title: Differential effects of polyamine depletion by DENSpm and DFMO on beta cell stress reponses and type 1 diabetes outcomes in mice

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

summary: Type 1 diabetes (T1D) is an autoimmune disease leading to dysfunction and loss of insulin-secreting β cells.  In β cells, polyamines have been implicated in causing cellular stress and dysfunction.  An inhibitor of polyamine biosynthesis, difluoromethylornithine (DFMO), has been shown to delay T1D in mouse models and preserve β cell function in humans with recent-onset T1D.  Another small molecule, N1,N11-diethylnorspermine (DENSpm), both inhibits polyamine biosynthesis and accelerates polyamine metabolism and is currently being tested for efficacy in cancer clinical trials.  In this study, we show that DENSpm depletes intracellular polyamines as effectively as DFMO in mouse β cells.  RNA sequencing analysis, however, suggests that the cellular reponses to DENSpm and DFMO differ, with the two sharing similar effects on cellular proliferation, but the latter showing greater effects on mRNA translation and protein folding pathways.  In the low-dose streptozotocin-induced mouse model of T1D, DENSpm administration did not prevent or delay diabetes outcome, but did result in improvements in glucose tolerance and reductions in islet oxidative stress.  In non-obese diabetic (NOD) mice, short-term DENSpm administration resulted in slight reduction in insulitis and proinflammatory Th1 cells in the pancreatic lymph nodes.  Longer term treatment resulted in a dose-dependent increase in mortality.  Notwithstanding the efficacy of both DFMO and DENSpm in reducing potentially toxic polyamine levels in β cells, our results highlight the discordant T1D outcomes that result from differing mechanisms of polyamine depletion and, more importantly, that toxic effects of DENSpm may limit its utility in T1D treatment.

overall_design: MIN6 β cells were treated with vehicle, 5 mM DFMO, or 10 μM DENSpm with or without a proinflammatory cytokine mix (100 ng/lg IFN-γ, 50 mg/ml TNF-α, and 25 ng/ml IL-1β) for 24 h prior to RNA isolation.

first: Raghavendra

last: Mirmira

first: Batoul

last: Hammound


title: Unmethylated Cyc1 downregulates hyphal specific genes and upregulates hyphal suppressors in Candida albicans

status: Public on Jan 01 2024

city: Singapore

first: Guisheng

last: Zeng

address: 8A Biomedical Grove, #05-13 Immunos Building, Immunos

department: Infectious Diseases Labs

country: Singapore

institute: Agency for Science, Technology and Research

type: Expression profiling by high throughput sequencing

summary: Our genetic screen reveals that deletion of CTM1, which abolishes the lysine trimethylation of cytochrome c (Cyc1), results in inhibition of hyphal morphogenesis in Candida albicans. Similar results are observed in the unmethylatable Cyc1 mutant (cyc1K79A). To elucidate how unmethylated Cyc1 inhibits hyphal growth, we performed RNA-Seq analysis by comparing WT (BWP17), ctm1∆/∆, and cyc1K79A cells grown in yeast and hyphal condition. Consistent with previous published data, many hyphal specific genes (HSGs), such as ALS3, ECE1, HWP1, and UME6, are upregulated while three major hyphal suppressor genes, TUP1, NRG1, and RFG1, are downregulated when WT cells switch from yeast to hyphal growth. Similar changes are observed in ctm1Δ/Δ and cyc1K79A cells upon hyphal induction, even though most mutant cells maintain yeast morphology throughout the induction. Further comparisons reveal that the basal transcriptional levels of HSGs are much lower in ctm1Δ/Δ and cyc1K79A cells than those in WT cells. Upon hyphal induction, the levels of HSGs in ctm1Δ/Δ and cyc1K79A cells increase but still remain lower than their basal levels in WT cells. In contrast, the hyphal suppressor genes (especially NRG1) exhibit much higher basal transcriptional levels in ctm1Δ/Δ and cyc1K79A cells than in WT cells. Their transcriptional levels reduce upon hyphal induction but still remain higher than the basal levels in WT cells. Together, these data suggest that unmethylated Cyc1 inhibits hyphal morphogenesis via transcriptional regulation of HSGs and hyphal suppressor genes.

overall_design: Three C. albicans strains, including WT (BWP17), ctm1∆/∆, and cyc1K79A, were grown in YPD at 30°C overnight and subjected to hyphal induction with 10% fetal bovine serine (FBS) and incubation at 37°C for 1-2 h. Three types of samples (overnight yeast cultures, 1 h and 2 h hyphal induction cultures) from each strains were taken for RNA-Seq. We then performed gene expression profiling analysis using data obtained from RNA-Seq of there different strains at three timeppoints.


title: Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-players game

city: Palaiseau

first: Nicolas

last: Lapalu

address: 22 place de l'agronomie

department: SPE

country: France

institute: INRAE

summary: During infection, plant pathogenic fungi secrete a set of molecules collectively known as effectors, involved in overcoming the host immune defense system and in disease establishment. Effector genes are concertedly expressed as waves all along plant pathogenic fungi lifecycle. However, little is known about how coordinated expression of effector genes is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in the regulation of effector expression was recently investigated. In Leptosphaeria maculans, causing stem canker of oilseed rape, we established that the repressive histone modification H3K9me3 (trimethylation of Lysine 9 of Histone H3), deposited by the histone methyltransferase KMT1, was involved in the regulation of expression of genes highly expressed during infection, including effectors. Nevertheless, inactivation of KMT1 did not induce expression of these genes at the same level as observed during infection of oilseed rape, suggesting that a second regulator, such as a transcription factor (TF), might be involved. Pf2, a TF belonging to the Zn2Cys6 fungal specific TF family, was described in several Dothideomycete species as essential for pathogenicity and effector gene expression. We identified the orthologue of Pf2 in L. maculans, LmPf2, and investigated the role of LmPf2 together with KMT1 in L. maculans, by inactivating and over-expressing LmPf2 in a wild type (WT) strain and a ∆kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis. Transcriptomic analyses during axenic growth showed that LmPf2 is involved in the control of effector gene expression. We observed an enhanced effect of the over-expression of LmPf2 on effector gene expression in a ∆kmt1 background, suggesting a synergic role between KMT1 and LmPf2.

overall_design: Eight different transformants (i.e., two mutants inactivated for KMT1 or LmPf2 and two transformants in which LmPf2 was over-expressed in a WT background (WT_oPf2) or a ∆kmt1 background (∆kmt1_oPf2).

first: Colin

last: Clairet

first: Jessica

last: Soyer

first: Isabelle

last: Fudal


title: High-throughput Drug Screening Identifies Ketotifen as a Potential Therapeutic Agent for Neuroendocrine Prostate Cancer

city: Shanghai

first: Qi

last: Wang

state: Shanghai

address: Shanghai Pu Dong district, Dongfang Rd. No.1630

country: China

institute: Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine

summary: We performed a high-throughput drug screening and identified Ketotifen, originally an FDA-approved antidepressant, as candidate therapeutic agent for NEPC. RNA-seq was performed of LASCPC-01 cells treated with Ketotifen or PBS.

overall_design: mRNA profiles of LASCPC-01 cells treated with PBS or Ketotifen

first: Yiyi

last: Ji

first: Bo

last: Liu

first: Lei

last: Chen

first: Yinjie

last: Zhu

first: Wei

last: Xue


title: Dietary amino acid source elicits sex-specific metabolic response to diet-induced NAFLD in murine model.

city: Toulouse

first: Laurence

last: Gamet-Payrastre

address: 180 chemin de Tournefeuille

summary: Non-alcoholic fatty liver disease (NAFLD) is a sexually dimorphic disease influenced by dietary factors. Here, we assess the metabolic and hepatic effects of dietary amino acid (AA) source in Western diet (WD)-induced NAFLD in male and female mice. The AA source was either casein or a free AA mixture mimicking the composition of casein. As expected, males fed a casein-based WD displayed glucose intolerance, fasting hyperglycemia, and insulin-resistance and developed NAFLD associated with changes in hepatic gene expression and dysbiosis. In contrast, males fed the AA-based WD showed no steatosis, a similar gene expression profile as males fed a control diet, and a distinct microbiota composition compared to males fed a casein-based WD. Females were protected against WD-induced liver damage, hepatic gene expression, and gut microbiota changes regardless of the AA source. Thus, free dietary AA intake prevents the unhealthy metabolic outcomes of a WD in a sex-specific manner.

overall_design: Six-week-old male and female C57BL/6J mice were purchased from Charles Rivers Laboratories (L’Arbresle, France), kept 1 week for acclimatization, and then randomly allocated to the different experimental groups. Mice (n=12 per group and per sex) were fed a chow diet (CD; 70% carbohydrate, 4% fat, and 14% protein, Figure S1a), a Western diet (WD; 61% carbohydrate, 20% fat, and 14% protein, Figure S1a) or diets identical to the CD or WD except for protein being replaced by a free amino acid mixture mimicking the amino acid composition of casein (SAAJ INRAE, Jouy) for 15 weeks.

last: Payrastre

first: Anne

last: Fougerat

first: Clémence

last: Rives

first: Claire

last: Naylies

first: Anne-Marie

last: Loustau

first: Yannick

last: Lippi


title: Comprehensive gene expression analysis using gastric mucosa with autoimmune gastritis

city: Tsukiji, Chuo-ku

first: Chihiro

last: Takeuchi

state: Tokyo

department: Division of Epigenomics

country: Japan

institute: National Cancer Center Research Institute

summary: In this study, we aimed to reveal whether gastric mucosa with AIG has a specific gene expression profile, involving in its histology and chronic inflammation. To approach this, we performed comprehensive analysis of gene expression using gastric mucosa with atuoimmune gastritis, that with H. pylori-associated gastritis and healthy mucosa without any inflammation. Potential mechanisms of the gene expression changes in gastric mucosa with AIG were also explored.

overall_design: Biopsy samples were obtained from gastric mucosa with autoimmune gastritis and H. pylori-associated gastritis, and normal mucosa. The samples were put into RNA later and were frozen at -80C for further use. The samples were homogenized and total RNA was extracted.

first: Junichi

last: Sato

first: Nobutake

last: Yamamichi


title: Normal hematopoietic stem and progenitor cells in murine acute myeloid leukemia model in vivo

city: Philadelphia

first: Peter

last: Kurre

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

country: USA

institute: Children's Hospital of Philadelphia

summary: Bone marrow inflammation has been linked to acute myeloid leukemia (AML) progression. Studies have demonstrated that leukemic blasts propagate acute inflammation in the AML niche, but the involvment of normal hematopoietic stem and progenitor cells (HSPCs) in the inflammatory crosstalk is not well understood. To better model compartmental inflammation in AML, we first established a highly penetrant, immunocompetent, fully congenic system. Using the monoblastic AML cell line C1498 (CD45.2+), we grafted non-condition C57BL/6J (CD45.1) mice, avoiding changes in BM niche function. We then fluoresence-activated cell sorting (FACS)-sorted residual normal HSPCs for single-cell RNA-sequencing analysis. We show that residual normal HSPCs from C1498-grafted mice expresses key inflammatory signature and are enriched in inflammatory signaling related pathways. Overall, we show that normal HSPCs engages in inflammatory signaling in AML niche.

