title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ets1 ATAC-Seq]

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: The gene regulatory network (GRN) underlying CTL differentiation and whether Tex responses can be functionally reinvigorated are incompletely understood. Here, we systematically mapped causal GRNs via single-cell CRISPR (scCRISPR) screens in vivo and discovered checkpoints for CTL differentiation.

overall_design: We used ATAC seq to compare chromatin accessibility profiles of Ets1 KO and Spike Tpex and Tex OT-I T cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor.

first: Peipei

last: Zhou

first: Hao

last: Shi

first: Hongling

last: Huang


title: Cardiomyocyte-Specific Disruption of the Circadian BMAL1–REV-ERBα/β Regulatory Network Impacts Distinct miRNA Species in the Murine Heart

status: Public on Nov 15 2023

city: Birmingham

first: Lamario

middle: J

last: Williams

state: AL

address: 1825 University Boulevard, Room 121

department: Medicine

country: USA

institute: University of Alabama at Birmingham

type: Non-coding RNA profiling by high throughput sequencing

summary: Circadian clocks are cell autonomous timekeeping mechanisms that govern critical biological processes.  Regarding the heart, the cardiomyocyte circadian clock regulates a diverse array of processes, ranging from transcription and translation, to signaling, metabolism, electrophysiology, and contractility.  The importance of this mechanism is underscored by observations that genetic disruption of the cardiomyocyte circadian clock in murine models leads to adverse cardiac remodeling, heart failure, and reduced lifespan.  However, the precise molecular links between the cardiomyocyte circadian clock and cardiac physiology/pathology have not been characterized fully.  Given that recent studies have highlighted that small RNA species (such as miRNAs) influence both cardiac physiology and pathology, we sought to determine the extent to which cardiomyocyte circadian clock disruption impacts cardiac small RNA species.  Accordingly, hearts were collected from cardiomyocyte-specific Bmal1 knockout (CBK) and littermate control (CON) mice at distinct times of the day.  Small RNA-seq revealed 47 differentially expressed miRNA species in CBK hearts (in the absence of significant time-of-day-dependent effects).  Subsequent bioinformatic analyses predicted that differentially expressed miRNA species in CBK hearts potentially influence processes such as circadian rhythmicity, cellular signaling, and metabolism.  Of the induced miRNAs in CBK hearts, 7 were predicted to be targeted by the transcriptional repressors REV-ERB/ (integral circadian clock components that are directly regulated by BMAL1).  Similar to CBK hearts, cardiomyocyte-specific Rev-erb/ double knockout (CM-RevDKO) mouse hearts exhibited increased let-7c-1-3p, miR-23b-5p, miR-139-3p, miR-5123, and miR-7068-3p levels.  Importantly, 19 putative targets of these 5 miRNAs were commonly repressed in both CBK and CM-RevDKO heart (of which 16 are targeted by let-7c-1-3p).  These observations suggest that disruption of the BMAL1–REV-ERB/ axis in the heart leads to induction of a subset of miRNAs, whose predicted mRNA targets have established functions in biological processes such as metabolism and cellular signaling.

overall_design: Comparative gene expression profiling analysis of small RNA-seq data for biventricular heart tissue isolated from cardiomyoycte-specific BMAL1 knockout (CBK) and littermate control (CON) mice. Heart tissue samples were harvested at different times of the day denoted as zeitgeber time (ZT).

first: Mary

last: Latimer

first: Gobinath

last: Shanmugan

first: Bryce

last: Carpenter

first: Mitchell

last: Lazar

first: Pieterjan

last: Dierickx

first: Martin

last: Young


title: TMEM106B reduction or partial depletion does not rescue GRN haploinsufficiency in mouse and iPSC-derived human microglia cell models [Mouse MG]

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

type: Expression profiling by high throughput sequencing

summary: Heterozygous mutations in the granulin (GRN) gene result in haploinsufficiency of the progranulin (PGRN) protein, a leading cause of frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP). Polymorphisms in the TMEM106B gene have been associated with disease risk in GRN mutation carriers and protective TMEM106B variants are associated with reduced levels of TMEM106B, suggesting that lowering TMEM106B might be therapeutic in the context of FTLD. Here we tested the impact of full deletion and partial reduction of TMEM106B in mouse and iPSC-derived human cell models of GRN deficiency. In vitro, TMEM106B deletion did not reverse transcriptomic and proteomic profiles in GRN-deficient microglia, with the exception of a small set of immune-related proteins in the NF-κB pathway.  In vivo, neither homozygous nor heterozygous Tmem106b deletion normalized disease-associated gene expression in sorted microglia, lipid abnormalities, or histopathology in Grn knock-out mice. Furthermore, Tmem106b reduction with antisense oligonucleotide (ASO) treatment was poorly tolerated in Grn knock-out mice. These data provide novel insight into TMEM106B and GRN  function in microglia cells but do not support lowering TMEM106B levels as a viable therapeutic strategy for treating FTLD-GRN.

overall_design: Comparative RNA-seq data for full deletion or partial reduction of Tmem106b in mice with Grn deficency.

first: Sara

middle: L

last: Dominguez

first: Arundhati

last: Sengupta-Ghosh

first: Brad

middle: A

last: Friedman

first: Amy

last: Easton


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ikzf1 ATAC-Seq]

state: TN

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We used ATAC seq to compare chromatin accessibility profiles of Ikzf1 KO and Spike Tpex and Tex OT-I T cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: EZH2 is a key component of Hepatoblastoma tumor cell growth

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: To understand molecular mechanisms driving HB pathogenesis, we hypothesize that pathologic activation of Enhancer of Zeste Homolog 2 contributes to hepatoblastoma propagation. Here we demonstrate that EZH2 promotes proliferation in HB cell lines through interaction with β-catenin, the most frequently mutated gene in HB. We demonstrate that canonical and noncanonical EZH2 signaling occur in HB tumor cells, likely driven by aberrant EZH2 expression. We use comparison groups of liver cancer, hepatocytes, and dermal fibroblasts to establish the hepatoblastoma identity of our patient-derived cell lines.

overall_design: Comparison of patient-derived hepatoblastoma cell lines with hepatocytes, hepatocellular carcinoma, and dermal fibroblasts using bulk RNAseq.

first: Kathryn

last: Glaser


title: TMEM106B reduction or partial depletion does not rescue GRN haploinsufficiency in mouse and iPSC-derived human microglia cell models [Mouse ASO]

summary: Heterozygous mutations in the granulin (GRN) gene result in haploinsufficiency of the progranulin (PGRN) protein, a leading cause of frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP). Polymorphisms in the TMEM106B gene have been associated with disease risk in GRN mutation carriers and protective TMEM106B variants are associated with reduced levels of TMEM106B, suggesting that lowering TMEM106B might be therapeutic in the context of FTLD. Here we tested the impact of full deletion and partial reduction of TMEM106B in mouse and iPSC-derived human cell models of GRN deficiency.  In vitro, TMEM106B deletion did not reverse transcriptomic and proteomic profiles in GRN-deficient microglia, with the exception of a small set of immune-related proteins in the NF-κB pathway.  In vivo, neither homozygous nor heterozygous Tmem106b deletion normalized disease-associated gene expression in sorted microglia, lipid abnormalities, or histopathology in Grn knock-out mice. Furthermore, Tmem106b reduction with antisense oligonucleotide (ASO) treatment was poorly tolerated in Grn knock-out mice. These data provide novel insight into TMEM106B and GRN  function in microglia cells but do not support lowering TMEM106B levels as a viable therapeutic strategy for treating FTLD-GRN.

overall_design: Comparative RNA-seq data for mice treated with Tmem106b ASOs.

first: Łukasz

last: Kiełpiński


title: Integrated transcriptomic and metabolomic analysis to reveal the mechanism of ischemic tolerance in TIA patients

city: Guangzhou

first: Chi Kwan

last: Tsang

address: Building #3, 613 Huangpu avenue west

department: Clinical Neuroscience Institute

country: China

institute: Jinan University

summary: Background: Transient ischemic attack (TIA) induces ischemic tolerance that can reduce the subsequent ischemic damage and improve prognosis of stroke patients. However, the underlying mechanisms remain elusive. Recent advances in plasma metabolomics analysis have made it a powerful tool to investigate human pathophysiological phenotypes and mechanisms of diseases. In this study, we aimed to identify the bioactive metabolites from the plasma of TIA patients for determination of their prophylactic and therapeutic effects on protection against cerebral ischemic stroke, and the mechanism of TIA-induced ischemic tolerance against subsequent stroke. Methods: Metabolomic profiling using liquid chromatography-mass spectrometry was performed to identify the TIA-induced differential bioactive metabolites in the plasma samples of 20 patients at day 1 (time for basal metabolites) and day 7 (time for established chronic ischemic tolerance-associated metabolites) after onset of TIA. Mouse MCAO-induced stroke model was used to verify their prophylactic and therapeutic potentials. Transcriptomics changes in circulating neutrophils of TIA patients were determined by RNA-sequencing. Multivariate statistics and integrative analysis of metabolomics and transcriptomics were performed to elucidate the potential mechanism of TIA-induced ischemic tolerance. Findings: Plasma metabolomics analysis identified five differentially upregulated metabolites associated with TIA-induced ischemic tolerance, namely all-trans 13,14 dihydroretinol (atDR), 20-carboxyleukotriene B4, prostaglandin B2, cortisol and 9-KODE. They were associated with the metabolic pathways of retinol, arachidonic acid, and neuroactive ligand-receptor interaction. Prophylactic treatment of MCAO mice with these five metabolites significantly improved neurological functions. Additionally, post-stroke treatment with atDR or 9-KODE significantly reduced the cerebral infarct size and enhanced sensorimotor functions, demonstrating the therapeutic potential of these bioactive metabolites. Mechanistically, we found in TIA patients that these metabolites were positively correlated with circulating neutrophil counts. Integrative analysis of plasma metabolomics and neutrophil transcriptomics further revealed that TIA-induced metabolites are significantly correlated with specific gene expression in circulating neutrophils which showed prominent enrichment in FoxO signaling pathway and upregulation of the anti-inflammatory cytokine IL-10. Finally, we demonstrated that the protective effect of atDR-pretreatment on MCAO mice was abolished when circulating neutrophils were depleted. Interpretation: TIA-induced ischemic tolerance is associated with upregulation of plasma bioactive metabolites which can protect against cerebral ischemic damage and improve neurological functions through a positive role of circulating neutrophils.

overall_design: To elucidate the potential mechanism of TIA-induced ischemic tolerance, we performed transcriptomic analyses in the circulatory neutrophils as well as metabolomic analyses in the plasma samples collected from 20 TIA patients at day 1 and day 7 after their TIA onset. We performed gene expression profiling analysis using data obtained from RNA-sequencing of the two time points. Integrative analyses of the transcriptomic and metabolomic data were then conducted.

first: Rongrong

last: Liu

first: Siwei

last: Luo

first: Yu-Sheng

last: Zhang

first: Chi

middle: K


title: TMEM106B reduction or partial depletion does not rescue GRN haploinsufficiency in mouse and iPSC-derived human microglia cell models.