overall_design: C1498 mice were generated by injecting C1498 cells (CD45.2; 1E6 cells per recipient) into healthy non-conditioned C57BL/6J mice (CD45.1; 8-12 weeks; female; Jacksons Laboratory). PBS-injected mice serve as control. Mice were sacrificed 21-day after injection. Bone marrow hematopoietic stem and progenitor cells (HSPCs; CD45.1+ Lin- cKit+ Sca1+) were fluorescent-activated cell sorting (FACS)-sorted for gene expression assay.

first: Ding-Wen

first: Jian-Meng

last: Fan

first: Seul

last: Jung

first: Empar

last: Baltasar-Pérez


title: RREB1 Regulates Neuronal Proteostasis and Microtubule Network Function [RNA-seq]

city: La Jolla

first: Susan

last: Ackerman

state: CA

address: 9500 Gilman Drive

department: CMM

institute: UCSD

summary: To establish molecular pathways disrupted by loss of RREB1 in Purkinje cells, RNA-seq was performed on mRNA isolated from Purkinje cells and differential expression analysis was performed.

overall_design: Cerebella from 3 Rpl22fl/+;PCP2-Cre and 4 Rpl22fl/+;PCP2-CRE;nm3888-/- mice were collected. HA tagged ribosomes were immunoprecipitated from fresh tissue and nascent mRNA transcripts were isolated .

first: Emily

last: Griffin

first: Thomas

last: Jucius

first: Su-Eon

last: Sim

first: Belinda

middle: S

last: Harris

first: Sven

last: Heinz

middle: L


title: RREB1 Regulates Neuronal Proteostasis and Microtubule Network Function

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Sire modulates developmental kinetics and transcriptome in the bovine embryo

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

summary: The impact of sire on pre-implantation embryonic development in cattle remains poorly understood. This study evaluated differences in embryos produced from sires with varying capacities to produce blastocysts. Sires classified as high (HP) and low-performing (LP) based on their ability to produce embryos were used in order to better understand how sire regulates embryonic development. By monitoring embryo development, it was determined that the most common arrest stage was the 5-6 cell stage. Embryos (4-6 cells) from HP and LP sires were analyzed for autophagic activity, where embryos for LP sires exhibited increased autophagy than HP-derived embryos. Transcriptome analysis of 4-cell embryos found that embryos from LP sires might have issues in sperm mitochondrial clearance, histone retention, and DNA damage, while HP sires have increased expression of genes involved in transcription, chromosome segregation, and cell division. In conclusion, LP sires have an increased proportion of embryos arresting at the 5-6 cell stage, and these embryos have higher rates of cellular stress due to paternal contributions from the spermatozoon.

overall_design: Bovine embryos at 2-4 cell stage from high and low performing sires

first: MS

first: Kelsey

middle: N

last: Lockhart

first: Jessica

last: Drum

first: Ahmed

middle: Z

last: Balboula

first: Christine

middle: M

last: Spinka

middle: E

last: Spencer


title: RREB1 Regulates Neuronal Proteostasis and Microtubule Network Function [ChIP-seq]

summary: RREB1 regulates neuronal proteostasis and the microtubule network

overall_design: Cerebella from 2 Tg(Rreb1/3V5)20/J mice were collected. Tissues were homogenized, genomic DNA was sheared, and an aliquot of each sample was set aside as input. A V5 antibody was used to perform ChIP on the transgene. DNA was then isolated from input and ChIP samples and sent in for sequencing.


title: Gene expression profiling of ATRA-resistant NB4-MR4 subclone (R4 cell line)  treated with a CHK1 inhibitor i(MK-8776).

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Acute promyelocytic leukemia (APL) is a hematological disease characterized by a balanced reciprocal translocation that leads to the synthesis of the oncogenic fusion protein PML-RARα. APL is mainly managed by a differentiation therapy based on the administration of all-trans retinoic acid (ATRA) and arsenic trioxide (ATO). However, therapy resistance, differentiation syndrome, and relapses require the development of new low-toxicity therapies based on the induction of blasts differentiation. Here, we performed a high-throughput gene expression profile of the ATRA-resistant acute promyelocytic leukemia (APL) cellline (aka R4) treated with a CHK1 inhibitor or DMSO as control.

overall_design: We performed a whole mRNA transcriptome analysis by Affymetrix microarray of R4 cells  treated with MK-8776 (4 μM) for 96 h or DMSO as control. Two biological replicates were performed for each condition.

first: Alessandra

last: Di Masi


title: CD39+ CD4+ conventional T cells with exhaustion traits and cytotoxic potential infiltrate tumors and expand upon CTLA4 blockade

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

summary: CD4+ conventional T (Tconv) lymphocytes display an important role in tumor immunity; however, their contribution to tumor elimination remains poorly understood. Here we describe a subset of tumor-infiltrating Tconv cells characterized by the expression of CD39. In mouse cancer models CD39+ Tconv cells accumulate with tumor growth but are absent in lymphoid organs. Compared to tumor CD39- Tconv cells, CD39+ cells exhibit a cytotoxic and exhausted signature at the transcriptomic level, confirmed by high protein expression of co-inhibitory receptors and transcription factors related to exhaustion. Additionally, CD39+ Tconv cells show an increased production of INFg, Granzyme B, Perforin and CD107a, but a reduced production of TNF upon in vitro stimulation.  In vivo, CTLA-4 blockage induces the expansion of CD39+ Tconv cells in the tumor, while maintaining their features of cytotoxicity and exhaustion. In breast cancer patients, CD39+ Tconv cells are found in tumors, and at lower frequency in the adjacent non-tumoral mammary tissue. CD39+ Tconv cells are also present in metastatic but not detected in non-metastatic lymph nodes and blood. Human tumor CD39+ Tconv cells constitute a heterogeneous cell population with features of exhaustion, impaired TNF production, and high expression of co-inhibitory receptors and CD107a. High gene expression of CD4 and ENTPD1 (CD39) in human tumor tissues correlates with higher overall survival rate in breast cancer patients. Our results identify CD39 as a biomarker of CD4+ T cells with characteristics of both exhaustion and cytotoxic potential and put forward CD39+ Tconv cells as pivotal players of the immune response against tumors.

overall_design: B16F10-OVA tumors from 9 FOXP3-GFP tumor-bearing mice were processed for RNA sequencing. Tumors were shaped into 3 pools and purified CD4+ T cells were obtained by positive selection (CD39neg, CD39pos and Tregs)

first: Sabrina

last: Bossio

first: Carolina

last: Abrate

first: Eliane

last: Piaggio

last: Montes


title: Role of MEF2C in the Endothelial Cells Derived from Human Induced Pluripotent Stem Cells

city: Sacramento

first: Julian

last: Halmai

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

summary: Human induced pluripotent stem cells (hiPSCs) not only provide an abundant source of vascular cells for potential therapeutic applications in vascular disease but also constitute an excellent model for understanding the mechanisms that regulate the differentiation and the functionality of vascular cells. Here, we reported that myocyte enhancer factor 2C (MEF2C) transcription factor, but not any other members of the MEF2 family, was robustly upregulated during the differentiation of vascular progenitors and endothelial cells (ECs) from hiPSCs. Vascular endothelial growth factors (VEGF) strongly induced MEF2C expression in endothelial lineage cells. The specific upregulation of MEF2C during the commitment of endothelial lineage was dependent on the extracellular signal regulated kinase (ERK). Moreover, knockdown of MEF2C with shRNA in hiPSCs did not affect the differentiation of ECs from these hiPSCs, but greatly reduced the migration and tube formation capacity of the hiPSC-derived ECs. Through a chromatin immunoprecipitation-sequencing, genome-wide RNA-sequencing, quantitative RT-PCR, and immunostaining analyses of the hiPSC-derived endothelial lineage cells with MEF2C inhibition or knockdown compared to control hiPSC-ECs, we identified TNF-related apoptosis inducing ligand (TRAIL) and transmembrane protein 100 (TMEM100) as novel targets of MEF2C. This study demonstrates an important role for MEF2C in regulating human EC functions and highlights MEF2C and its downstream effectors as potential targets to treat vascular malfunction-associated diseases.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for MEF2C in hiPSC-derived Ecs

first: Ping

last: Zhou


title: Angptl-7 knockdown RNA sequencing of 4T1 orthotopic transplants into rat mammary fat pads

city: Seattle

first: Kevin

middle: J

last: Cheung

state: WA

address: 1100 Fairview Ave N

department: Public Health Sciences

institute: Fred Hutchinson Cancer Center

summary: These samples are derived from tissues obtained from 4T1 spheroids transplanted orthotopically into the mammary fat pads of SRG OncoRats. 4T1 cell lines were established by viral transduction that stably express either a non-targeting control shRNA (NT4) or an shRNA targeting Angptl-7.  4T1 cells were cultured as spheroids in suspension for 24-hours prior to transplantation in 2% matrigel. 600,000 cells in a 1:1 mixture of matrigel and DMEM/F12 were transplanted orthotopically into the right T4 fat pads of SRG rats.  At day 27 post transplanation, primary tumors. The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing.

overall_design: 4T1 cells transduced with either non-targeting control shRNA (n=4 animals) or Angptl7 knockdown shRNA (n=3 animals) were transplanted into the mammary fat pads of SRG rats. Tumors were dissected into necrotic core and non-necrotic rim regions, and regions were separately submitted for RNA-sequencing.

first: Ami

last: Yamamoto

first: Yin

last: Huang

first: Brad

last: Krajina


title: The rDNA antisense transcript PAPAS promotes lactogenic differentiation of mammary epithelial cells and suppresses breast cancer

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

country: Germany

institute: Friedrich Schiller University Jena

summary: PAPAS is an antisense transcript of rRNA genes and mediates silencing of the locus in non-dividing cells. Here, we have analyzed PAPAS function in lactogenic differentiation of mammary epithelial cells (HC11 cells) and in mammary cancer cells (4T1). Using doxycycline (Dox) inducible shRNA against PAPAS, we found that the knockdown perturbs differentiation and inhibits expression of lactogenic genes. In contrast, Dox-inducible overexpression of PAPAS in 4T1 cells suppresses genes required for ribosome biogenesis and slows down the neoplastic growth.

overall_design: Comparative gene expression analysis of total RNA-Seq data for murine mammary epithelial cells (untransformed cell line HC11 and cancer cell line 4T1).

first: Holger

last: Bierhoff

first: Marco

last: Groth

first: Clara

last: Stanko


title: Repeat elements activating lncRNAs drives zygotic genome activation

first: Wenju

last: Liu

address: 1239  siping road

institute: University of Tongji

summary: Vertebrate life begins with fertilization, then the zygote genome is activated after transient silencing, termed zygotic genome activation (ZGA). The mechanism of how ZGA initiates is far from clear although it underlay the mystery of totipotency and start of life. The specific property of the minor ZGA implied the possible critical role of ncRNA in the initiation of ZGA. Here we delineated the expression profile of the lncRNAs in the mouse early embryo development and elucidated their critical role in the minor ZGA. LncRNAs showed closer correlation with minor ZGA, they activated earlier than the protein coding genes (PCGs) and suppressed quickly after ZGA. H3K9me3 enrichment prior the ZGA could explain the suspended expression of major ZGA PCGs albeit they possess the PolII pre-configuration. The PolII enriched MuERV-L was found around the TSS of the minor ZGA lncRNAs, and they were responsible for the activation of the minor ZGA lncRNAs and the subsequent embryo development. Our work suggested the MuERV-L mediated minor ZGA lncRNA activation as a critical driver between the epigenetic reprogramming triggered by fertilization and the embryo developmental program, thus provided clues for understanding totipotency and starting of life.

overall_design: Total RNA profiles of  mouse early embryonic samples were generated by deep sequencing.

first: Kang

last: Chen


title: Reversal of C9orf72 mutation-induced transcriptional dysregulation and pathology in cultured human neurons by allele-specific excision

status: Public on Jan 02 2024

city: San Francisco

first: Claire

last: Clelland

institute: UCSF

type: Methylation profiling by high throughput sequencing

summary: Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived iPSC line and a WT line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 FTD/ALS in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding SNP in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using ddPCR, we determined that transcription from the mutant allele is upregulated at least ten-fold, and that sense transcription is independently regulated from each allele whereas antisense transcription is regulated by the opposite allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all DPRs, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including ASOs and CRISPR gene editing.

overall_design: Single molecule sequencing of the C9orf72 repeat region from CRISPR edited patient iPSCs using PacBio No-Amp protocol

first: Patrick

last: Issagholian-Lewin


title: Hematologic DNMT3A Reduction and High Fat Diet Synergize to Promote Weight Gain and Tissue Inflammation

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: In the aging hematopoietic system, blood cell production becomes dominated by a limited number of hematopoietic stem cell (HSC) clones. While somatic mutations in the de novo DNA methyltransferase 3A (DNMT3A) frequently drive clone dominance, the aging milieu also likely contributes to selection of variant HSCs. The detrimental impact of clonal hematopoiesis on organismal health is thought to be mediated by differentiated progeny of variant HSCs through mechanisms as yet poorly understood. Here, we examined the interaction between high fat diet (HFD) as an inflammatory stressor and a hematopoietic system haploinsufficient for DNMT3A. Strikingly, HFD accelerated weight gain in mice harboring bone marrow with reduced DNMT3A. Moreover, distal tissues of such mice including pancreas, adipose, and spleen, harbored high levels of mutant macrophages that impacted tissue function. Aberrant DNA methylation and pro-inflammatory transcriptional activation in mutant-derived myeloid cells correlated with increased IL-6 and TNFa signaling. Together, these findings identify synergism between HFD and DNMT3A haploinsufficiency that, through increased inflammatory myeloid cell functions, can contribute to deterioration in organismal health.

overall_design: RNA-seq performed on in vitro differentiated macrophages derived from the bone marrow of male 13-week-old DNMT3A-HET or wild-type mice.

first: Jaime

last: Reyes


title: A cell-free pipeline for recreating methylation patterns   radically enhances DNA transformation in bacteria

city: Wuerzburg

first: Chase

last: Beisel

address: Josef-Schneider-Str. 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: We report a method for bypassing restriction modification systems to increase DNA transformation in batceria and develop a high-throughput way to determine the optimal methylation pattern for DNA transformation.

overall_design: Submitted barcoded amplicons from transformed Bifidobacterium breve cells for high-throughput Amplicon EZ sequencing performed by Genewiz to determine the frequency of each barcode.

first: Justin

last: Vento

first: Deniz

last: Durmusoglu


title: 3,3',5-Triiodothyroacetic acid (TRIAC) induces embryonic ζ-globin expression via thyroid hormone receptor α

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital


title: 3,3',5-Triiodothyroacetic acid (TRIAC) induces embryonic ζ-globin expression via thyroid hormone receptor α (RNA-seq)

summary: Next Generation Sequencing Facilitates Quantitative Analysis of K562 cells treated with DMSO and TRIAC

overall_design: mRNA profiles of K562 cells were generated by deep sequencing, in duplicate, using Illumina Navoseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays.

first: Huiqiao

first: Hao

last: Yuan


title: Friend or Foe? Primary Tumor represses distant metastases' growth via exosomal miRNA-1

city: Seoul

first: Je-Yoel

last: Cho

address: 1, Gwanak-ro, Gwanak-gu

department: Biochemistry

country: South Korea

institute: Seoul National University

type: Non-coding RNA profiling by high throughput sequencing

summary: Recently, exosome has been treated as a key mechanism for cell-to-cell communication. We thus demonstrated the roles of exosomes for the encoding messages between primary tumors and metastases. To investigate the difference between pTDE miRNA (primary tumor-derived exosomal miRNA) and mDE miRNA (metastases-derived exosomal miRNA), we isolated exosomal miRNA from each cell lines. Next, we performed small RNA sequencing for miRNA profiling. Compared with pTDE and mDE miRNAs, miR-1 is specifically abundunt in pTDE and also shows therapeutic effects to repress the growth of metastases after primary tumor resection.

overall_design: Profiling both pTDEs and mDE miRNAs, we isolated exosomal miRNAs from CHMp (primary tumor) and CHMm (metastases) with two replicates.

first: HuiSu

last: Kim

first: Kang-Hoon

last: Lee

first: Keun-Hong

last: Son

first: Tae-Jin

last: Shin


title: Transcriptional, Metabolic, Physiological and Developmental Responses to Nitrogen Limitation in Switchgrass (Panicum virgatum)

status: Public on Dec 31 2023

city: Invergowrie / Dundee

first: Raul

last: Huertas

state: Perth and Kinross

address: Errol Road

department: Environmental and Biochemical Sciences

country: United Kingdom

institute: The James Hutton Institute

summary: Sustainable production of switchgrass (Panicum virgatum) as a bioenergy crop hinges in part on efficient use of soil macronutrients, especially nitrogen (N). This study investigated the physiological, metabolic and transcriptomic responses of switchgrass to N limitation. Moderate N limitation marked a tipping point for large changes in plant growth, root-to-shoot ratio, root system architecture and total nitrogen content. Integration of transcriptomic and metabolic data revealed that N limitation reduced switchgrass photosynthetic capacity and carbon(C)-fixation activities. Switchgrass balanced C-fixation with N-assimilation, transport and recycling of N compounds by rerouting C-flux from glycolysis, the oxidative branch of the pentose phosphate pathway (OPPP) and from the tricarboxylic acid (TCA) cycle in an organ specific manner. The energy and reduction power so generated, and C-skeletons appear to be directed towards N uptake, biosynthesis of energy storage compounds with high C/N ratio such as sucrose, non-N-containing lipids, and various branches of secondary metabolism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from switchgrass plants grown under optimal nutritional conditions or with different nitrogen limitation regimes (mild, moderate and severe) for four weeks.

last: Ding

first: Ivone

last: Torres-Jerez

first: Nick

last: Krom

first: Yuhong

last: Tang

first: Wolf

last: Scheible

first: Michael

last: Udvardi


title: Single-cell transcriptomic analysis of lung mesenchymal cells with mesenchyme-specific deletion of transcriptional regulator Sin3a

city: San Diego

first: David

middle: James

last: McCulley

address: 9500 Gilman Drive, MC 0735, Leichtag Building, Room 132

institute: University of California, San Diego

summary: Congenital diaphragmatic hernia (CDH) is a common and severe congential malformation characterized by defects in diaphragm, lung, and pulmonary vascular developent. Despite the frequency and severity of CDH, the underlying developmental mechanisms are not understood. We identified SIN3A loss of function sequence variants in two patients with CDH. To understand the genetic and developmental mechanisms of CDH, we generated Sin3a conditional knockout mice that lack Sin3a expression in the lung mesenchyme. SIN3A has been shown to play a critcal role during development, directing cell lineage specification and cell cycling. We found that loss of SIN3A resulted in impaired mesenchymal cell differentiation from bulk lung transcriptomic analysis in Sin3a CKO mice. To investigate the impact of loss of SIN3A in mesenchymal cell differentation, we performed fluorescent activated cell sorting (FACS) to isolate cells that underwent recombination of Sin3a. We then performed single-cell transcriptomic analysis on sorted mesenchymal cells from embryonic day 16 (E16) Sin3a CKO and control lungs. In this dataset are expression data from FACS-isolated recombined lung mesenchymal cells of Sin3a CKO and control mice. Sin3a CKO mice have conditional deletion of Sin3a in the lung mesenchyme directed by Tbx4rtta; tetocre (Tbx4rtta; tetocre; Sin3a flox/flox CKO). Control mice are heterozygous for Sin3a in the lung mesenchyme (Tbx4rtta; tetocre; Sin3a flox/WT). These data were used to identify transcriptional changes due to loss of Sin3a in the lung mesenchyme.

overall_design:
2 controls and 2 Sin3a CKO lungs were collected at E16. We generated comparisons in differential gene expression between control and Sin3a CKO samples at this stage.
contributor: University of Wisconsin-Madison Gene Expression Center
contributor: University of Wisconsin-Madison Gene Bioinformatics Center

first: Gia

last: Stokes

first: Rabi

last: Murad


title: Induced Endothelial Cell Cycle Arrest Prevents Arterio-venous Malformations in Hereditary Hemorrhagic Telangiectasia (Bulk RNA-Seq)

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

summary: Distinct endothelial cell cycle states (early G1 vs. late G1) provide different “windows of opportunity” to enable the differential expression of genes that regulate venous and arterial specification, respectively. Endothelial cell cycle control and arterial-venous identities are disrupted in vascular malformations including arteriovenous (AV) shunts which is a hallmark of hereditary hemorrhagic telangiectasia (HHT). We show how endothelial cell late G1 arrest induced by Palbociclib modulates the expression of genes regulating arterio-venous identity and prevents AVM development induced by BMP9/10 inhibition.

overall_design: Eyes from P7 pups of control (group 1), BMP9/10 Abs-treated (group 2), and BMP9/10 Abs + CDK4/6i (group 3) treated animals were dissected out and primary retinal ECs were FACS-isolated and prepared for bulk RNA sequencing of total RNA.

first: Gael

last: Genet

first: Nafiisha

first: Umadevi

first: Nicholas

last: Chavkin

first: Karen

last: Hirschi


title: Impaired activation of plasmacytoid dendritic cells via Toll-Like receptor 7/9 and STING is mediated by melanoma-derived immunosuppressive cytokines and metabolic drift.