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: CUT&Tag analysis on H3K27me3 in mouse embryonic medial ganglionic eminence (MGE) under deletion of Ezh2 gene

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

summary: Enhancer of zeste homolog 2 (Ezh2) is the methyltransferase component of the Polycomb Repressive Complex 2 (PRC2), which is critical for trimethylation of histone 3 at lysine 27 (H3K27me3) and results in gene repression. Mutations in EZH2 and dysregulation of H3K27me3 can lead to neurodevelopmental abnormalities such as Weaver Syndrome and ataxia-telangiectasia. During cortical neurogenesis, H3K27me3 is a critical epigenetic modification that regulates cellular maturation rate, and in turn, determines when precursor cells exit the cell cycle. Loss of function studies reveal that Ezh2 plays a critical role in epigenetic regulation of neuronal fate and maturation in some brain regions, but a role for Ezh2 in forebrain GABAergic interneurons has not been explored. Here, we removed Ezh2 from the medial ganglionic eminence (MGE) to study its role in interneuron development.

overall_design: WT and Ezh2 KO mice (Nkx2.1-CreC/+;Ezh2;Ai9F/+) were created by Nkx2.1-CreC/C;Ezh2F/+ males crossed to Ai9F/F;Ezh2F/+ females. Bulk CUT&Tag analysis was performed to assess H3K27me3 using an H3K27me3 antibody in each genotype.


title: Single cell ATAC-seq analysis in mouse embryonic medial ganglionic eminence (MGE) under deletion of Ezh2 gene (10X Genomics Multiome)

overall_design: WT, Het, and Ezh2 KO mice (Nkx2.1-CreC/+;Ezh2;Ai9F/+) were created by Nkx2.1-CreC/C;Ezh2F/+ males crossed to Ai9F/F;Ezh2F/+ females. Single nuclei from embryonic day 12.5 (e12) and 15.5 (e15) from each genotype were prepared to analyze chromatin accessibility using 10X Genomics Multiome pipeline.


title: TMEM106B reduction or partial depletion does not rescue GRN haploinsufficiency in mouse and iPSC-derived human microglia cell models [Human iMG]

overall_design: Comparative RNA-seq data for full deletion of TMEM106B in hiPSC-derived microglia with GRN deletion.

first: Gaia

last: Ruggeri

first: Maheswara

middle: R

last: Emani


title: Regulation of Hippo/YAP axis by CXCR7 in the tumorigenesis of gastric cancer

city: Xinxiang

first: Zhongbo

last: li

state: Henan

institute: Xinxiang medical university

summary: The Hippo pathway is crucial in organ size control and tumorigenesis. The dys-regulation of Hippo/YAP axis is vastly observed in gastric cancer, while the effective therapeutic targets for Hippo/YAP axis are still not clear. It is important and urgent to identify reliable drug targets and the underlying mechanisms, which could inhibit the activity of Hippo/YAP axis and gastric cancer progression. In our current study, we demonstrate the membrane receptor CXCR7 (C-X-C chemokine receptor 7) is an important modulator for Hippo/YAP axis. The activation of CXCR7 could stimulate gastric cancer cell progression through Hippo/YAP axis in vitro and in vivo, while pharmaceutical inhibition of CXCR7 via ACT-1004-1239 could block the tumorigenesis in gastric cancer. Molecular studies reveal that the activation of CXCR7 could dephosphorylate YAP, facilitate YAP nuclear accumulation and transcriptional activation in gastric cancer. CXCR7 functions via G-protein Gαq/11 and Rho GTPase to activate YAP activity. Interestingly, ChIP assay shows that YAP could bind to the promoter region of CXCR7 and facilitate its gene transcription, which indicates CXCR7 is both the upstream signaling and downstream target for Hippo/YAP axis in gastric cancer. In general, we identified a novel positive feedback loop between CXCR7 and Hippo/YAP axis, while blockade of CXCR7 could be a plausible strategy for gastric cancer.

overall_design: gastric cancer cell mRNA samples were summarized in six samples, divided into two groups, siControl and siCXCR7

first: Tianshi

last: Wang

first: Yinlu

last: Ding

first: Jian

last: Zhu


title: Single cell 10X Genomics Multiome analysis in mouse embryonic medial ganglionic eminence (MGE) under deletion of Ezh2 gene


title: Modulation of Recovery from Neonatal Hyperoxic Lung Injury by Sex as a Biological Variable

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Recovery from lung injury during the neonatal period requires the orchestration of many biological pathways. Modulation of biological pathways can drive the developing lung towards proper repair or persistent maldevelopment after injury that can lead to a disease phenotype. Sex as a biological variable can modulate these pathways differently in the male and female lung exposed to neonatal hyperoxia. In this study, we assessed the contribution of cellular diversity in the male and female neonatal lung following injury. Our objective was to investigate sex and cell-type specific transcriptional changes that drive repair or persistent injury in the neonatal lung at single-cell resolution and delineate the alterations in the immune-endothelial cell communication networks in the developing lung using single cell RNA sequencing (sc-RNAseq) in a murine model of hyperoxic lung injury. We generated transcriptional profiles of >55,000 cells isolated from the lungs of postnatal day 1 (PND 1) andpostnatal day 21 (PND 21) neonatal male and female C57BL/6 mice exposed to 95% FiO2between PND 1-5 (saccular stage of lung development).We show the presence of sex-based differences in the transcriptional states of lung endothelial and immune cells at PND 1 and PND 21. Furthermore, we demonstrate that biological sex significantly influences the response to injury, with a greater number of differentially expressed genes showing sex-specific patterns than those shared between male and female lungs. Pseudotime trajectory analysis highlighted genes needed for lung development that were altered by hyperoxia. Finally, we show intercellular communication between endothelial and immune cells at saccular and alveolar stages of lung development with sex-based biases in the cross-talk and identify novel ligand-receptor pairs. Our findings provide valuable insights into the cell diversity, transcriptional state, developmental trajectory, and cell-cell communication underlying neonatal lung injury, with implications for understanding lung development and therapeutic interventions while highlighting the crucial role of sex as a biological variable.

overall_design: C57BL/6N neonatal mice were exposed to room air (21% O2) or hyperoxia (95% FiO2) from PND 1-5 and then moved to room air. Mice were euthanized at PND 1 or PND 21. Single cell suspension was prepared for each of the four groups: male room air, female room air at PND 1 and male room air, female room air, male hyperoxia and female hyperoxia at the PND 21. Each sample was comprised of pooled lung tissue from three mice.

first: Manuel

middle: C

last: Gutierrez

first: Xiaoyu

last: Dong

first: Connor

last: Leek

first: Krithika

last: Lingappan


title: Genomic analysis of IDH-mutant astrocytoma progression to grade 4 in the treatment setting reveals changes in cell cycle, growth factor, and DNA repair pathways

first: Kirsi

middle: J.

last: Rautajoki

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University


title: Single cell RNA-seq analysis in mouse embryonic medial ganglionic eminence (MGE) under deletion of Ezh2 gene (10X Genomics Multiome)

overall_design: WT, Het, and Ezh2 KO mice (Nkx2.1-CreC/+;Ezh2;Ai9F/+) were created by Nkx2.1-CreC/C;Ezh2F/+ males crossed to Ai9F/F;Ezh2F/+ females. Single nuclei from embryonic day 12.5 (e12) and 15.5 (e15) from each genotype were prepared to analyze transcriptome using 10X Genomics Multiome pipeline.


title: Female murine airway epithelium is more susceptible to cigarette smoke-induced injury.

city: Baltimore

first: Baishakhi

last: Ghosh

state: MD

address: 615 N Wolfe St, E7209

department: Environmental Health and Engineering

institute: Johns Hopkins University - Bloomberg School of Public Health

summary: Our study discusses the importance of studying sex-specific differences in the response of the airway epithelium to chronic injury. It focuses on tracheal epithelial cells from male and female mice exposed to chronic cigarette smoke and found evidence of sex-specific differences in gene expression and epithelial plasticity. Understanding these differences could lead to more effective personalized treatments for respiratory diseases.

overall_design: Mice tracheal epithelial cells (mTECs) from 7– to 8 – week old male and female FVB/NJ mice were isolated, expanded, and differentiated on an air-liquid interface (ALI) for 10 to 14 days. The differentiated epithelium was exposed to cigarette smoke or humidified air for ten days. Phenotypic parameters of epithelial plasticity such as transepithelial electrical resistance, paracellular permeability, ciliary beat frequency, and cellular velocity were quantified. Total RNA was isolated and sequenced on NovaSeq S4 6000 Illumina platform. Quality control and data management were performed, including trimming reads and aligning them to the reference mouse genome. Differentially expressed genes were analyzed for biological pathways by g: Profiler.

first: Pratulya

middle: P

last: Chengala

first: Sonya

last: Shah

first: Bonnie

last: Yeung-Luk

first: Daniel

last: Chen

first: Vaishnavi

last: Karanam

first: Venkataramana

last: Sidhaye


title: LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: We compared gene panel sequencing and DNA methylation analysis with RNA sequencing results from 125 patients. We could demonstrate improvement of diagnostic accuracy and clinical patient benefit by the addition of RNA sequencing fom fresh frozen tumor tissue.

overall_design: 125 pLGG tumors were profiled on IlluminaHumanMethylation 850k arrays.