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

institute: University of Verona

summary: Plasmacytoid dendritic cells (pDCs) infiltrate a large set of human cancers. IFN-α produced by pDCs might induce growth arrest and apoptosis in tumor cells and modulates innate and adaptive immune cells involved in anti-cancer immunity. Moreover, pDC-derived  effector molecules exert tumor cell killing. However, the activation state and clinical relevance of pDCs infiltration in cancer is still largely controversial. In Primary Cutaneous Melanoma (PCM), pDCs density decreases over disease progression and collapses in metastatic melanoma (MM). Moreover, the residual circulating pDC compartment is defective in IFN-α production. Here, based on a set of microscopic, functional and in silico analysis, we demonstrated that the melanoma secretome directly impairs type I interferon and CXCL10 production by pDCs via TLR-7/9 and cGAS-STING signaling pathways. As proposed byBased on bulk transcriptomic data, we could confirmed that TGF-β and a metabolic drift represent relevant mechanisms enforcing pDC-mediated melanoma escape.

overall_design: Bulk RNA sequencing (RNA-seq) analysis of healthy pDCs, cultured in RPMI or in melanoma conditioned medium (SN-mel146; SN-mel336 ) and either left untreated or stimulated with R848 for 2 hours.

first: Matilde

last: Monti

first: Giorgia

last: Ferrari

first: Valentina

last: Grosso

first: Francesco

last: Missale

first: Mattia

last: Bugatti

first: Valeria

last: Cancila

first: Stefania

last: Zini

first: Francesca

last: Consoli

first: Matteo

last: Orlandi

first: Claudio

last: Tripodo

first: William

last: Vermi


title: Lung mesenchymal cells with lung-mesenchyme specific deletion of Sin3a

first: David

last: McCulley

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

overall_design: Refer to individual Series


title: Interferon-gamma is Quintessential for NOS2 and COX2 Expression in ER- Breast Tumors that Lead to Poor Outcome

city: Frederick

last: Wink

state: MD

address: 1050 Boyles St

department: CCR

institute: NCI

summary: Previously, we have proved the NOS2 and COX2 genes play an important role in ER-negative breast cancer. In this study, we utilized the scRNAseq technique to investigate how cancer cells react to cytokines with and without IFNG combination treatments.

overall_design: Synchronized MDA-MB-231 cells were treated with cytokines with and without IFNG for 48 hours

first: Robert

middle: Y

last: Cheng

first: Lisa

last: Ridnour

first: Adelaide

first: Ana

last: Gonzalez

first: Elise

last: Femino

first: Helene

last: Rittscher

first: Veena

last: Somasundarum

middle: F

last: Heinz

first: Leandro

last: Coutinho

first: M

middle: C

last: Rangel

first: Elijah

last: Edmondson

first: Donna

last: Butcher

last: Kinders

first: Xiaoxian

last: Li

first: Stephen

middle: T

last: Wong

first: Daniel

middle: W

last: McVicar

first: Steven

middle: K

last: Anderson

first: Milind

last: Pore

last: Hewitt

first: Timothy

middle: R

last: Billiar

first: Sharon

last: Glynn

first: Jenny

last: Chang

last: Lockett

first: Stefan

last: Ambs


title: Effects of oocyte-specific PIK3CA* transgene knock-in in ovaries

city: Omaha

first: So-Youn

last: Kim

state: Nebraska

address: DRC2 4016, 601 South Saddle Creek RD

institute: University of Nebraska Medical center

summary: To investigate the transcriptomic changes during the development and growth of ovarian granulosa cell tumors derived by oocyte-specific PIK3CA* transgene overexpression

overall_design: Temporal transcriptomic analysis of RNA-seq data with tumor samples harvested at postnatal day 8, 50 and 65


title: 3,3',5-Triiodothyroacetic acid (TRIAC) induces embryonic ζ-globin expression via thyroid hormone receptor α (ChIP-seq)

city: Shanghai

first: Shanhe

last: Yu

summary: To characterize genome-wide THRA traget genes in K562 cells.

overall_design: Examination of THRA traget genes in K562 cells.

first: Huiqiao

last: Chen

first: Hao

last: Yuan


title: Transcriptomic analysis of lung mesenchymal cells with lung-mesenchyme specific deletion of Sin3a

first: David

last: McCulley

summary: Congenital diaphragmatic hernia (CDH) is a common and severe congential malformation characterized by defects in diaphragm, lung, and pulmonary vascular developent. Despite the frequency and severity of CDH, the underlying developmental mechanisms are not understood. We identified SIN3A loss of function sequence variants in two patients with CDH. To understand the genetic and developmental mechanisms of CDH, we generated Sin3a conditional knockout mice that lack Sin3a expression in the lung mesenchyme. SIN3A has been shown to play a critcal role during development, directing cell lineage specification and cell cycling. We found mesenchymal progenitor cells in Sin3a CKO mice have altered expression of cell cycle progression genes from bulk lung transcriptomic analysis. To investigate changes in gene expression that occur specifically in lung mesenchymal cells, we performed fluorescent activated cell sorting (FACS) to isolate cells that underwent recombination of Sin3a. We then performed transcriptomic analysis on sorted mesenchymal cells from embryonic day 16 (E16) Sin3a CKO and control lungs. In this dataset are expression data from FACS-isolated recombined lung mesenchymal cells of Sin3a CKO and control mice. Sin3a CKO mice have conditional deletion of Sin3a in the lung mesenchyme directed by Tbx4rtta; tetocre (Tbx4rtta; tetocre; Sin3a flox/flox CKO). Control mice are heterozygous for Sin3a in the lung mesenchyme (Tbx4rtta; tetocre; Sin3a flox/WT). These data were used to identify transcriptional changes due to loss of Sin3a in the lung mesenchyme.

overall_design:
4 controls and 4 Sin3a CKO lungs were collected at E16. We generated comparisons in differential gene expression between control and Sin3a CKO samples at this stage.
contributor: University of Wisconsin-Madison Gene Expression Center
contributor: University of Wisconsin-Madison Gene Bioinformatics Center

first: Gia

last: Stokes


title: Cellular composition of murine mitral valves during autoimmune valvular carditis

city: Minneapolis

first: Bryce

last: Binstadt

state: Minnesota

address: 2-200 WMBB Bench 8

institute: University of Minnesota

summary: To characterize the cell types that compose the mitral valve during the development of autoimmune valvular carditis, we utilized scRNA sequencing. Live cells from inflamed valves of K/B.g7 mice or uninflamed B.g7 controls were collected and analyzed at 3-, 8-, and 25 weeks of age.

overall_design: Live single cells were sorted from digested mitral valves using fluorescence-activated cell sorting (FACS) and analyzed using scRNA sequencing.

first: Binstadt

last: Bryce A

first: Meier

last: Lee A

first: Auger

last: Jennifer L

first: Firulyova

last: Maria M

first: Zaitsev

last: Konstantin

first: Yellamilli

last: Amritha

first: Osinski

last: Victoria

first: Faragher

last: Jessica L


title: Enriched Single-Nucleus RNA-Sequencing Reveals Unique Attributes of Distal Convoluted Tubule Cells

city: Portland

first: Xiao-Tong

last: Su

state: OR

address: 3181 SW Sam Jackson Park Road, LBRB 540, L334

institute: Oregon Health and Science University

summary: Distal convoluted tubule (DCT) cells display a remarkable ability to adapt to the dietary potassium intake. We  applied single-nucleus RNA-seq to map the plasticity of enriched mouse DCT cells in response to dietary potassium restriction

overall_design: Kidney DCT cells of the NCC-Cre-INTACT mice were isolated by Fluorescence-activated nuclei sorting (FANS) according to the presence or absence of mCherry signal and analyzed using scRNAseq.

first: Jonathan

last: Nelson

middle: H

last: Ellison


title: Multi-level profiling of the Fmr1 KO rat unveils altered behavioral traits along with aberrant glutamatergic function

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

summary: Fragile X Syndrome (FXS) is the most common cause of inherited intellectual disabilities and the most prevalent monogenic cause of autism. Although the knockout (KO) of the Fmr1 gene homolog in mice is primarily used for elucidating the neurobiological substrate of FXS, there is limited association of the experimental data with the pathophysiological condition in humans. The use of Fmr1 KO rats offers additional translational validity in this regard. Therefore, we employed a multi-level approach to study the behavioral profile and the glutamatergic and GABAergic neurotransmission status in pathophysiology-associated brain structures of Fmr1 KO rats, including the recordings of evoked and spontaneous field potentials from hippocampal slices, paralleled with next-generation RNA sequencing (RNA-seq). We found that these rats exhibit hyperactivity and cognitive deficits, along with characteristic bidirectional glutamatergic and GABAergic alterations in the prefrontal cortex and the hippocampus. These results are coupled to affected excitability and local inhibitory processes in the hippocampus, along with a specific transcriptional profile, highlighting dysregulated hippocampal network activity in KO rats. Overall, our data provide novel insights concerning the biobehavioral profile of FmR1 KO rats and translationally upscales our understanding on pathophysiology and symptomatology of FXS syndrome.

overall_design: RNA sequencing analysis for Hippocampus samples deriving from Wild Type and FMR1-KO animals in triplicates

first: Dimitrios

first: Katerina

last: Antoniou


title: FMRP targets in human neurons

city: Madison

first: Xinyu

last: Zhao

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

summary: FMRP-bound RNAs in hPSC-derived 8 wk neurons were identified using crosslinking immunoprecipitation (CLIP) and Illumina sequencing.

overall_design: FMRP targets in hPSC-derived 8 wk neurons were isolated by CLIP from three hPSC lines and cDNA libraries were sequenced on Illumina HiSeq 2500 platform.


title: Cell-free DNA 5-hydroxymethylcytosine is highly sensitive for MRD assessment in acute myeloid leukemia

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

summary: Measurable residual disease (MRD) is an important biomarker in acute myeloid leukemia (AML). However, MRD cannot be detected in many patients using current methods. We developed a highly sensitive 5-hydroxymethylcytosine (5hmC) signature in cell-free DNA by analyzing 115 AML patients and 86 controls. The 5hmC method detected MRD in 20 of 29 patients with negative MRD by multiparameter flow cytometry and 11 of 14 patients with negative MRD by molecular methods. MRD detection by the 5hmC method was significantly associated with relapse-free survival. This novel method can be used in most AML patients and may significantly impact AML patient management.

overall_design: Analyze 5-hydroxymethyl cytosine (5hmC) genome-wide distribution in plasma cell-free DNA from AML patients.

first: Jianming

last: Shao


title: scRNA sequencing revealed the effect of celecoxib on thioacetamide-induced liver fibrosis in mice

city: Chengdu

first: Linhao

last: Zhang

state: Sichuan

address: No. 37 Guoxue Lane

department: Gastroenterology

institute: West China Hospital, Sichuan University

summary: Aims: We sought to discover the effect of celecoxib on thioacetamide-induced liver fibrosis in mice with single cell RNA sequencing (scRNA-seq). Methods: A fibrotic mouse model was established by intraperitoneal injection of thioacetamide, and celecoxib was used as the treatment. Mice livers were collected and analyzed with scENA-seq. Results: scRNA-seq revealed prominent transcriptomic changes especially in B cells in liver fibrosis and after celecoxib treatment. KEGG pathways of the B-cell receptor signaling pathway and antigen processing and presentation were enriched, and the gene expression of receptors such as CXCR4 was altered. Conclusions: Celecoxib might modulate intrahepatic B cells to ameliorate liver fibrosis.

overall_design: A mouse model of liver fibrosis was established by intraperitoneal injection of thioacetamide (TAA) for 12 weeks, and 7.5 mg/kg celecoxib (C7.5) or 30 mg/kg celecoxib (C30) treatment was given orally by gavage started from 5th week of TAA injection to fibrotic mice.  Mice were allocated to the control group, TAA group, TAA+C7.5 and  TAA+C30 group with 1 in each according to the treatment. Hepatic nonparenchymal cells were isolated from one mouse for each group (control, TAA, TAA+C7.5, and TAA+C30 groups) and subjected to scRNA-seq.

first: Chengwei

last: Tang


title: Influenza A virus infection sustainably rewires pneumocyte gene regulatory network responses to different pneumococcal serotypes in secondary Streptococcus pneumoniae infection

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research

summary: Background: Pneumococcal secondary infection following influenza A virus (IAV) pneumonia is a synergistic complication with high mortality. While varying invasiveness of pneumococcal serotypes is an important pathogenic factor, serotype-specifc immediate-early transcriptional responses of the IAV-perturbed alveolar epithelium have not been adressed. We comprehensively analyzed gene transcription in alveolar type II epithelial cells (AECII) isolated from mice infected with IAV and/or S. pneumoniae (S.pn.) serotypes 4, 7F and 19F.    Results: IAV, 14 days post infection, rendered the lung susceptible to invasive secondary S.pn. infection with serotypes 4 and 7F but not 19F. Only secondary 7F infection induced exacerbated cytokine/chemokine responses. IAV/7F infection induced superior protein expression of type I and II interferons, acesserbated expression in IAV/serotype 4 infection. Inference of a scale-free-like ARACNE gene co-expression network revealed interferon-response network modules in AECII and network-mapping unfolded S.pn. serotype-specific transcriptional network responses/usage. Secondary S.pn. infection abrogated the IAV-induced pneumocyte proliferative configuration and preceeding IAV infection rendered the transcriptional response to 7F infection comparable to that towards serotype 4. This related especially to network genes correlating with the expression of two master regulators of interferon responses: Irf7 and Stat1. Epigenetic ATAC-seq analysis of AECII in resolved IAV infection identified enhanced expression of ARACNE network genes Hist1h2bf, Igtp, Mki67, Rasl10b, H2-Q6 and H2-Q7 to be associated with increased chromatin accessability at promoter regions.    Conclusions: We show that AECII sustainably retain an IAV-associated transcriptional configuration with epigenetic involvement, that serotype-specifically affects proliferation and accelerates and enhances the AECII transcriptional response, mainly to interferons, in secondary S.pn. infection.

overall_design: In total 42 microarrays were analyzed belonging to 14 experimental conditions with 3 independent replicates per condition.

first: Julia

middle: D

last: Boehme

first: Kristin

last: Schultz

first: Lars

last: Melcher

first: Katharina

last: Schott

first: Elif

last: Gelmez

first: Andrea

last: Kröger

first: Sabine

last: Stegemann-Koniszewski

first: Dunja

last: Bruder


title: Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

institute: Duke University

summary: DNA methyltransferases DNMT3A- and DNMT3B-mediated de novo DNA methylation critically regulates epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote macro-oligomer formation, leading to aberrant DNA methylation that in turn contributes to pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the hotspot mutation-induced functional mis-regulation of DNMT3A remains unclear. Here, we report the crystal structure of DNMT3A methyltransferase (MTase) domain, revealing a molecular basis for its DNMT3B-distinct oligomerization behavior. Introducing DNMT3B-converting mutations to DNMT3A R882 mutants also led to structure determination of R882H- and R882C-mutated DNMT3A, which show enhanced intermolecular contacts than wild-type DNMT3A. Consistently, our in vitro and genomic DNA methylation analyses reveal that the DNMT3B-converting mutations eliminate the gain-of-function effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutation-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

overall_design: TF-1 cell line was stably expressed with Myc-tagged DNMT3A (isoform 1), either wild-type (WT) or AML-associated hotspot mutant (R882C or R882H) or the one carrying an additional macro-oligomerization-decreasing mutation, namely, R676K (WT-K), R882C/R676K (R882C/K), R882C/M674T/R676K (CTK), R882H/R676K (R882H/K) or R882H/M674T/R676K (R882H/TK). 100,000 of TF-1 cells were subjected to CUT&Tag using anti-Myc tag antibody (CST #2276s). 5,000 of NIH-3T3 cells with stable expression of Myc-tagged WT DNMT3A1 were added to all TF-1 cell groups as spike-in normalization control.

first: Guo

last: Yiran

first: Wang

last: Greg


title: Potential cyclooxygenase-2-independent mechanisms of the anti-proliferation and anti-fibrotic effects of celecoxib on the human intrahepatic biliary epithelial cell line HIBEpiC assessed by bulk-RNA sequencing

summary: This experiment utilized next-generation sequencing (NGS) to identify potential cyclooxygenase-2-independent mechanisms of the anti-proliferation and anti-fibrotic effects of celecoxib on the human intrahepatic biliary epithelial cell line HIBEpiC. HIBEpiC cells were cultured in vitro. Treatments were vehicle, 20 ng/mL of TGF-β (T20), combination of 10μM of celecoxib plus 20 ng/mL of TGF-β (C10+T20), or combination of 10μM of 2,5-dimethyl-celecoxib plus 20 ng/mL of TGF-β (DC10+T20) before NGS. The gene expression were analyzed. Overall, the results suggested that celecoxib had a COX-2-independent inhibitory effect on the proliferation and profibrotic behavior of TGF-β-stimulated CXCL12+ HIBEpiC cells, probably because of the regulation of the cell cycle and several other signaling pathways.

overall_design: HIBEpiC cells were cultured in vitro. Treatments were vehicle, 20 ng/mL of TGF-β (T20), combination of 10μM of celecoxib plus 20 ng/mL of TGF-β (C10+T20), or combination of 10μM of 2,5-dimethyl-celecoxib plus 20 ng/mL of TGF-β (DC10+T20). Vehicle: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% Bovine Serum Albumin (BSA) and 0.1% DMSO for 28 hours. T20: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% BSA and 0.1% DMSO for 4 hours, and then the TGF-β were added to the final concentration of 20 ng/mL for further 24 hours incubation. C10+T20: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% BSA and 10μM of celecoxib (final concentration of DMSO: 0.1%) for 4 hours, and then the TGF-β were added to the final concentration of 20 ng/mL for further 24 hours incubation. DC10+T20: HIBEpiC cells were cultured in RPMI 1640 medium with 0.5% BSA and 10μM of 2,5-dimethyl-celecoxib (final concentration of DMSO: 0.1%) for 4 hours, and then the TGF-β were added to the final concentration of 20 ng/mL for further 24 hours incubation. The cell experiments were performed in triplicate. Then, the cells were harvested for NGS.


title: Malignant A-to-I RNA editing by ADAR1 drives T-cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing

city: LA JOLLA

first: QINGFEI

last: JIANG

address: 2880 TORREY PINES SCENIC DR

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

summary: Leukemia initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for developing targeted approaches to eliminate LICs and prevent relapse. Here, we show that the RNA editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine (A-to-I) editing is a common attribute of relapsed T-ALL regardless of molecular subtypes. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL PDX models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA to avoid detection by the innate immune sensor MDA5. Moreover, we uncovered that the cell intrinsic level of MDA5 dictates the dependency on ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents an effective therapeutic strategy for eliminating T-ALL LICs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T-ALL patient samples following ADAR1 knockdown by shRNA.

first: Maria

last: Rivera

first: Haoran

first: Jessica

last: Pham

first: Jane

last: Isquith

first: Qingchen

last: Zhou

first: Larisa

last: Balaian

first: Roman

last: Sasik

first: Sabina

last: Enlund

first: Adam

last: Mark

first: Wenxue

last: Ma

first: Frida

last: Holm

first: Kathleen

last: Fisch

first: Dennis

last: Kuo

first: Catriona

last: Jamieson

first: Qingfei

last: Jiang


title: Parthenolide induces ROS-dependent cell death in human gastric cancer cells

city: HEFEI

first: wang

last: hiuru

state: State...

address: NO 17 Lujiang ROAD , HEFEI

department: The First Affiliated Hospital of USTC

institute: USTC

summary: Parthenolide (PN), a key active ingredient of feverfew, has been used to treat gastrointestinal disorders. However, the mechanism of the cytotoxic effect exerted by PN on tumor cells is not elucidated now. MGC-803 cells treated with and without PN were separately subjected to high throughput RNA sequencing (RNA-Seq).

first: Huiru

last: Wang

first: Yang

last: Chen


title: Essential roles of LINE-1 in the regulation of neural progenitor cells

city: La Jolla

first: Fred

last: Gage

address: 10010 N Torrey Pines Rd

department: Laboratory of Genetics

institute: Salk Institute

summary: Knockdown of LINE-1s induced neural differentiation, therefore the project seeks molecular underlying mechanims after applying shRNs against LINE-1s in mouse neural progenitor cells

overall_design: shRNAs against young LINE-1s and old LINE-1s were introduced into mouse neural progenitor cells. In addition, full-length LINE-1 was simultaneously introduced with shRNA targeting young LINE-1.

first: Tomohisa

last: Toda

first: Sara

middle: B

last: Linker

first: Tracy

middle: A

last: Bedrosian


title: Transcriptomic analysis of lungs with mesnchyme-specific deletion of Sin3a transcriptional regulator

first: David

last: McCulley

summary: Congenital diaphragmatic hernia (CDH) is a common and severe congential malformation characterized by defects in diaphragm, lung, and pulmonary vascular developent. Despite the frequency and severity of CDH, the underlying developmental mechanisms are not understood. We identified SIN3A loss of function sequence variants in two patients with CDH. To understand the genetic and developmental mechanisms of CDH, we generated Sin3a conditional knockout mice that lack Sin3a expression in the lung mesenchyme. SIN3A plays a critcal role during development, directing cell lineage specification and cell cycling. Despite this role, SIN3A sequence variants have not been reported in patients with CDH or other congential malformations. We found that Sin3a CKO mice have abnormal lung stucture at birth into adulthood. To determine the role of Sin3a in lung mesenchymal development, we performed transcriptomic analysis of Sin3a CKO and control lungs at embryonic day 16 (E16) when cell cycling defects were first evident, postnatal day 0 (P0) when lung defects were first evident, and P3 when lung phenotyopes worsened. In this dataset are expression data from dissected embryonic and postnatal lungs of Sin3a CKO and control mice. Sin3a CKO mice have conditional deletion of Sin3a in the lung mesenchyme directed by Tbx4rtta; tetocre (Tbx4rtta; tetocre; Sin3a flox/flox CKO). Control mice are heterozygous for Sin3a in the lung mesenchyme (Tbx4rtta; tetocre; Sin3a flox/WT). These data were used to identify transcriptional changes due to loss of Sin3a in the lung mesenchyme.