first: Emily

last: Hardin

first: Simone

last: Schmid

first: Alexander

last: Sommerkamp

first: Carina

last: Bodden

first: Anna-Elisa

last: Heipertz

first: Philipp

last: Sievers

first: Andrea

last: Wittmann

first: Till

last: Milde

first: Stefan

middle: M

last: Pfister

first: Andreas

last: von Deimling

first: Svea

last: Horn

first: Nina

last: Herz

first: Michèle

last: Simon

first: Ashwyn

last: Perera

first: Amedeo

last: Azizi

first: Ofelia

last: Cruz

first: Sarah

last: Curry

first: An

last: Van Damme

first: Miklos

last: Garami

first: Darren

last: Hargrave

first: Antonis

last: Kattamis

first: Barbara

last: Faganel Kotnik

first: Päivi

last: Lähteenmäki

first: Katrin

last: Scheinemann

first: Antoinette

middle: Y

last: Schouten-van Meeteren

first: Astrid

last: Sehested

first: Elisabetta

last: Viscardi

first: Ole

last: Wormdal

first: Michal

last: Zapotocky

first: David

last: Ziegler

first: Arend

last: Koch

first: Pablo

last: Hernáiz Driever

first: Olaf

last: Witt

last: Capper

first: Felix

last: Sahm

middle: T

last: Jones

first: Cornelis

last: van Tilburg


title: Genomic analysis of IDH-mutant astrocytoma progression to grade 4 in the treatment setting reveals changes in cell cycle, growth factor, and DNA repair pathways [mutations]

first: Kirsi

last: Rautajoki

summary: As the progression of low-grade diffuse astrocytomas into grade 4 tumors significantly impacts patient prognosis, a better understanding of this process is of paramount importance for improved patient care. In this project, we analyzed matched IDH-mutant astrocytomas before and after progression to grade 4 from six patients (discovery cohort) with genome-wide sequencing and 21 additional patients with targeted sequencing. The Cancer Genome Atlas (TCGA) data from 595 diffuse gliomas provided supportive information. All patients in our discovery cohort received radiation, all but one underwent chemotherapy, and no patient received temozolomide before progression to grade 4 disease. One case in the discovery cohort exhibited a hypermutation signature associated with the inactivation of the MSH2 and DNMT3A genes. In other patients, the number of chromosomal rearrangements and deletions increased in grade 4 tumors. Tumor progression was associated with upregulation of cell cycle progression, migration, and DNA damage repair-related genes. The cell cycle checkpoint genes CDKN2A or RB1 were most commonly inactivated, followed by activating growth factor receptor gene alterations in cases with homozygous CDKN2A deletion. We also detected progression-related alterations in DNA repair pathway genes associated with the promotion of error-prone DNA repair, thus facilitating tumor progression. The homologous recombination repair gene RAD51B was hemizygously deleted in all but one progressed tumor in our discovery cohort. In our retrospective analysis of patient treatment and survival timelines, the combination of postoperative radiation and chemotherapy (mainly temozolomide) outperformed radiation especially in the grade 3 tumor cohort, in which it was typically given after primary surgery. Our results support previous notions that treatment contributes to tumor evolution and suggest that altered DNA repair has a role in treatment resistance and tumor progression.

overall_design:
Examination of five IDHmut astrocytoma patient cases with mutation data from matched grade 2-3 and progressed grade 4 tumors.
**Raw data not provided due to patient privacy**

first: Serafiina

last: Jaatinen

first: Anja

last: Hartewig

first: Aliisa

last: Tiihonen

first: Matti

last: Annala

first: Iida

last: Salonen

first: Masi

last: Valkonen

first: Vili

last: Simola

first: Elisa

last: Vuorinen

first: Anni

last: Kivinen

first: Minna

last: Rauhala

first: Riikka

last: Nurminen

first: Kendra

last: Maass

first: Sirpa-Liisa

last: Lahtela

first: Arja

last: Jukkola

first: Olli

last: Yli-Harja

first: Pauli

last: Helén

first: Kristian

middle: W

last: Pajtler

first: Pekka

last: Ruusuvuori

first: Joonas

last: Haapasalo

first: Wei

last: Zhang

first: Hannu

last: Nykter


title: Genomic analysis of IDH-mutant astrocytoma progression to grade 4 in the treatment setting reveals changes in cell cycle, growth factor, and DNA repair pathways [ssRNA-seq]

first: Kirsi

last: Rautajoki

overall_design:
Examination of six IDHmut astrocytoma patient cases with mutation data from matched grade 2-3 and progressed grade 4 tumors.
**Raw data not provided due to patient privacy**

first: Serafiina

last: Jaatinen

first: Anja

last: Hartewig

first: Aliisa

last: Tiihonen

first: Matti

last: Annala

first: Iida

last: Salonen


title: YAP and TAZ couple osteoblast precursor mobilization to angiogenesis and mechanoregulation in fetal bone development

first: Joseph

last: Collins

address: 36th and Hamilton Walk

department: Department of Bioengineering

institute: University of Pennsylvania

summary: Fetal bone development occurs by endochondral conversion of avascular cartilage to vascularized bone at the growth plate. This requires coordinated mobilization of osteoblast precursors with blood vessels. In adult bone, vessel-adjacent osteoblast precursors are maintained by mechanical stimuli; however, the mechanisms by which these cells mobilize and respond to mechanical cues during embryonic development are unknown. Here, we unify osteoblast precursor co-mobilization and mechanotransduction in a single signaling pathway, via the mechanosensitive transcriptional regulators YAP and TAZ. We show that YAP and TAZ spatially couple osteoblast precursor mobilization to angiogenesis, regulate vascular loop morphogenesis to control growth plate remodeling, and mediate mechanoregulation of load-induced osteogenesis in embryonic bone. Mechanistically, YAP and TAZ uniquely regulate a subset of osteoblast-lineage cells, identified by single-cell RNA sequencing as vessel-associated osteoblast precursors. Among these cells, YAP and TAZ regulate expression of the angiogenic chemokine, Cxcl12. Functionally, in 3D human cell co-culture, CXCL12 treatment rescued angiogenesis impaired by stromal cell YAP/TAZ depletion.  Together, these data establish new functions of the vessel-associated osteoblast precursors in endochondral bone development.

overall_design: Fetal forelimbs were generated from E17.5 mice from 3 genotypes - 2 control and 1 experimental. 1) YAPfl/fl; TAZfl/fl - hereafter WT(fl/fl) (n = 4 embryos), 2).YAPWT/WT; TAZWT/WT; Osx-cre - hereafter WT(Osx-cre) (n=4 embryos), 3)   YAPfl/fl; TAZfl/fl; Osx-Cre - hereafter YAP/TAZ Osx cKO (n=3 embryos)

first: Annemarie

last: Lang

first: Cristian

last: Parisi

first: Yasaman

last: Moharrer

first: Madhura

last: Nijsure

first: Jong

middle: H

last: Kim

first: Saima

last: Ahmed

first: Gregory

last: Szeto

first: Ling

last: Qin

first: Riccardo

last: Gottardi

first: Nathaniel

last: Dyment

first: Niamh

last: Nowlan

first: Joel

middle: D

last: Boerckel


title: MicroRNAs in Pyrus stigma tissue and stigma exudates

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: In many plant species, flower stigma secretions are important in early stages of sexual reproduction. Previous chemical analysis and proteomic characterization of these exudates provided insights into their biological function. Nevertheless, the presence of nucleic acids in the stigma exudates has not been previously reported. Here we studied the stigma exudates of Pyrus communis, Pyrus pyrifolia and Pyrus syriaca, and showed them to harbor extracellular RNAs of various sizes. RNA sequencing revealed, for the first time, the presence of known Rosaceae mature micro-RNAs (miRs), also abundant in the stigma source tissue. Predicted targets of the exudate miRs in the Arabidopsis thaliana genome include genes involved in various biological processes. Several of these genes are pollen transcribed, suggesting possible involvement of exudate miRs in transcriptional regulation of the pollen. Moreover, extracellular miRs can potentially act across kingdoms and target genes of stigma interacting organisms/microorganisms, thus opening novel applicative avenues in HortSciences.

sample_organism:
Pyrus pyrifolia
Pyrus communis
Pyrus syriaca

overall_design: Stigma tissue and stigma exudates were collected from 2 independent pooled flowers of Pyrus pyrifolia, a single pool of Pyrus communis flowers, and 3 independent pools of Pyrus syriaca flowers. Small RNAs were purified and sequenced using Illumina technology.

first: Vivek

last: Ambastha

first: Ifat

last: Matityhu

first: David

last: Honys

first: Yehoram

last: Leshem


title: Effect of hypoxia on gene expression among HK-2 cells and 786-0 cells

city: Nanjing

first: Yu

last: Zhang

state: China/Jiangsu

address: No. 87 Dingjiaqiao, Gulou District

department: Department of Pathology

institute: School of Medicine, Southeast University

summary:
Although both of renal interstitial fibrosis (RIF) and renal carcinoma (RCC) are in hypoxic microenvironments, they underwent several contrary  pathologicall changes. To investigate the potent targets in the RIF and RCC through transcriptome alterations of hypoxia compared with normoxia, we established hypoxia cell culture models, primarily simulating hypoxia microenvironments in RIF and RCC. By bioinformatics analysis, a certain number of significant differentially expressed genes (DEGs) among RIF and RCC were recognized.
We then performed gene expression profiling analysis using data obtained from RNA-seqencing of 2 different cells cultured in hypoxia and normoxia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HK-2 cells and 786-0 cells in hypoxia and normoxia respectively.

first: Pingsheng

last: Chen


title: Targeting FLT3-TAZ Signaling to Suppress Drug Resistance in Blast Crisis Chronic Myeloid Leukemia

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: Although the development of tyrosine kinase inhibitors (TKIs), including BCR-ABL1 targeted therapies, rendered chronic myeloid leukemia (CML) a manageable condition, acquisition of drug resistance during blast crisis (BC) progression remains a critical challenge. Here, we elucidate the significance of FLT3 signaling in the acquisition of drug resistance in BC-CML. Mechanistically, FLT3 expression in CML cells activated FLT3-JAK-STAT3-TAZ-TEAD-CD36 pathway, which conferred resistance to wide range of tyrosine kinase inhibitors (TKIs). Remarkably, a subgroup of BC-CML patients who expressed FLT3 showed strong correlation with the prognostic factors of CML independent of recurrent BCR-ABL1 mutations. We demonstrate that combining FLT3 inhibitors with BCR-ABL1 targeted therapies or single treatment with ponatinib can overcome drug resistance and promote cell death in patient-derived FLT3+ BC-CML cells and mouse xenograft models. Our findings reveal the mechanism of FLT3-mediated drug resistance in BC progression and suggest the inclusion of FLT3 as a therapeutic target for this defined group of patients.

overall_design: RNA-seq of K562 cells with indicated conditions

first: Jae-Seok

first: Hwa-Ryeon


title: Association of immune related expression profile with sensitivity to neoadjuvant chemotherapy using docetaxel, cisplatin and 5-fluorouracil in esophageal squamous cell carcinoma.