overall_design:
4 controls and 4 Sin3a CKO lungs were collected at each timepoint (E16, P0, and P3). We generated comparisons in differential gene expression between control and Sin3a CKO samples at each stage.
contributor University of Wisconsin-Madison Gene Expression Center
contributor University of Wisconsin-Madison Gene Bioinformatics Center

first: Gia

last: Stokes


title: FEAR antiviral response pathway is independent of interferons and countered by poxvirus proteins

city: Dallas

first: Dustin

last: Hancks

address: 6000 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: The human facilitates chromatin transcription (FACT) complex is a chromatin remodeller composed of human suppressor of Ty 16 homologue (hSpt16) and structure-specific recognition protein-1 subunits that regulates cellular gene expression. Whether FACT regulates host responses to infection remained unclear. We identify a FACT-mediated, interferon-independent, antiviral pathway that restricts poxvirus replication. Cell culture and bioinformatics approaches suggest that early viral gene expression triggers nuclear accumulation of SUMOylated hSpt16 subunits required for the expression of E26 transformation-specific sequence-1 (ETS-1)-a transcription factor that activates virus restriction programs. However, biochemical studies show that poxvirus-encoded A51R proteins block ETS-1 expression by outcompeting structure-specific recognition protein-1 binding to SUMOylated hSpt16 and by tethering SUMOylated hSpt16 to microtubules. Furthermore, A51R antagonism of FACT enhances poxvirus replication in human cells and virulence in mice. Finally, we show that FACT also restricts rhabdoviruses, flaviviruses and orthomyxoviruses, suggesting broad roles for FACT in antiviral immunity. Our study reveals the FACT-ETS-1 antiviral response (FEAR) pathway to be critical for eukaryotic antiviral immunity and describes a unique mechanism of viral immune evasion.

overall_design: A549 cells stably expressing control (pLKO1) or hSpt16 shRNA from transduced lentiviruses were mock-infected or infected with DA51RFA51R or DA51R strains for 1 h (MOI = 50). Following infection, complete media was added and incubated until 4 hpi when cells were lysed and total RNA was extracted for library preparations. All infection treatments were performed in triplicate for a total of 18 samples (libraries) to be analyzed. Control

first: Don

last: Gammon

first: Emily

last: Rex

first: Sruthi

last: Chappidi

first: Chelsea

last: Pinkham


title: Structure-guided functional suppression of AML-associated DNMT3A R882 mutations [methylation]

first: Yiran

last: Guo

type: Methylation profiling by genome tiling array

overall_design: TF-1 cell line was stably expressed with DNMT3A (isoform 1), including wild-type (WT) or AML-associated hotspot mutant (either R882C or R882H) or the one carrying an additional macro-oligomerization-decreasing mutation, namely, R676K (i.e., WT-K), M674T/R676K (WT-TK), R882C/R676K (CK), R882C/M674T/R676K (CTK), R882H/R676K (HK), or R882C/M674T/R676K (HTK). The total genomic DNA was extracted, subjected for bisulfite conversion, and then analyzed with the Illumina Infinium Methylation EPIC arrays. Replicated samples (n = 3-4) were used per group.

first: Greg


title: Vitamin A treatment rescues neonatal infection-induced durably impaired lymph node function (scRNA-Seq)

city: Nanjing

first: Mangge

last: Zou

address: No.6 Building, Life Science TechTown, 568 Longmian Avenue Jiangning District

institute: Legend Biotech

summary: Gut-draining mesenteric and celiac lymph nodes (mLNs and celLNs) critically contribute to peripheral tolerance towards food and microbial antigens by efficiently supporting the de novo induction of regulatory T cells (Tregs). These tolerogenic properties of mLNs and celLNs are stably imprinted within stromal cells (SCs) by microbial signals and vitamin A (VA), respectively. In the present study, we demonstrated that a transient neonatal gastrointestinal infection long-lastingly affects the functionality of celLN by permanently abrogating the efficient Treg-inducing capacity of celLN SCs. The neonatal infections durably shifted the heterogeneity of celLN SCs with permanently altered expression of genes involved in chemotaxis and inflammatory responses, resulting in a lastingly skewed dendritic cell (DC) composition. Mechanistically, transiently reduced VA levels caused the long-lastingly impaired celLN function, which could be rescued by an early-life VA supplementation. Together, our data highlight the therapeutic potential of VA treatment post gastrointestinal infections in infants.

overall_design: Single cell RNA-seq on FACS-isolated CD45-CD24-celiac lymph node stromal cells of PBS-treated and Yersinia-treated mice

first: Joern

last: Pezoldt

first: Carolin

last: Wiechers

first: Marina

last: Pils

first: Juhao

last: Yang

first: Michael

last: Beckstette

first: Juliane

last: Mohr

first: Lars

last: Philipsen

first: Andreas

last: Mueller

first: Lianxu

last: Hao

first: Till

last: Strowig

first: Aline

last: Dupont

first: Mathias

last: Hornef

first: Petra

last: Dersch

first: Jens

last: Raila

first: Jochen

last: Huehn


title: Vitamin A treatment rescues neonatal infection-induced durably impaired lymph node function (RNA-Seq DC)

overall_design: RNA-seq with 3 replicates per condition migratory or resident dendritic cells ex vivo isolated from lymph node.


title: Vitamin A treatment rescues neonatal infection-induced durably impaired lymph node function (RNA-Seq FSC)

overall_design: RNA-seq with 3 replicates per condition fibroblastic stromal cells ex vivo isolated from lymph node.


title: SMCHD1 variants induce variegated expression in Facio Scapulo Humeral Dystrophy and Bosma Arhinia and microphtalmia syndrome (Methylation).

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

institute: Aix-Marseille Université - Marseille Medical Genetics

summary: Determination of SMCHD1 epi-signature in type 2 Facio Scapulo Humeral Dystrophy (FSHD2) and Bosma Arhinia and Microphtalmia Syndrome (BAMS).

overall_design: By combining RNA Seq, DNA methylation profiling and ChIP-Seq, we showed that SMCHD1 regulates repressed chromatin but also cis-regulatory elements and enhancers.

first: Frédérique

first: Camille

last: Laberthonnière

first: Raphaël

last: Chevalier


title: The M1 aminopeptidase NPEPPS is a novel regulator of cisplatin sensitivity

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Platinum-based chemotherapeutics are used in many combination regimens in cancer. Despite extensive use across diverse cancer types, there is room for improved efficacy and patient selection for treatment. Here, we use bladder cancer to address both issues. A multi-omic assessment of five human bladder cancer cell lines and their chemotherapy resistant derivatives, coupled with in vitro whole-genome CRISPR screens were used to define functional drivers of treatment resistance. We identified 46 genes that sensitized the resistant cell lines to cisplatin plus gemcitabine (GemCis), a standard combination therapy in bladder cancer. Most genes were involved with DNA damage and repair pathways, which have previously been associated with enhanced sensitivity to cisplatin. Evaluating expression of the 46 genes in the whole transcriptome and proteome data in parental and resistant lines identified the puromycin sensitive aminopeptidase, NPEPPS, as a novel hit. Depletion of NPEPPS resulted in sensitizing resistant bladder cancer cells to cisplatin in vitro and in xenograft experiments. Pharmacologic inhibition of NPEPPS with tosedostat in cells and in chemoresistant, bladder cancer patient-derived tumoroids improved response to cisplatin. Prior work found NPEPPS in a protein complex with volume regulated anion channels (VRACs) in several cell line models. Interestingly, depletion of two VRAC subunits, LRRC8A and LRRC8D, known importers of intracellular cisplatin, enhanced resistance to cisplatin. Our findings support NPEPPS as a novel and druggable driver of cisplatin resistance with the potential for rapid translation to clinical investigation.

overall_design: Examination of five bladder cancer cell lines with parental along with their gemcitabine, cisplatin and gemcitabine + cisplatin resistant derivatives.

first: Robert

last: Jones

first: Hedvig

last: Vekony

first: Annie

last: Jean

first: Tahlita

last: Zuiverloon

first: Dan

last: Theodorescu

first: James

last: Costello


title: Single-cell Transcriptomes of RPE-specific AAV-GFP/AAV-PDGF-D mouse RPE-choroid complex

status: Public on Dec 30 2023

city: Guangzhou

first: Zhen

last: Xiong

address: No.7 Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

summary: Purpose: PDGF-D is a potent angiogenic and immune-related factor. It has been demonstrated that PDGF-D play roles in the pathological process of ocular angiogenesis and degenerative diseases. In our previous study, we established a retinal pigment epithelial (RPE) cell-specifc AAV-PDGF-D/GFP mouse model to study PDGF-D's role in age-related macular degeneration (AMD). In this study, we utilized the single-cell transcriptiome seqeuncing technique to explore the cell types of immune cells attracted by PDGF-D overepxression using the same animal models, with emphases on the impact of PDGF-D overexpression on individual cell's behaviour.

overall_design: scRNA-seq of mouse RPE-choroid complex received subretina injection of RPE-specific AAV-GFP and AAV-PDGF-D , which were collected after 4-weeks injection of AAVs.

first: Jianing

last: Zhang

first: Wanhong

last: Li

first: Xuri


title: LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase–like 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here we show that LOXL2 interacts with RUVBL1, RUVBL2, BAF53, and DMAP1, a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).

overall_design: ChIP-seq (5 samples), RNA-seq (8 samples) and ATAC-seq (2 samples)  of MDA-MB-231 cells. shControl means shRNA Control, shLOXL2 means knock-down of LOXL2 and shRUVBL2 means know knock-down of RUVBL2.

first: Gemma

last: Serra-Bardenys

first: Sandra

last: Peiró


title: The M1 aminopeptidase NPEPPS is a novel regulator of cisplatin sensitivity. CRISPR Synthetic Lethal Screen.

overall_design: Whole genome CRISPR screening in bladder cancer cell lines to identify synthetic lethal interactions with gemcitabine and cisplatin combination therapy.