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

summary: Neoadjuvant chemotherapy (NAC) followed by surgery is one of the standard therapeutic approaches for patients with locally advanced esophageal carcinoma in Japan. Recently, JCOG1109 study revealed that NAC with docetaxel, cisplatin and 5-fluorouracil (5-FU) (DCF-NAC) is superior to NAC with cisplatin and 5-FU, and has become the standard preoperative chemotherapy. By using microarray, we have previously investigated expression profiles of endoscopic biopsies of patients with esophageal squamous cell carcinoma (ESCC) before DCF-NAC (preNAC) and identified 17 molecules as predictive biomarkers for pathologically complete response to DCF-NAC. Here, we re-grouped our previous dataset based on the histopathological response grade with an addition of several microarray profiles (altogether 5 non-tumors, 12 highly resistant cancers and 27 sensitive cancers) and re-analyzed by bioinformatic web tools, including DAVID, GSEA, UALCAN and CIBERSORTx. We identified 204 genes as differentially expressed genes (DEGs) between highly resistant and sensitive groups. A number of DEGs were related to immune response and expressed higher in sensitive group. By UALCAN, 28 of the top 50 DEGs showed that their high expression were associated with favorable prognosis (p<0.25). Among them, 18 DEGs reached significance (p<0.05), suggesting that patients with high expression of these genes might have benefited from chemotherapy and thus had better outcome. We further showed distribution of the cells expressing CXCL9 mRNA, one of the prognosis related DEGs, in preNAC biopsy tissues of DCF-sensitive case. In conclusion, our data may provide useful information to establish predictive and effective methods for DCF-NAC in ESCC.

overall_design: 200ng of RNA samples from endoscopic biopsies before neoadjuvant chemotherapy were subjected to gene expression microarray.

first: Shusaku

last: Kurogi

first: Hajime

last: Fujishima

first: Tomotaka

last: Shibata

first: Shoichi

last: Fumoto

first: Kohei

last: Nishiki

first: Kosuke

last: Suzuki

first: Tsuyoshi

last: Etoh

first: Norio

last: Shiraishi

first: Yuka

last: Hirashita

first: Takafumi

last: Fuchino

first: Chisato

last: Nakada

first: Tomohisa

last: Uchida

first: Masafumi

last: Inomata

first: Masatsugu

last: Moriyama

first: Naoki

last: Hijiya


title: Next Generation Sequencing Facilitates Quantitative Analysis of Klebsiella pneumoniae strain HKE9, HKE9-M-rpoS,HKE9-C-M-ropS

city: Xi'an

first: Bei

last: Han

state: Shaanxi

address: NO 76 Yanta West Road

department: School of Public Health

institute: Xi'an Jiaotong University

summary: Compared with HKE9, HKE9-M-rpoS (rpoS knockout in hypervirulent Klebsiella pneumoniae strain HKE9) had 624 genes expressed significantly different, among which 148 genes were significantly up-regulated and 476 genes were significantly down-regulated, 586 genes on chromosomes, 10 genes on circular plasmid and 28 genes on linear plasmid; HKE9-C-M-rpoS had 746 genes expressed significantly different, among which 286 genes were significantly up-regulated and 460 genes were significantly down-regulated, 727 genes on chromosomes, 11 genes on circular plasmid and 8 genes on linear plasmid. Compared with HKE9-M-rpoS, HKE9-C-M-rpoS (rpoS complement in strain HKE9-M-rpoS) had 509 genes expressed significantly different, among which 324 genes were significantly up-regulated and 185 genes were significantly down-regulated, 458 genes on chromosomes, 3 genes on circular plasmid and 48 genes on linear plasmid.

overall_design: A fresh culture of hypervirulent Klebsiella pneumoniae strain HKE9, HKE9-M-rpoS (rpoS knockout in strain HKE9), and HKE9-C-M- rpoS (rpoS complement in strain HKE9-M-rpoS) strains were grown to OD600 of 0.6. Total RNA was extracted using RNAprotect Bacteria Reagent and RNeasy minikit (Qiagen, DE). RNA quality was monitored on 1% agarose gels. RNA purity (OD260/OD280, OD260/OD230) was checked using the NanoPhotometer® spectrophotometer (Implen, USA). RNA integrity was measured using Bioanalyzer 2100 (Agilent, CA). A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and then transcriptome sequencing was performed at Novaseq 6000 in Gene Denovo Co. Ltd(Guangzhou, China). Quality trimmed reads were mapped to the HKE9 using Bowtie2 (version 2.2.8), reads mapped to ribosome RNA were removed. Retained reads were aligned with reference genome to identify known genes and calculated gene expression by RSEM. To evaluate reproducibility between samples, the correlation coefficient among replicas was calculated. Values closer to one indicated better reproducibility. Principle component analysis (PCA) was performed with the R package gmodels (http://www.r-project.org) to reveal the relationship between samples. The gene expression level was further normalized by using the fragments per kilobase of transcript per million (FPKM) mapped reads method to eliminate the influence of different gene lengths and amount of sequencing data on the calculation of gene expression. The edgeR package (http://www.r-project.org/) was used to identify differentially expressed genes (DEGs) across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05. DEGs were then subjected to an enrichment analysis of GO functions (http://www.geneontology.org) and KEGG pathways (http://www.genome.jp/kegg), and q values < 0.05 were using as threshold.

first: Han

last: Bei

first: Da

last: Rong

first: Zhou

last: Yi

first: Cheng

last: Yue


title: Identifying novel genes related to the peritubular capillary rarefaction in renal interstitial fibrosis through chip sequencing

first: Yu

last: Zhang

summary: Renal interstitial fibrosis (RIF) is the prominent pathological characteristics of deteriorative chronic kidney disease (CKD), leading to  peritubular capillary (PTC) rarefaction accompanied by significant hypoxia. However, the underlying mechanisms remain elusive. To deal with this, we constructed the chip sequencing of HK-2 cells in hypoxia to explore critical  genes modulated by HIF-1α through peak annotation. Several biomarkers have been identified on the basis of bioinformatics and deserve further research.

overall_design: HK-2 cells were cultured in hypoxia and normoxia

first: Pingsheng

last: Chen


title: Transgenic porcine model reveals two roles for LGR5 during lung development and homeostasis

city: Raleigh

first: Jorge

last: Piedrahita

state: NORTH CAROLINA

address: 1060 William Moore Drive, BPC Suite 200

institute: North Carolina State University

overall_design: Refer to individual Series


title: Comparative RNA-sequencing analysis of the prostate in a mouse model of benign prostatic hyperplasia with bladder outlet obstruction

city: GuiYang

first: XiaoHu

last: Tang

address: No. 83 Zhongshan East Road

institute: Guizhou Provincial People's Hospital

summary: Effects of excessive testosterone and estradiol on gene expression of mice prostate

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BPH mice induced with excessive testosterone and estradiol

first: Xiaohu

first: Guangheng

last: Luo


title: Transgenic porcine model reveals two roles for LGR5 during lung development and homeostasis [Bulk RNA-seq]

summary: Stem cell dynamics in the lung govern homeostasis, repair, and regeneration, yet there is still much unknown about the mechanisms of these processes. Furthermore, incongruencies between murine and human physiology limit the translation of some findings. In this work, we address these limitations by using a transgenic pig model to identify two populations of LGR5+ cells in the lung that are present in the human but that are absent from the mouse. Using RNA sequencing, 3D imaging, organoid models, and differentiation assays, we determine that in the fetal lung, epithelial LGR5 expression is transient in a subpopulation of developing lung bud tips. While epithelial LGR5 expression is absent from postnatal lung, it is reactivated in some organoids derived from basal airway cells. A separate population of LGR5+ cells is mesenchymal, surrounds developing and mature airways, is closely associated with nerve fibers, and acts as a multipotent progenitor cell capable of supporting the airway basal cell niche. These results point to two roles for LGR5 in orchestrating stem and progenitor cell dynamics, and provide a physiologically relevant model for further studies on the role of these populations in repair and regeneration.

overall_design: RNA-Seq

first: Kathryn

last: Polkoff

first: Nithin

last: Gupta

first: Yanet

last: Murphy

first: Ross

last: Lampe

first: Jaewook

last: Chung

first: Amber

last: Carter

first: Jeremy

last: Simon

first: Katherine

last: Gleason

first: Adele

last: Moatti

first: Laura

last: Edwards

first: Alon

last: Greenbaum

first: Aleksandra

last: Tata

first: Purushothama


title: Identification of miRNAs Involved in intracranial aneurysm rupture in cigarette smoking patients

city: Baoding

first: Hanbin

last: Wang

state: Hebei province

address: 212 Yuhua East Road

institute: Affiliated Hospital of Hebei University

summary: To investigate the role of smoking in the rupture of intracranial aneurysms (IA), plasma miRNA profiles of smoking IA patients, non-smoking IA patients, and healthy volunteers were analyzed.

overall_design: Comparative plasma miRNA profiling analysis of RNA-seq data for smoking IA patients, non-smoking IA patients, and healthy volunteers.

first: Lijian

last: Zhang

first: Chunhui

last: Li

first: Luxuan


title: Direct Selection of an Allosteric RNA-Cleaving DNAzyme for a Protein Target: A Specific DNAzyme for Eosinophil Peroxidase to Monitor Airway Eosinopilia

city: Hamilton

first: Monsur

last: Ali

state: ON

address: ETB 303, Biointerface Institute, 1280 Main St West

department: Biointerfaces Institute

country: Canada

institute: McMaster University

summary:
In this project, in vitro selection was carried out to generate DNAzymes for Eosinophil peroxidase using a synthetic DNA library. Total 15 rounds of selections were carried out. The DNA molecules obtain in round 15, was applied in Illumina MiSeq deep sequencing which provided fastq files. Sequencing samples were prepared from each parallel SELEX experiment by PCR tagging with Illumina sequencing primers. Samples were size purified by agarose gel electrophoresis prior to being quantified by measuring absorbance at 260 nm. Tagged samples were pooled and paired-end sequenced on an Illumina MiSeq high-throughput DNA sequencer. Sequence data processing was performed on a Windows 10 computer running Ubuntu 20.04 under WSL2. Raw paired-end reads were trimmed of sequencing and library primers using cutadapt 3.4. Trimmed paired-end reads were then: 1) merged into a consensus sense read; 2) dereplicated; and, 3) clustered at 90% identity using USEARCH v11.0.667_i86linux32. Sequence frequencies and ranking lists were generated using custom Python scripts. Multiple sequence alignments were performed using MUSCLE v3.8.1551 and converted to sequence logos using WebLogo 3.7.8. Processed sequencing data and cluster linkage data were stored on a MySQL 8.0.22 database. Analysis of sequence copy number, frequency, cluster linkage and data plots were performed using the database and Microsoft Excel
Top 20 sequences were tested for cleavage performance. The most active DNAzyme was characterized and optimized. At the end,  fluorescence and lateral flow assays were developed and evaluated in real patients' sputums.

overall_design: A random DNA library conatining approximately 10^14 individual sequences were prepared by chemical synthesis and was employed in the in vitro selection to isolate DNAzymes that specifically catalyze the hydrolysis of a fluorogenic substrate. Total 15 rounds of selections were carried out and the DNA pool of round 15 was deep sequenced by Illumina Miseq.

first: Manali

last: Mukharjee

last: Radford

first: Zil

last: Patel

first: Yingfu

first: Alfredo

last: Capretta

first: Parameswaran

last: Nair

first: John

last: Brennan


title: Keloid Transcriptome

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Eevaluation of intra- and inter-keloid fibroblast heterogeneity by analyzing their gene expression using transcriptomic analysis

overall_design: Comparison between nodular or extensive keloids, each of them being separated into four regions: on one side center versus periphery, on the other side papillar (or superficial) and reticular (or deep) regions . This leads to four fibroblast subtypes: central papillary (CP), central reticular (CR), peripheral papillary (PP) and peripheral reticular (PR) all compared to control skin from superficial/papillary (Pap) or deep/reticular (Ret) dermis

first: K

last: Serror

first: L

last: Michel


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ets1 scRNAseq]

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary: The gene regulatory network (GRN) underlying CTL differentiation and whether Tex responses can be functionally reinvigorated are incompletely understood. Here, we systematically mapped causal GRNs via single-cell CRISPR (scCRISPR) screens in vivo and discovered checkpoints for CTL differentiation.

overall_design: We used scRNA-seq to compare transcriptional heterogeneity of sgNTC (‘spike for sgEts1’)- or sgEts1-transduced OT-I T cells from the dual-color transfer system at day 7 post adoptive transfer into B16-OVA tumors

first: Peipei

last: Zhou

first: Hao

last: Shi

first: Hongling

last: Huang


title: Transgenic porcine model reveals two roles for LGR5 during lung development and homeostasis [scRNA-seq]

first: Jorge

last: Piedrahita

first: Kathryn

last: Polkoff

first: Nithin

last: Gupta

first: Yanet

last: Murphy

first: Ross

last: Lampe

first: Jaewook

last: Chung

first: Amber

last: Carter

first: Jeremy

last: Simon

first: Katherine

last: Gleason

first: Adele

last: Moatti

first: Laura

last: Edwards

first: Alon

last: Greenbaum

first: Aleksandra

last: Tata

first: Purushothama


title: The transcription factor Rpn4 activates its own and efflux pumps’ expression to confer fluconazole resistance in Candida auris

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: The goal of this RNA-Seq study is to elucidate Rpn4’s function in regulating C. auris fluconazole resistance.

overall_design: mRNA profiles of ubr2Δ, mub1Δ, and WT cells.

first: Eve

last: Chow

first: Jianbin

last: Wang

first: Jiaxin

last: Gao


title: BCL2 inhibition reveals a dendritic cell-specific immune checkpoint that controls tumor immunosurveillance

first: Pierre

last: de la Grange

summary: We developed a screening platform in which immortal dendritic cell (DC) precursors can be genetically manipulated and then de-immortalized and differentiated into DCs for functional in vitro assays, as well for adoptive transfer into syngeneic tumor-bearing mice to explore their capacity to instate immunosurveillance. A genome-wide CRISPR screen led to the identification of BCL2 as an endogenous inhibitor of DC function. Knockout of BCL2 in DCs enhanced antigen presentation and the expression of activation markers in vitro, as well as the capacity of DCs to control tumor growth in vivo and to synergize with PD-1 blockade. These effects where phenocopied by the pharmacological BCL2 inhibitors venetoclax and navitoclax, both of which required DCs of the cDC1 subtype to efficiently reduce the growth of orthotopic lung cancers and fibrosarcomas. Thus, solid tumors failed to respond to venetoclax and navitoclax in mice constitutively devoid of cDC1 cells due to the knockout of Batf3, and this defect was reversed by the infusion of DCs. Moreover, depletion of cDC1 cells by systemic injection of cytochrome c reduced the therapeutic efficacy of BCL2 inhibitors alone or in combination with PD-1 blockade. In vivo treatment with venetoclax caused cDC1 cells to express several activation markers, both in mice and in patients. In conclusion, genetic and pharmacological BCL2 inhibition unveils a DC-specific immune checkpoint that restrains tumor immunosurveillance

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cas9-expressing inducible-immortalized dendritic cells that were treated with venetoclax or DMSO, as well as  its derivatives that are KO of Bcl2.

first: Liwei

last: Zhao

first: Peng

last: Liu

first: Oliver

last: Kepp

first: Guido

last: Kroemer


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Rbpj_ATAC-seq]

first: Hongbo

last: Chi

overall_design: We used ATAC seq to compare chromatin accessibility profiles of Rbpj KO and Spike Tpex and Tex OT-I T cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor

first: Peipei

last: Zhou

first: Hao

last: Shi

first: Hongling

last: Huang


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ikzf1_scRNAseq]

overall_design: We used scRNA-seq to compare transcriptional heterogeneity of sgNTC (‘spike for sgIkzf1’)- or sgIkzf1-transduced OT-I T cells from the dual-color transfer system at day 7 post adoptive transfer into B16-OVA tumors


title: Nuclear Location Bias of HCAR1 Drives Cancer Malignancy through Numerous Routes [RNA-seq]

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: The involvement of G-Protein-Coupled Receptors’ (GPCR) location bias in diverse cellular functions and their misregulation in pathology is an underexplored territory. HCAR1, a GPCR for lactate is linked to cancer progression, mainly due to Warburg effect, but its mechanism of action remains elusive. Here, we show HCAR1 has a nuclear localization, capable of signaling intranuclearly to induce nuclear-ERK and AKT phosphorylation concomitant with higher cancer cell proliferation and survival. We determine its nuclear interactome, proving its involvement in protein-translation and DNA-damage repair. Nuclear HCAR1 (N-HCAR1) directly interacts with chromatin/DNA promoting expression of genes involved in cellular migration. Notably, we show N-HCAR1 particularly regulates a broader transcriptomic signature than its PM counterpart, emphasizing on the facts that functional output of N-HCAR1 is larger than PM localized HCAR1. Our study presents several unprecedented processes by which a GPCR through location-biased activity regulate various cellular functions and how cancer cells exploit these.

overall_design: RNAseq of HeLa cells transfected with shRNA (scr = shScrambled, b = shHCAR1b and dl = KD+δS305A) with a lentiviral shRNA against HCAR1 targeting 3’UTR regions of the gene. Transfected Hela cells were treated with either PBS (P) or lactate (L), representing six conditions, with 3 to 5 biological replicates per condition.

first: Mohammad

last: Nezhady

first: Sylvain

last: Chemtob


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [microarray]

overall_design: In total 15 samples were analyzed: sgNTC (4 samples), sgRbpj (4 samples), sgIrf1 (4 samples), sgRbpj + sgIrf1(3 samples),


title: Nuclear Location Bias of HCAR1 Drives Cancer Malignancy through Numerous Routes

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


title: Bulk RNA Sequencing of XIST-knockdown A431 Cells

first: Erica

last: Darrah

address: 5200 Eastern Ave.

department: Molecular Rheumatology

institute: Johns Hopkins School of Medicine

summary: Systemic Lupus Erythematosus (SLE) is among the most sex-biased autoimmune diseases identified to date, affecting 9-times more women than men. Recognition of self-RNA by Toll-like receptor 7 (TLR7) is implicated as a central pathogenic process leading to the aberrant production of type-I interferon (IFN) in SLE, but the specific RNA molecules contributing to this process have not been defined. Given the role of self-RNA and biological sex in SLE pathogenesis, we investigated which sex-biased self-RNAs are potentially responsible for aberrant TLR7 activation in SLE. We used recent revelations about TLR7 sequence specificity and publicly available RNA sequencing data to identify sex-biased sources of self-RNA containing TLR7 ligands. We found X-inactive specific transcript (XIST) to be a particularly rich source of TLR7 ligands that is specifically expressed in women. We then investigated the capacity of XIST to act as a TLR7 ligand in vitro and found that multiple fragments of XIST induce IFNα production in a TLR7-dependent manner more than control RNA of equal length. Furthermore, we found that RNA isolated from XIST-knockout cells have significantly reduced capacity to stimulate TLR7 compared to RNA from wild-type cells. Finally, we used flow cytometry and publicly available RNA sequencing data to investigate the connection between XIST and SLE disease variables. We found that higher XIST expression correlated with SLE disease status, higher SLE disease activity index (SLEDAI) scores, and the interferon signature. Our data suggest that XIST is a source of TLR7 ligands that may underlie the sex bias in SLE.

overall_design: Fourteen samples were analyzed, including 3 biological replicates of each of the WT and XIST KD cell lines and 4 biological replicates of the pCAS and XIST 2KD cell lines. The parental cell line (reference sample) is denoted WT, and the pCAS cell line was treated with a scrambled guide RNA as control.

first: Jonathan

last: Crawford

first: C

last: Talbot

first: Erika

first: Linda

last: Orzolek


title: Nuclear Location Bias of HCAR1 Drives Cancer Malignancy through Numerous Routes [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for flag tag targeting the C or N terminal region of Hcar1 in HeLa cells with lactate or PBS. Both C- and N-terminus flag tagged cells were used for ChIP-seq studies. Two samples from each terminus tagged cells were used for either lactate or vehicle (PBS); in total 4 samples per treatment group (C and N terminal flag ChIP seq duplicates were grouped and compared to input), and only shared peaks between C and N were used for further bioinformatic analysis.


title: Expression signatures of Arabidopsis thaliana roots under low or high phosphate conditions.

city: Seeland

first: Anja

last: Hartmann

state: Saxony-Anhalt

address: Corrensstraße 3

department: PZB

institute: IPK Gatersleben

summary: To cope with limiting phosphorus (P) availability, plants have evolved a series of mechanisms to recycle internal P sources and to acquire P from the soil. One of these mechanisms is the release of low-molecular weight carboxylates, such as malate, which helps to liberate phosphate desorbed to aluminum and iron oxides. As malate release into the rhizosphere and root apopplast also increases iron availability. To identity  genes involved in this interaction, we investigated time-dependent changes in the transcriptome of Arabidopsis thaliana roots exposed to sufficient and deficient phoshate levels .

overall_design: Gene expression of Arabidopsis thaliana root tissues was measured after transferring seven-day-old seedlings for 0, 1, 2, 4 and 6 days to 625 µM phosphate (sufficient P; control) or 100 µM phosphate (P-deficient condition). Three biological replicates were used.

first: Ricardo

middle: F

last: Giehl

first: Nicolaus

last: von Wirén


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer

department: Immunology


title: Mixed hepatocellular – cholangiocarcinoma derives from liver progenitor cells and depends on senescence and IL6 trans-signaling, bulk RNA sequencing

first: nofar

last: rosenberg

address: Hadassah University Hospital

institute: Hebrew university

summary: Mixed hepatocellular – cholangiocarcinoma (HCC-CCA) is a highly malignant primary liver cancer of increasing incidence for which the cell of origin and molecular pathogenesis have not yet been fully elucidated. Here, by linking YFP to the progenitor cell specific promoter of Foxl1 in Mdr2-KO mice, we generated a lineage tracing mouse model for liver cancer to monitor the development of mixed HCC-CCA tumors following a prolonged period of liver inflammation. In this model of chronic hepatitis, we demonstrate that liver progenitor cells are the source of mixed HCC-CCA tumors but not of hepatocellular carcinoma (HCC). Moreover, we show that IL6, originating from senescent hepatic cells, is involved in progenitor cell proliferation and development of mixed HCC-CCA tumors via IL6 trans-signaling. These findings could form the basis for the development of novel therapeutic approaches for treatment of mixed HCC-CCA liver cancer.