title: Kir4.1 channels contribute to astrocyte CO2/H+-sensitivity and the drive to breathe

status: Public on Dec 29 2023

city: Farmington

first: William

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Astrocytes in the retrotrapezoid nucleus (RTN) stimulate breathing in response to CO2/H+, however, it is not clear how these cells detect changes in CO2/H+. Considering Kir4.1/5.1 channels are CO2/H+-sensitive and important for several astrocyte-dependent processes, we consider Kir4.1/5.1 a leading candidate CO2/H+ sensor in RTN astrocytes. To address this, we show that RTN astrocytes express Kir4.1 and Kir5.1 transcripts. We also characterized respiratory function in astrocyte-specific inducible Kir4.1 knockout mice (Kir4.1 cKO); these mice breathe normally under room air conditions but show a blunted ventilatory response to CO2, which could be partly rescued by viral mediated re-expression of Kir4.1 in RTN astrocytes. At the cellular level, astrocytes in slices from astrocyte-specific inducible Kir4.1 knockout mice are less responsive to CO2/H+ and show a diminished capacity for paracrine modulation of respiratory neurons. These results suggest Kir4.1/5.1 channels in RTN astrocytes contribute to respiratory behavior.

overall_design: Examination of cells from rostral ventrolateral medulla brainslices from 4-OH tamoxifen injected Kir4.1 cKO mice

first: Colin

last: Cleary

first: Daniel

last: Mulkey


title: SMCHD1 variants induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome (ChIP-Seq).

first: Frederique

last: Magdinier

overall_design: By combining RNA Seq, DNA methylation profiling and ChIP-Seq, we showed that SMCHD1 regulates repressed chromatin but also cis-regulatory elements and enhancers. Samples are analyzed using two biological replicates

first: Camille

last: Laberthonnière

first: Raphael

last: Chevalier


title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells

city: Montreal

first: Mehdi

last: Amiri

state: Quebec

address: 1160 Pine Avenue West

country: Canada

institute: McGill University

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

overall_design: Refer to individual Series


title: NGS-based miRNome reveals regulation in the miR-34/miR-449 cluster targetome in sinonasal cancers.

status: Public on Dec 28 2023

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

institute: University of Verona


title: Effect of K7M2 derived extracellular vesicles on gene expression of primary bone marrow derived macrophage

first: Chuangzhong

last: Deng

state: Guangdong China

address: 651 Dongfeng East Rd

department: Department of Musculoskeletal Oncology

institute: Sun Yat-sen University Cancer Center

summary: To profile the molecular changes that are caused by osteosarcoma cell-derived EVs macrophages, we performed RNA-seq of BMDMs treated with K7M2-EVs or the PBS control.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of three independent experiments.
Comparative gene expression profiling analysis of RNA-seq data for BMDMs treated with K7M2-EVs (10 μg) or PBS control for 24 hours

first: Jin

last: Wang


title: Consequences of chromatin replication on RNAPII activity and transcriptional outcome [ChrRNAseq]

status: Public on Dec 26 2023

city: Seville

first: Cristina

last: González-Aguilera

state: Seville

address: Avenida Américo Vespucio, 24

institute: CABIMER - CSIC

summary: In the nucleus of the eukaryote cell, the genetic material is organized in the form of chromatin where DNA associates with nucleosomes, formed by an octamer of histone proteins, to provide the correct environment to regulate gene expression, maintain cellular identity and avoid disease. Despite the important role of chromatin organization in cellular function, in each cell division chromatin is totally disorganized. Nucleosomes are evicted ahead of the replication fork and will have to be recycled together with newly synthetized histones to maintain nucleosome density in the two daughter strands. This produce changes in chromatin accessibility and a dilution in epigenetic information. To date, it is not clear how these chromatin and epigenetic changes can affect gene expression. Here, we have used the cutting-edge technology ChOR-seq (Chromatin Occupancy after Replication and sequencing) and ChrRNA-seq (Chromatin-associated RNA-seq) to investigate the distribution and abundance of the RNA Polymerase II (RNAPII) in newly replicated chromatin and nascent RNA levels in human cells.

overall_design: Study of the transcriptional outcome after chromatin replication by chromatin-associated RNA sequencing (ChrRNA). All experiments were done in duplicates.

first: Federica

last: Bruno

first: Cristóbal

last: Guisado

middle: G

last: Aguilera


title: Differences in the microbiome of the small intestine of Leghorn lines divergently selected for antibody titer to sheep erythrocytes suggest roles for commensals in host humoral response

city: Raleigh

first: Shelly

last: Nolin

state: NC

address: 147 Scott Hall, 2711 Founders, Ashwell Lab

department: Prestage Dept of Poultry Science

institute: NC State University

summary: For forty generations, two lines of White Leghorn chickens have been selected for high (HAS) or low (LAS) antibody response to a low dose injection of sheep red blood cells (SRBCs).  Their gut is home to billons of microorganisms and the largest number of immune cells in the body; therefore, the objective of this experiment was to gain understanding of the ways the microbiome may influence the differential antibody response observed in these lines.  We achieved this by characterizing the small intestinal microbiome of HAS and LAS birds, determining their functional microbiome profiles, and by using machine learning to identify microbes which best differentiate HAS from LAS and associating the abundance of those microbes with host gene expression.  Microbiome sequencing reveals greater diversity in LAS but statistically higher abundance of several strains, particularly those of lactobacillus, in HAS.  Enrichment of microbial metabolites implicated in immune response such as lactic acid, short chain fatty acids, amino acids, and vitamins were different between HAS and LAS.  The

overall_design: Characterize the microbiome of intestinal segments of chickens from genetic lines selected for high and low antibody response to sheep red blood cells via 16S sequencing and associate microbiome differences with antibody response phenotype.

first: Paul

last: Siegel

first: Christopher

last: Ashwell


title: mTOR-CNP-Tight junction/Ion pump/Aquaporin axis, a target of FSH signaling, controls the initial formation of follicular antrum

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

summary:
Background: The initial formation of follicular antrum (iFFA) is a milestone in folliculogenesis, which serves as a boundary between gonadotropin (GTH) -independent folliculogenesis and GTH-dependent folliculogenesis and endows the follicle's ability to acquire response to GTHs and continue to survive. However, iFFA is a barren field in folliculogenesis research, which do not match its physiological significance.
Methods:In this study, transcriptome sequencing was used to comprehensively analyze the changes in the life activities of cells in the ovary during iFFA, and then the regulatory mechanism of iFFA was deduced based on the results of omics analysis, and it was systematically verified by experiments.
Result: Herein, we conducted in vivo and in vitro experiments to studied iFFA in a mouse model, and revealed that: (1) iFFA is a physiological process of active cell proliferation, increased energy expenditure, enhanced secretory activity and increased moisture absorption, accompanied by complex changes in epigenetic modification, bioclock regulation, and cell junctions; (2) iFFA and blastocoel formation may be conservatively regulated in fluid accumulation, and tight junctions, ion pumps and aquaporins underlie the structural, kinetic and transport foundations for fluid accumulation during iFAA, respectively; (3) mTOR-CNP is the main signal cascade regulating iFFA, it initiated iFFA by targeting tight junction/ion pumps/aquaporins and follicular cell proliferation; (4) FSH controls iFFA by targeting the intra-ovarian mTOR-CNP cascade; (5) mTOR activator could be used as an improver to increase the efficiency of in vitro follicular culture technology.
Conclusion: Overall, this study elucidated the changes in follicular cells' life activities in preparation for iFFA, proposed the model of "Dam-Pump-Pipe" to explain the accumulation of follicular fluid, and confirmed that FSH-mTOR-CNP-Tight junction/Ion pumps/Aquaporins is the core cascade controlling iFFA. These findings would help to fill in the gaps in iFFA research, and enrich the theory of folliculogenesis regulation.

overall_design: Ovarian mRNA profiles of Postnatal day 14，15 and 16 mice .There are 9 samples represented three time points PD14 (n=3), PD15 (n=3) and PD16 (n=3)

first: Xiaodong

first: Shanshan

last: Zhou

first: Zian

last: WU

first: Changjiu

last: He


title: Consequences of chromatin replication on RNAPII activity and transcriptional outcome [HU]

overall_design: Analysis of S2P RNAPII distribution and abundance in newly replicated and mature chromatin by ChOR-seq in HeLa S3 cells. All experiments were done in duplicates. Replicated chromatin was labelled in early S and treated with hydroxyurea (HU) to slow down replication fork speed. Chromatin of Drosophila melanogaster S2 cells were used as spike-in.


title: Consequences of chromatin replication on RNAPII activity and transcriptional outcome [ChOR-seq and EdU-seq]

overall_design: Analysis of total RNAPII and S2P RNAPII distribution and abundance in newly replicated and mature chromatin by ChOR-seq in HeLa S3 cells. All experiments were done in duplicates. Replicated chromatin was labelled in early S. Chromatin of Drosophila melanogaster S2 cells were used as spike-in.

last: Coronel Guisado


title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells [Ribo-Seq]

summary: The integrated stress response (ISR) is critical for cell survival under stress. In response to diverse environmental cues, eIF2αbecomes phosphorylated, engendering a dramatic change in mRNA translation. The activation of ISR plays a pivotal role in the early embryogenesis but the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESC) is largely unexplored. We employ a multi-omics approachconsisting of ribosome profiling, proteomics, and metabolomics inwild-type(eIF2α+/+)andphosphorylation-deficient mutant eIF2α(eIF2αA/A)mouse ESCs (mESCs) to investigate phosphorylated (p)-eIF2α-dependent translational control of naïve pluripotency. We show a transient increase in p-eIF2α in the naïve epiblast layer of E4.5 embryos. Absence of eIF2α phosphorylation engenders an exit from naive pluripotency following 2i (two chemical inhibitors of MEK1/2 and GSK3α/β) withdrawal. p-eIF2α controls translation of mRNAs encoding proteins which govern pluripotency, chromatin organization, and glutathione synthesis.Thus, p-eIF2αacts as a key regulator of the naïve pluripotency gene regulatory network.

overall_design: To delineate the mechanisms by which phosphorylation of eIF2α controls the naïve state of pluripotency, we performed ribosome profiling (Ribo-Seq) and RNA-Seq  on eIF2αA/A (KI) and eIF2α+/+ (WT) mouse embryonic stem cells (mESCs) grown in LIF/2i and LIF conditions

first: Soroush

last: Tahmasebi

first: Nahum

last: Sonenberg


title: Inducible degradation of the Mediator subunit Med19 reveals a dedicated role in the regulation of developmental genes expression

city: Toulouse

first: muriel

last: BOUBE-TREY

address: 4bis av Hubert Curien

institute: CNRS INSERM

summary: In the Drosophila wing imaginal disc, by using a inductible degradable version of  Med19 degradation with RNAseq, we got access to the early consequences of Med19 depletion on gene expression. We showed that less than a quarter of the genes expressed in the wing disc were deregulated after Med19 loss. Strikingly, these genes exhibit a spatio-temporal expression pattern like transcription factors or Notch responsive genes that reveals Med19 dedicated role in the regulation of developmental gene transcription.

overall_design: RNAseq was done on drosophila wing discs from female ub> Med19AID L3 larvae that were either fed with Auxin analog NAA (AIDUbAux) to induce M19 degradation, or not (AIDUb) as a control. A second control was performed to monitor Auxin effect on drosophila wing discs from female Med19AID L3 larvae that were fed with Auxin (AIDAux).

first: Emmanuelle

last: Guillou

first: Muriel

last: Boube

first: Denis

last: Jullien


title: The Receptor Binding Domain of SARS-CoV-2 Omicron Subvariants Targets Siglec-9 to Decrease the Immunogenicity by Preventing Phagocytosis of Macrophages

first: Xin

address: Zhongshan 2nd Road

institute: Sun Yat-Sen University

summary: SARS-CoV-2 Omicron infection results in a milder clinical feature compared to the Delta strain. The development of Omicron specific vaccine has also been hampered due to the low immunogenicity. By reverse-mutating the amino acids in the Omicron receptor binding domain (RBD), we identified that the mutation from Phenylalanine 375 (F375) in the Omicron spike to Serine 375 (S375) in Delta and other early strains significantly enhances the immune response in the manner of vaccines. Interestingly, the new evolution of the 371FAPF375FAF sequence in Omicron exhibited a potent inhibitory effect on macrophage uptake of the RBD nanoparticle or spike-pseudovirus particles. Omicron RBD enhances binding to Siglec-9 on macrophages to reduce the immunogenicity and increase the immune evasion, which could be abrogated by Serine 375 mutation. Based upon these observations, we further developed a bivalent Omicron RBD with S375 mutation and Delta RBD nanoparticle vaccine, which elicited potent and broad neutralizing antibodies in mice, rabbits, and rhesus macaques. Our research suggests that manipulating the Siglec-9 pathway could be a promising approach to enhancing vaccine response. Importantly, our findings suggest that Omicron subvariants have developed a new strategy to evade immune surveillance by impairing the phagocytosis and antigen presentation processes of macrophages.

overall_design: WT or Siglece-/- BMDMs were pretreated with XBB.1 or XBB.1(S375) RBD NPs for 24 hours before stimulation with LPS (100 ng/ml) for 48 hours. Total RNA was isolated and assayed by RNA sequencing. Triplicates analyzed for each condition.

first: Zhang

last: Hui

first: He

last: Xin

first: Xi

last: Zhihui


title: The RHW1-ZCN4 regulatory pathway confers natural variation of husk leaf width in maize

status: Public on Dec 25 2023

city: Beijing

first: Aiai

last: Xia

address: NO2 Yuanmingyuan West Road, Haidian, Beijing

department: Plant Genetics and Breeding

institute: China Agricultural University

summary: Maize husk leaf - the outer leafy layers covering the ear - modulates kernel yield and quality. Despite its importance, however, the genetic controls underlying husk leaf development remain elusive. Our previous genome-wide association study identified a single nucleotide polymorphism located in the gene RHW1 (Regulator of Husk leaf Width) that is significantly associated with husk leaf-width diversity in maize. Here, we further demonstrate that a polymorphic 18-bp InDel (insertion/deletion) variant in the 3' untranslated region of RHW1 alters its protein abundance and accounts for husk leaf width variation. RHW1 encodes a putative MYB-like transcriptional repressor. Disruption of RHW1 altered cell proliferation and resulted in a narrower husk leaf, whereas RHW1 overexpression yielded a wider husk leaf. RHW1 positively regulated the expression of ZCN4, a well-known TFL1-like protein involved in maize ear development. Dysfunction of ZCN4 reduced husk leaf width even in the context of RHW1 overexpression. The InDel variant in RHW1 is subject to selection and is associated with maize husk leaf adaption from tropical to temperate regions. Overall, our results identify that RHW1-ZCN4 regulates a pathway conferring husk leaf width variation at a very early stage of husk leaf development in maize.

overall_design: RNA-seq liabraries were prepared using early developing ears (length, 0–0.5 cm) of rhw1-1, OE#1, and wild-type plants


title: Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells [RNA-Seq]

first: Mehdi

last: Amiri

department: Biochemistry


title: Immune evasion in lung metastasis of leiomyosarcoma: upregulation of EPCAM inhibits CD8⁺ T cell infiltration

status: Public on Dec 22 2023

city: Fukuoka

first: Masaya

last: Kanahori

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Orthopaedic Surgery

institute: Kyushu University

summary:
Background: Leiomyosarcomas are among the most common histological types of soft tissue sarcoma (STS), with no effective treatment available for advanced patients. Lung metastasis, the most common site of distant metastasis, is the primary prognostic factor. We analysed the immune environment targeting lung metastasis of STS to explore new targets for immunotherapy.
Methods: We analysed the immune environment of primary and lung metastases in 38 patients with STS using immunohistochemistry. Next, we performed gene expression analyses on primary and lung metastatic tissues from six patients with leiomyosarcoma. Using human leiomyosarcoma cell lines, the effects of the identified genes on immune cells were assessed in vitro.
Results: Immunohistochemistry showed a significant decrease in CD8⁺ cells in the lung metastases of leiomyosarcoma. Among the genes upregulated in lung metastases, epithelial cellular adhesion molecule (EPCAM) showed the strongest negative correlation with the number of CD8⁺ cells. Transwell assay results showed that the migration of CD8⁺ T cells was significantly increased in the conditioned media obtained after inhibition or knock down of EPCAM.
Conclusions: EPCAM was upregulated in lung metastases of leiomyosarcoma, suggesting inhibition of CD8⁺ T cell migration. Our findings suggest that EPCAM could serve as a potential novel therapeutic target for leiomyosarcoma.

overall_design:
To investigate changes in gene expression in human leiomyosarcoma cell lines in which EPCAM was inhibited or knocked down, we created three clones of TYLMS-1 cells treated with tumour necrosis factor-α converting enzyme inhibitor (TAPI) + γ-secretase inhibitor (DAPT), three clones of untreated TYLMS-1 cells (dimethyl sulfoxide added), three clones of TYLMS-1 cells transfected with siEPCAM, and three clones of TYLMS-1 cells transfected with scrambled siRNA, for a total of 12 TYLMS-1 cell clones.
We then performed differentially expressed genes analysis using data obtained from RNA-seq of 12 TYLMS-1 cell clones: comparing gene expression in TAPI + DAPT treated cells and untreated cells, and in siEPCAM-transfected cells and scrambled siRNA-transfected cells.

first: Eijiro

last: Shimada

first: Yoshihiro

last: Matsumoto


title: Vitamin A treatment rescues neonatal infection-induced durably impaired lymph node function

first: Mangge

last: Zou


title: NGS-based miRNome reveals regulation in the miR-34/miR-449 cluster targetome in sinonasal cancers [RIP-seq]

first: Marzia

last: Rossato

summary: Using NGS-based miRNome, followed by AGO2-RIP-seq, the miR-34c and miR-449a and their direct targets were identified as factors involved in the development and progression of sinonasal cancers (SNCs). Both miR-34c and miR-449a were independent prognostic biomarkers and were associated with patient outcome.

overall_design: AGO2-RIP-seq, to identify the miR-34c/miR-449a  targetome

first: Marco

last: Tomasetti

first: Massimo

last: Re


title: Uncovering the divergent epigenetic background of KRAS-mutant NSCLC in mouse and human cell lines

city: Austin

first: Eleftherios

last: Bochalis

address: 2515 Speedway

department: College of Pharmacy

institute: The University of Texas at Austin

summary:
Illumina miRNA-seq method to uncover the expression profile of NSCLC in-vitro experimental models consisting of cell lines A549, H460 compared to healthy BEAS-2B cell line, and lung tissue (NSCLC and paired normal) from urethane treated 6-week-old FVB/NJ mice.
We aimed to uncover the divergent epigenetic background of KRAS-mutant NSCLC in mouse and human cell lines, extensively used as biological models in relevant research. To that end, we have comprehensively mapped the functional miRNA and lncRNA landscape of human (A549 and H460) and mouse (experimentally developed LUAD) NSCLC models and correlated current results with LRF/ZBTB7A expression

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total RNA was extracted from cell lines and mice and library preparation was performed by QIAseq miRNA library kit. Adapters were ligated to 3’ and 5’ ends of miRNAs and subsequently, universal cDNA synthesis reaction with Unique Molecular Indices (UMI) assignment, cDNA cleanup, library amplification and library cleanup, were performed. Downstream RNA sequencing reactions were performed in Illumina iSeq 100 instrument (Illumina, Inc., US) in single-ended mode with 75 bp sequence length and total reads ranging from 1.0 to 1.5 million per sample.

first: Argyro

last: Sgourou

first: Katerina

last: Athanasopoulou

first: Vasiliki

last: Chondrou

first: Irene

last: Dereki

first: Argyri

last: Chroni


title: C57Bl6J retina lysates

status: Public on Dec 19 2023

first: Mike

last: Sapieha

address: 5415 Boul. L'Assomption

institute: Hôpital Maisonneuve-Rosemont

summary: Diabetic retinopathy (DR) is one of the main causes of blindness in working age populations in industrialized countries. It is estimated that close to 100 million individuals worldwide suffer from DR. Regrettably, relatively little is known of the cellular processes at play during late stages of the disease, especially concerning diabetic macular edema (DME). Streptozotocin-induced diabetic retinopathy (STZ) allows to reproduce experimentally in the mouse retina the retina vascular leakage and neuroegeneration features observed in human pathological retina with non-proliferative DR. Using agnostic and orthogonal approaches, in our work we demonstrate that in contrast to healthy retina, the STZ diabetic retina engages pathways of cell cycle arrest, resulting in cellular senescence. These findings combined with further pharmacological approaches provide mechanistic evidence supporting that targeting selectively senescent vessels in DR represents a potential treatment for high vascular permeability in DME.

overall_design: 2 samples were analyzed: control citrate (2 replicates), streptozotocin-induced diabetes or STZ (2 replicates)

first: Przemyslaw

first: Sergio

last: Crespo-Garcia

first: Manuel

last: Buscarlet


title: Chronic stress dampens Lactobacillus johnsonii-driven suppression on cancer stemness and enhances colorectal tumorigenicity

status: Public on Dec 20 2023

first: Qiuhua

last: Cao

address: No. 639 Longmian Avenue, Jiangning District, Nanjing, Jiangsu Province, China

institute: China Pharmaceutical University

summary: More than one-half of all colorectal cancer cases and deaths are due to modifiable risk factors, while psychological stress stands out as an important factor with mechanism unclear. Polymorphic microbiomes have pivotal roles in CRC. We therefore explored the impact of chronic stress on CRC, and the involvement of gut microbiome and its metabolites in this process.

overall_design: The colon mRNA profile of  AOM/DSS-induced mice that treatd with calm and chronic restraint stress by deep sequencing.

first: Yong

last: Yang

first: Xinghua

last: Gao