overall_design: HCC tumors were compared to Mix tumors , both from human and mouse. Each type of tumor had at least 3 replicates

first: Eithan

last: Galun


title: Mixed hepatocellular – cholangiocarcinoma derives from liver progenitor cells and depends on senescence and IL6 trans-signaling, single-cell RNA sequencing

overall_design: Cells from non-tumor tissue, HCC tumor and HCC-CCA mixed tumor were prepared for single-cell RNA-Seq, one sample from each source.


title: Rpb9 plays a critical role in global co-transcriptional splicing (Fraction RNA-seq)

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: In order to measure the impact of Rpb9 on co-transcriptional splicing, we treated HeLa cells with control siRNA or siRpb9, and for comparative analysis, we also depleted Rpb1 and confirmed by Western blotting the knockdown efficiency in all cases. To measure co-transcriptional splicing, we fractionated HeLa cells into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from each compartment, spiked in with in vitro transcribed EGFP and FireFly luciferase RNA for data normalization, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq, which showed excellent reproducibility .

overall_design: Characterization of co-transcriptional splcing  after Rpb9 knock-down  in Hela cells

first: Changwei

last: Shao

first: Xiang-Dong

last: Fu


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Rbpj_scRNAseq]

first: Hongbo

last: Chi

overall_design: We used scRNA-seq to compare transcriptional heterogeneity of sgNTC (‘spike for sgRbpj’)- or sgRbpj-transduced OT-I Tcells from the dual-color transfer system at day 7 post adoptive transfer into B16-OVA tumors

first: Peipei

last: Zhou

first: Hao

last: Shi

first: Hongling


title: Mixed hepatocellular – cholangiocarcinoma derives from liver progenitor cells and depends on senescence and IL6 trans-signaling.

overall_design: Refer to individual Series


title: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [scCRISPR]

overall_design: We used scCRISPR to identify the TF regulatory network of transcriptional heterogeneity of OT-I Tcells  at day 7 post adoptive transfer into B16-OVA tumors

last: Huang


title: mRNA transcriptome analysis of hypoxia with shSETDB1 in hela cells

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Purpose: The goals of this study are to compare NGS-derived Hela with shSETDB1 and shcontrol in hypoxia transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods

overall_design: Methods: mRNA profiles of shControl hela and shSETDB1 with or hypoxia (1% O2) for 12 hours were generated by deep sequencing, in duplicate.  GSEA was performed, qRT–PCR validation was performed

first: Sungryul

last: Park

first: Jenog

first: Jong-Hwan

first: Seon-Young


title: Total RNA transcriptome analysis of hypoxia with sgSETDB1 in hela cells

summary: Purpose: The goals of this study are to compare NGS-derived Hela with sgSETDB1 and shcontrol in hypoxia transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods

overall_design: Methods: mRNA profiles of sgControl hela and sgSETDB1 with or hypoxia (1% O2) for 6 hours were generated by deep sequencing, in duplicate.  Hierarchical clustering was performed, qRT–PCR validation was performed


title: Advancing Cell Therapies: Single-Cell Profiling in Rhesus Macaque Plasma B Cells

status: Public on Nov 14 2023

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

summary: Engineered long lived plasma cells have the potential to be a new area of cell therapy. A key step in developing this cell therapy is testing in a model with an intact immune system similar to humans. To that end, we have developed methods to purify, expand, and differentiate non-human primate (NHP; rhesus macaque) B cells ex vivo. We consistently achieved 10-fold expansion of NHP B cells using a readily available commercial supplement. After only seven days in culture, large percentages of cells in NHP B cell cultures were differentiated. These cells expressed surface markers found in human antibody secreting cells (CD38 and CD138) and secreted immunoglobulin G. From single cell transcriptome analysis of NHP, we verified the presence of plasma cell markers commonly shared with humans, and have unearthed less recognized markers such as CD59 and CD79A. In addition, we identified unique NHP plasma cell markers that are absent in humans including the immune checkpoint molecule CD274 (PD-L1, Programmed Death-Ligand 1). Furthermore, we found that MHC class I molecules were upregulated in NHP plasma cells, in contrast to the pattern observed in humans. Lastly, we also identified the serotypes (AAVD-J) and established the conditions for efficient transduction of NHP B cells with AAV vectors, achieving an editing rate of approximately 60%. We envision that this work will accelerate proof-of-concept in vivo studies using engineered protein-secreting B cells in the NHP model.

overall_design: Ex vivo differentiated B cells day 7

first: Richard

last: James


title: Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines (RNA-Seq)

city: Bethesda

first: Mingan

last: Sun

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3.

overall_design: We generated RNA-seq, ATAC-seq and ChIP-seq data in S2, K167 and/or D17-c3 cells.

first: Lesley

last: Brown

first: Pedro

last: Rocha

first: Ming-an

first: Judith

last: Kassis


title: Single-cell Transcriptome Analysis Reveals the Dynamic Populations of Vascular Cells in Neointimal Hyperplasia

city: Shanghai

first: Guangzheng

address: No. 197, Ruijin Second Road

department: Ruijin Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Neointimal hyperplasia (NIH) are the major causes of re-stenosis in coronary intervention. Fibroblasts, vascular smooth muscle cells and endothelial cells are the main disease-causing cells in NIH. However, Yet how these cells contribute to the pathophysiology of NIH remains elusive. This study was aimed at gaining new insights into the heterogeneity of these cells by using single-cell RNA sequencing and up-to-date analytical method.

overall_design: Carotid artery of each experimental group were harvested from both mice after 2 weeks postoperatively (six mice per sample and one sampple per group). Vessles were enzymatically digested to single-cell suspension, and then scRNA-seq libraries were built with the 10x Genomics platform.

first: Qun

last: Li


title: BH3 mimetics and azacitidine show synergistic effects on juvenile myelomonocytic leukemia

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Test the influence of azacytidine on leukemic cells after xenotransplantation

overall_design: ex vivo treatment

first: Melanie

last: Boerries

first: Miriam

last: Erlacher

first: Ying

last: Wu


title: Stereoselective RNA Reaction with Chiral 2'-OH Acylating Agents

city: Stanford

first: Lu

last: Xiao

state: California

address: 369 N-S Axis, Stauffer I, 109

institute: Stanford University

summary: The reactivity of RNA 2'-OH groups with acylating agents has recently been investigated for high-yield conjugation of RNA strands. To date, only achiral molecules have been studied for this reaction, despite the complex chiral structure of RNA. Here we prepare a set of chiral acylimidazoles and study their stereoselectivity in RNA reactions. Reactions performed with unfolded and folded RNAs reveal that positional selectivity and reactivity vary widely with local RNA macro-chirality. We further document remarkable effects of chirality on reagent reactivity, identifying an asymmetric reagent with 1000-fold greater reactivity than prior achiral reagents. In addition, we identify a chiral compound with higher RNA structural selectivity than any previously reported RNA-mapping species. Further, azide-containing homologs of a chiral dimethylalanine reagent were synthesized and applied to local RNA labeling, displaying 92% yield and 16:1 diastereoselectivity. The results establish that reagent stereochemistry and chiral RNA structure are critical elements of small molecule-RNA reactions, and demonstrate new chemical strategies for selective RNA modification and probing.

overall_design: 10 samples are analyzed, including replicates for each conditions: (1) A-case RNA library treated with 50mM S1; (2) A-case RNA library treated with 50mM R1; (3) A-case RNA library treated with 100µM S2; (4) A-case RNA library treated with 100µM R2;(5) A-case RNA library treated DMSO (as control); (6) U-case RNA library treated with 50mM S1; (7) U-case RNA library treated with 50mM R1; (8) U-case RNA library treated with 100µM S2; (9) U-case RNA library treated with 100µM R2;(10) U-case RNA library treated DMSO (as control);

first: Ryuta

last: Shioi

first: Sayantan

last: Chatterjee

first: Eric

last: Kool


title: Analysis of Genome-wide 5-Hydroxymethylation of Blood Samples Stored in Differing Anticoagulants: Opportunities for the Expansion of Clinical Resources for Epigenetic Research

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

type: Methylation profiling by high throughput sequencing

summary: Background: Elucidating epigenetic mechanisms could provide new biomarkers for disease diagnosis and prognosis. Technological advances allow genome-wide profiling of 5-hydroxymethylcytosines (5hmC) in liquid biopsies. 5hmC-Seal followed by NGS is a highly sensitive technique for 5hmC biomarker discovery in cfDNA. Currently, 5hmC Seal is optimized for EDTA blood collection. We asked whether heparin was compatible with 5hmC Seal as many clinical and biobanked samples are stored in heparin. Methods:  We obtained 60 samples in EDTA matched to 60 samples in heparin from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. Samples were comprised of 30 controls and 30 individuals who later were diagnosed with colon cancer. We profiled genome-wide 5hmC in cfDNA using 5hmC-Seal assay followed by NGS. The 5hmC profiling data from samples collected in EDTA were systematically compared to those in heparin across various genomic features. Results: cfDNA isolation and library construction appeared comparable in heparin vs. EDTA. Typical genomic distribution patterns of 5hmC, including gene bodies and enhancer markers, were comparable in heparin vs. EDTA.  5hmC analysis of cases and controls yielded highly correlated differential features suggesting that both anticoagulants were compatible with 5hmC Seal assay. Conclusions: While not currently recommended for the 5hmC-Seal protocol, blood samples stored in heparin were successfully used to generate analyzable and biologically relevant genome-wide 5hmC profiling. Our findings are the first to support opportunities to expand the biospecimen resource to heparin samples for 5hmC Seal and perhaps other PCR-based technologies in epigenetic research.

overall_design: Paired Comparison: We compared genomic distribution patterns of 5hmC between plasma collected in an EDTA tube and matched plasma collected in a heparin tube for 60 samples from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. Among the 60 samples, 30 of them were diagnosed later with colorectal cancer within one year of the 3rd sampling (i.e., T3 time point) of the PLCO Trial, and 30 individuals were age-, gender-, and race/ethnicity-matched controls who did not develop overt cancer followed for 15 years after the T3 blood collection time point.

last: Gao

first: Zhou

last: Zhang

first: Xiao-Long

first: Diana

last: West-Szymanski

first: Chang

last: Ye

first: Chuan

last: He

first: Wei

first: Marc

last: Bissonnette


title: DOCK1 insufficiency disrupts trophoblast function and pregnancy outcomes via DUSP4-ERK pathway

first: Yichi

last: Xu

address: 910 Hengshan

institute: International Peace Maternity And Child Health Hospital, IPMCH

summary: To investigate the role of DOCK1 in trophoblast regulation, we established HTR-8 lines in which DOCK1 has been knocked out by sgRNA using CRISPR/Cas9.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DOCK1-KO and its control in HTR-8 cells.


title: Single-Cell Profiling of Premature Neonate Airways Reveals a Continuum of Myeloid Differentiation

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

summary: Single-cell genomic technologies hold great potential to advance our understanding of lung development and disease. A major limitation lies in accessing intact cells from primary lung tissues for profiling human airway health. Sampling methods such as endotracheal aspiration that are compatible with clinical interventions could enable longitudinal studies, the enrollment of large cohorts, and the development of novel diagnostics. To explore single-cell RNA sequencing profiling of the cell types present at birth in the airway lumen of extremely premature neonates (<28 wk gestation), we isolated cells from endotracheal aspirates collected from intubated neonates within the first 1 hour after birth. We generated data on 10 subjects, providing a rich view of airway luminal biology at a critical developmental period. Our results show that cells present in the airways of premature neonates primarily represent a continuum of myeloid differentiation, including fetal monocytes (25% of total), intermediate myeloid populations (48%), and macrophages (2.6%). Applying trajectory analysis to the myeloid populations, we identified two trajectories consistent with the developmental stages of interstitial and alveolar macrophages, as well as a third trajectory presenting an alternative pathway bridging the distinct macrophage precursors. The three trajectories share many dynamic genes (N= 5,451), but also have distinct transcriptional changes (259 alveolar-specific, 666 interstitial-specific, and 285 bridging-specific). Overall, our results define cells isolated within the so-called “golden hour of birth” in extremely premature neonate airways, representing complex lung biology, and can be used in studies of human development and disease.

overall_design:
scRNA-seq of cells isolated from 10 premature neonatal endotracheal aspirates upon initial intubation.

Raw data is available from dbGaP (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs003427.v1.p1 or search for "phs003427.v1.p1" at http://www.ncbi.nlm.nih.gov/gap).

first: Holly

last: Welfley

first: Ranjit

last: Kylathu

first: Nahla

last: Zaghlou

first: Marilyn

last: Halonen

first: Fernando

last: Martinez

first: Mohamed

last: Ahmed


title: Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines [Micro-C]

first: Mingan

last: Sun

state: Maryland

summary: To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3; 5) Micro-C data.

overall_design: We generated RNA-seq, ATAC-seq, ChIP-seq and Micro-C data in S2, K167 and/or D17-c3 cells.

first: Lesley

last: Brown

first: Pedro

last: Rocha

first: Ming-an

first: Judith

last: Kassis


title: Ovarian cancer cell line (OVCAR-3): control vs. defined factors (OCT3/4, SOX2, KLF4, c-MYC) transfected

city: Taipei

first: YuAn

last: Chen

state: Taipei

address: 5F, No.2, Xuzhou Rd., Zhongzheng Dist

department: College of Medicine

country: Taiwan

institute: Graduate Institute of Medical Genomics and Proteomics, College of Medicine

summary: Transcriptional profiling of induced ovarian cancer initiating cell comparing control untransfected OVCAR-3 cells with iOVCAR-3 cells transfected with OCT3/4, SOX2, KLF4, and c-MYC genes. The aim of this study is to generate an induced ovarian cancer initiating cell (iOCICs) model by transducing defined factors into an OC cell line.

overall_design: Two-condition experiment, OVCAR-3 vs. iOVCAR-3 cells.


title: Analysis of hypoxia with sgSETDB1 in hela cells

first: Jong Hwan

last: Kim

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


title: Malnutrition affects the physiological status and function of pituitary gland in pregnant ewes

city: Hefei

first: Yanfeng

last: Xue

state: Anhui

address: Changjiang Western Road 130

institute: Anhui Agricultural University

summary: In the current study, 5 multiparous ewes during the late gestation were restricted to 30% feeding level to establish an undernutrition model while another 5 ewes were fed normally as controls. All the ewes were sacrificed and pituitary samples were collected to do transcriptome sequencing to investigate the metabolic changes.

overall_design: Compare the differences in transcriptome profiles between the pituitary sample from CON and TR ovis aries.

first: Shuai

last: Liu

first: Huizhen

last: Lu

first: Shengyong

last: Mao

first: Zijun

last: Zhang

first: Wen

last: Zhu

first: Jianbo

last: Cheng


title: Multi-ancestry genetic analysis of gene regulation in coronary artery prioritizes disease risk loci

city: Charlottesville

first: Clint

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in coronary artery disease (CAD). However, non-European populations are underrepresented in GWAS and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotype information to identify quantitative trait loci (QTL) for gene expression and splicing in coronary arteries obtained from 138 ancestrally diverse Americans.

overall_design: We integrated bulk RNA-sequencing and low-pass whole-genome seqeuncing to map allele-specific expression, eQTL and sQTL in coronary artery tissues from patients across a range of atherosclerosis disease stages. We leverage these molecular traits to perform colocalization based fine-mapping with CAD and related risk factors.

first: Chani

middle: J

last: Hodonsky


title: Effects of deoxycholic acid on gene expression in colonic tissue of colitis mice

status: Public on Nov 13 2023

city: Tianjin

first: Chen

last: Wang

state: Tianjin

address: 154 Anshan Road,Heping District,Tianjin,China

institute: Tianjin Medical University General Hospital

summary: To investigate the roles of deoxycholic acid in the regulation of cell function and gene expression of colonic tissue, we treated colitis mice with deoxycholic acid. Then, we performed gene expression profiling analysis using data obtained from RNA-seq of colonic tissue of colitis mice treated with or without deoxycholic acid.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colonic tissue of colitis mice with or without deoxycholic acid treatment.

first: Yu

last: Gu

first: Wenxiao

last: Dong

first: Qiao

last: Chu

first: Xin

last: Dai

first: Wentian

first: Bangmao

first: Tianyu

first: Weilong

last: Zhong

first: Hailong

last: Cao


title: Co-repressor CDYL confers forebrain identity to human cortical organoids by negatively regulating NNAT

first: Xi-Yin

address: College Road

department: Neuroscience Research Institute

institute: Peking University

overall_design: Refer to individual Series


title: SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks.

city: Marseille

first: Karel

last: Naiman

address: BD Lei Roure

institute: CRCM

summary: Nuclear pores complexes (NPCs) are genome organizers, defining a particular nuclear compartment enriched for SUMO protease and proteasome activities, and act as docking sites for DNA repair. In fission yeast, the anchorage of perturbed replication forks to NPCs is an integral part of the recombination-dependent replication restart mechanism (RDR) that resumes DNA synthesis at terminally dysfunctional forks. By mapping DNA polymerase usage, we report that SUMO protease Ulp1-associated NPCs ensure efficient initiation of restarted DNA synthesis, whereas proteasome-associated NPCs sustain the speed of restarted DNA polymerase. In contrast to Ulp1, this last function occurs independently of SUMO chains formation. By analyzing the role of the nuclear basket, the nucleoplasmic extension of the NPC, we reveal that the activities of Ulp1 and the proteasome cannot compensate for each other and affect the dynamics of RDR in distinct ways. Our work probes the mechanisms by which the NPC environment ensures optimal RDR.

overall_design: We mapped ribonucleotide-incorporation by the mutated DNA polymerase delta and epsilon at single-nucleotide resolution and used the data for following the replication fork restart by subsequent informatics analysis.

first: Kamila

last: Schirmeisen

first: Karine

last: Fréon

first: Laetitia

last: Besse

first: Shrena

last: Chakraborty

first: Antony

last: Carr

first: Karol

last: Kramarz

first: Sarah

last: Lambert


title: Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines (ATAC-Seq)

first: Mingan

last: Sun

first: Lesley

last: Brown

first: Pedro

last: Rocha

first: Ming-an

first: Judith

last: Kassis


title: Vancomycin Induced Gut Microbial Dysbiosis Alters Enteric Neuron-Macrophage Interactions During a Critical Period of Postnatal Development

city: Saint Louis

first: Ellen

middle: Merrick

last: Schill

state: MO

address: 660 S. Euclid Ave, Campus Box 8124

institute: Washington University

summary: Vancomycin is a broad-spectrum antibiotic widely used in cases of suspected sepsis in premature neonates. While appropriate and potentially lifesaving in this setting, early life antibiotic exposure alters the developing microbiome and is associated with increased risk of deadly complications, including late-onset sepsis (LOS) and necrotizing enterocolitis (NEC). Recent studies show that neonatal vancomycin treatment disrupts postnatal enteric nervous system (ENS) development in mouse pups, which is in part dependent upon neuro-immune interactions. This suggests that early life antibiotic exposure could disrupt these interactions in the neonatal gut. Notably, a subset of tissue-resident intestinal macrophages, muscularis macrophages, have been identified as important contributors to the development of the postnatal ENS. We hypothesized that vancomycin-induced neonatal dysbiosis impacts postnatal ENS development through effects on macrophages. Using a mouse model, we found that exposure to vancomycin in the first ten days of life, but not in adult mice, resulted in an expansion of pro-inflammatory colonic macrophages by increasing the recruitment of bone-marrow derived macrophages. Single cell RNA sequencing of neonatal colonic macrophages revealed that early-life vancomycin exposure was associated with an increase in immature and inflammatory macrophages, consistent with an influx of circulating monocytes differentiating into macrophages. Lineage tracing confirmed that vancomycin significantly increased non-yolk sac derived macrophage population. Consistent with these results, early life vancomycin exposure did not expand the colonic macrophage population nor decrease enteric neuron density in CCR2 deficient mice. Collectively, these findings demonstrate that early life vancomycin exposure alters macrophage number and phenotypes in distinct ways compared to vancomycin exposure in adult mice and results in altered ENS development.

overall_design: Mouse pups were treated with vancomycin daily from birth until DOL 11. Cx3CR1+ macrophages were isolated via FACS (selected cells were Live, CD45+ CX3CR1+ CD11c lo/negative). Macropahges from pups in the same litter were pooled.  Control vs. vanomycin treated macropahges were analyzed via RNA seqeuncing.

first: Rodney

last: Newberry


title: High-Throughput Methylome Analysis Reveals Differential Methylation During for Early and Late Onset Preeclampsia for Mothers and Their Newborn Children

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: Preeclampsia is a hypertensive disorder of pregnancy that affects approximately 2-5% of all pregnancies, contributes to 4 of the top 10 causes of pregnancy-related deaths, and remains a long-term risk factor for cardiometabolic diseases. Yet, little is still known about the molecular mechanisms that lead to this disease. There is evidence that some cases have a genetic cause. However, it is well appreciated that harmful factors in the environment, such as poor nutrition, stress, and toxins, may lead to epigenetics changes that can contribute to this disease. DNA methylation is one of the epigenetic modifications known to be fairly stable and impact gene expression. Using DNA from buccal swabs from pregnant women, we analyzed global DNA methylation among pregnancies complicated by preeclampsia at <32 weeks (early) and >37 weeks (late) against uncomplicated pregnancies, as well as newborns from these pregnancies. We found significant differentially methylated regions between pregnancies complicated by preeclampsia compared to normal pregnancies adjacent or within genes that are important for placentaton, embryonic development, cell adhesion, inflammation (e.g., the cadherin pathway) and many reported to be expressed in tissues relevant to preeclampsia (i.e. brain, heart, kidney, and placenta). As this study was performed on DNA extracted from cheek swabs, this opens the way to future studies in different tissues, aimed at identifying possible biomarkers of risk and early detection, develop targeted interventions, and reduce the progression of this life-threatening disease.

overall_design: The study included 6 groups: 1) Early-preeclampsia mothers (>32 weeks) N=10; 2) Children from early-preeclampsia mothers N=10; 3) Late-preeclampsia mothers (>37 weeks) N=9; 4) Children from late-preeclampsia mothers N=9; 5) Normal pregnancy mothers N=10; 6) Children from normal pregnancy mothers N=9

first: Cora

last: Layman

first: Samantha

last: Ward

middle: A

first: Kimberly

last: Nevonen

first: Mariam

last: Okhovat

first: Monica

last: Rincon

first: Amy

last: Valent

first: Lucia

last: Carbone

first: Kent

last: Thornburg


title: Co-repressor CDYL confers forebrain identity to human cortical organoids by negatively regulating NNAT [RNA-Seq]

city: Beijing

first: Xi-Yin

last: Zhang

summary: Epigenetic regulation is essential for the normal development of human cerebral cortex, and its disruptions would lead to diverse neurodevelopmental disorders. The epigenetic co-repressor CDYL exhibits widespread expression across various cell clusters within the human embryonic cortex, yet its roles in this intricate process have remained elusive. Here, we show that CDYL is critical for cortical neurogenesis, and CDYL deficiency led to an augmentation in the generation of GABAergic neurons instead of cortical progenitors and neurons in the cortical organoid model. Combining analysis of bulk RNA-seq and ChIP seq, we identified NNAT as a significant CDYL target by H3K27me3 modification, crucial for the fate determination of neural stem cells within human cortical organoids, distinctly diverging from the murine cortex at a similar developmental stage. Collectively, our study sheds light on the critical function of CDYL in the maintenance of cortical neural stem cell fate commitment during human corticogenesis through the inhibition of NNAT expression.

overall_design: cortical organoids generated from CDYL +/+ and CDYL -/- human ESCs are collected at day 30 and day 80; mouse cortex at E15.5 from control and Emx1-cre-Cdyl-loxp group were collected

first: Yaming

last: Yang

first: Bai-Rong

last: Chen

first: Yun

last: Wang


title: Gestational diabetes in mice induces hematopoietic memory that impacts the long-term health of the offspring

city: Cincinnati

first: Soona

last: Shin

state: Cincinnati

address: 3333 Burnet Ave, OH

institute: Cincinnati Children's Hospital Medical Center

summary: Gestational diabetes is a common medical complication of pregnancy that is associated with adverse perinatal outcomes and an increased risk of metabolic diseases and atherosclerosis in adult offspring. The mechanisms responsible for this delayed pathological transmission remain unknown. In mouse models, we found that the development of atherosclerosis in adult offspring born to diabetic pregnancy can be in part linked to hematopoietic alterations. Although they do not show any gross metabolic disruptions, the adult offspring maintain hematopoietic features associated with diabetes, indicating the acquisition of a lasting diabetic hematopoietic memory. We show that the induction of this hematopoietic memory during gestation relies on the activity of the pattern recognition receptor AGER and the NLRP3 inflammasome, which leads to increased placental inflammation. In adult offspring, we find that this memory is associated with DNMT1 upregulation and epigenetic changes in hematopoietic progenitors. Altogether, our results demonstrate that the hematopoietic system can acquire a lasting memory of gestational diabetes, and that this memory constitutes a new pathway connecting gestational health to adult pathologies.

overall_design: RNA-seq analysis on placental CD45+ cells isolated from Ctrl, WT(STZ) and Nlrp3(STZ) E17 embryos.

first: Vinothini

last: Govindarajah

first: Masahide

last: Sakabe

last: Good

first: Michael

last: Solomon

first: Ashok

last: Arasu

first: Nong

first: Xuan

first: H

middle: L

last: Grimes

first: Ady

last: Kendler

first: Mei

last: Xi

first: Damien

last: Reynaud


title: qPCR gene expression profiling of 84 key genes involved in brain micro-vessel treatment

city: Baltimore

first: jiekang

last: wang

state: MD

address: 365 homeland Southway unit 3A

institute: Johns Hopkins University

summary: The Mouse osteogenesis RT² Profiler PCR Array profiles the expression of 84 key genes involved in brain micro-vessel treatment. In this experiment, we established an ex vivo cerebral microvascular model and treated it with PDGF-BB. There are two samples: one is the control group, and the other is the PDGF-BB treated group.

overall_design: qPCR gene expression profiling. Cerebral microvascular from WT mice was treated by 20ng/ml PDGF-BB.

first: Jiekang


title: Gestational diabetes in mice induces hematopoietic memory that impacts the long-term health of the offspring.

overall_design: RRBS analysis on WT LSK cells isolated from the BM of adult offspring born to nomal and diabetic  pregnancy

first: Samantha


title: Differential expression of mRNAs  in the heart of ischemia-reperfusion mice

city: guangzhou

first: shuang

last: zheng

address: 11 Fengxin Road, Science City, Huangpu District, Guangzhou City

institute: Guangdong Laboratory Animal Monitoring Institute

summary: To identify the role of mRNA during myocardial ischemia-reperfusion in mice, we have employed high-throughput sequencing to detect mRNA expression. Samples were collected from the control group and the ischemia reperfusion groups , with 5 samples per group. The candidate mRNA that may affect the process of myocardial ischemia-reperfusion was screened by comparing the ischemia-reperfusion group and the control group.

overall_design: Total RNAs from the ventricular tissues of the control and ischemia-reperfusion groups were isolated using TRIzol® Reagent. Each group contains five independent samples. Subsequently, a total amount of 3 µg RNA per sample were used for high-throughput sequencing.

first: Shuang

last: Zheng

first: Xiang

last: Li

first: Weijiang

last: Tan

first: Feng


title: Co-repressor CDYL confers forebrain identity to human cortical organoids by negatively regulating NNAT [ChIP-Seq]

first: Xi-Yin

last: Zhang

first: Yaming

last: Yang

first: Bai-Rong

last: Chen

first: Yun


title: Serum Exosomal miRNA Signature in occupational medicamentosa-like dermatitis induced by trichloroethylene

first: Hui

last: Wang

address: 218 Jixi Road

institute: he First Affiliated Hospital of Anhui Medical University

summary: Occupational dermatitis medicamentosa-like of TCE (ODMLT) is a complex immune process which can cause serious damage of liver function, and becoming a serious occupational health problem in China. However, the pathogenesis of ODMLT remained undefined. The aim of the present study was to identify the expression profiles of circulating exosomal miRNAs in ODMLT patients and its role in the regulation of liver injury. The exosomes were isolated from the serum of patients and healthy individuals, and characterized by electron microscopy, nanoparticle tracking analysis, and Western blot and total RNA was extracted. Expression of exosomal miRNAs was evaluated with Agilent Human miRNA microarrays and the expression of selective serum exosomal miRNA were verified by qRT-PCR.

overall_design: Two disease stages (acute-stage and healed-stage) of the 5 ODMLT patients which were ODMLT-A and ODMLT-B group and 5 age- and sex-matched healthy control subjects. The blood was collected into serum-separating tubes and allowed to sit for 30-60min at room temperature prior to centrifugation.


title: A novel pathogenic mutation of MeCP2 impairs chromatin association independent of protein levels

city: Houston

first: Hu

state: TX

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

summary: Loss-of-function mutations in MECP2 cause Rett Syndrome (RTT), a severe neurological disorder that mainly affects girls. Mutations in MECP2 do occur in males occasionally and typically cause severe encephalopathy and premature lethality. Recently, we identified a missense mutation c.353G>A, p.Gly118Glu (G118E) in a young boy who suffered from progressive motor dysfunction and developmental delay. To determine whether this variant causes the clinical symptoms and study its functional consequences, we established two disease models, including patient-derived iPSCs and a knock-in mouse line. Given that G118E mutation is in the DNA binding domain of MeCP2 and could potentially disrupt its chromatin association, we performed Cut&Run using WT and G118E mouse cortical tissue to characterize the genome wide binding pattern of WT and mutant MeCP2 proteins. We observed a reduction of DNA binding of G118E MeCP2 in the known MeCP2 target loci, as well as in a genome-wide manner.

overall_design: Cleavage Under Targets & Release Using Nuclease (CUT&RUN) was performed using mouse cortical tissues collected from 3 Mecp2-G118E mice and 3 wild-type littermates.

first: Zhou

last: Jian

first: Li

last: Yan

first: Chen

last: Hu

first: Liu

last: Zhandong


first: Soona

last: Shin


title: The differentially expressed genes profile upon ZFX silencing in CML CD34+ cells

city: Suzhou

first: Xiuyan

address: 199 Ren'ai Road

institute: Soochow University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: In our previous study, the roles of zinc finger protein X-linked  (ZFX) in CML cells were revealed. We showed that ZFX expression was significantly higher in CML CD34+ cells than in control cells. Overexpression and gene silencing experiments indicated that ZFX promoted the in vitro growth of CML cells, conferred imatinib mesylate (IM) resistance to these cells, and enhanced BCR/ABL-induced malignant transformation.  To obtain molecular insights of how ZFX modulates the growth and imatinib response of CML stem and progenitor cells, we generated microarray data comparing ZFX silenced CML CD34+ cells with control (Scramble) cells.

overall_design: We recruited 3 CML patient bone marrow samples for CD34+ stem/progenitor cells enrichment with immunomagnetic beads. The CD34+ cells were transduced with concentrated lentivirus and then isolated using fluorescence-activated cell sorting (FACS). The transduced CD34+ cells were harvested for microarray analysis using Agilent whole human genome oligo-chips (4×180K) in Shanghai Biotechnology Corporation. The differentially expressed transcripts were determined based on Student’s t-test (P<0.05) and fold change (>2).

last: Zhao