title: High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails

city: San Francisco

first: Vivasvan

last: Vykunta

address: 513 Parnassus Avenue HSW901

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Enhancing site-specific transgene insertion efficiency by homology-directed repair (HDR) using high concentrations of double-stranded DNA (dsDNA) with Cas9 target sequences (CTSs) can be toxic to primary cells. Here, we develop single-stranded DNA (ssDNA) HDR templates (HDRTs) incorporating CTSs with reduced toxicity that boost knock-in efficiency and yield by an average of 2–3-fold relative to dsDNA CTSs. Using small-molecule combinations that enhance HDR, we could further increase knock-in efficiencies by an additional 2–3-fold on average. Our method works across a variety of target loci, knock-in constructs, and primary human cell types, reaching HDR efficiencies of >80–90%. We demonstrate application of this approach for both pathogenic gene variant modeling and gene-replacement strategies for IL2RA and CTLA4 mutations associated with Mendelian disorders. Finally, we develop a good manufacturing practice (GMP)-compatible process for non-viral chimeric antigen receptor (CAR)-T cell manufacturing, with knock-in efficiencies (46–62%) and yields (>1.5×109 modified cells) exceeding those of conventional approaches.

overall_design: Amplicon sequencing for detection of insertions and deletions after CRISPR-Cas9 mediated DNA modifications at CD5 target site

first: Brian

middle: R

last: Shy

first: Alexander

last: Marson


title: Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure

status: Public on May 12 2022

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

summary: Ultraviolet radiation (UV) is causally linked to cutaneous melanoma, yet the underlying epigenetic mechanisms, known as molecular sensors of exposure, have never been characterized in clinical biospecimen. DNA methylome, genome and transcriptome analyses of cutaneous melanoma in two cohorts identified UV-related alterations in regulatory regions and immunological pathways and revealed novel cancer driver genes affecting patient survival. TAPBP, the top gene and a member of the immunoglobulin superfamily, encompassed several CpG methylation sites altered by UV and independently validated by bisulfite pyrosequencing, providing cost-effective opportunities for clinical application. The DNA methylome also highlighted non UV-related aberrations underlying pathological differences between cutaneous and acral melanomas. Unsupervised epigenomic mapping demonstrated that non UV-mutant cutaneous melanoma more closely resembles acral rather than UV-exposed cutaneous melanoma, with the latter showing better patient prognosis than the other two forms. These gene-environment interactions in multi-ethnic backgrounds reveal translationally impactful mechanisms in melanomagenesis.

overall_design: 54 cutaneous and 17 acral melanoma samples prior to any treatment

first: AnnaLuiza

middle: S

last: Vicente

first: Alexei

last: Novoloaca

first: Vincent

last: Cahais

first: Zainab

last: Awada

first: Cyrille

last: Cuenin

first: Natália

last: Spitz

first: André

middle: L

last: Carvalho

first: Adriane

middle: F

last: Evangelista

first: Camila

last: Crovador

first: Rui

middle: M

last: Reis

first: Vinicius

last: Vazquez

first: Akram

last: Ghantous


title: Genome-wide DNA accessibility mapping using ATAC-seq in HEK293 in vector control, PC4 knockdown and  PC4 phosphorylation specific mutant and mimic

city: BENGALURU

first: TAPAS

middle: K

last: KUNDU

state: KARNATAKA

address: JAKKUR

department: MBGU

country: India

institute: JNCASR

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To assess the mechanisms by which PC4 mediates chromatin compaction in  cells and regulation of genome organization by its phosphorylation state, we measured the chromatin accessibility landscape using ATAC-seq of vector control 293 cells (Control/shNS), PC4 knockdown (KD/PC4 KD) and upon ectopic expression of Flag tagged PC4 (FP/PC4), Phosphomimic-PC4 (PM/PM-PC4) and phospho-mutant (MTP/MTP5) in PC4 knockdown cells.

overall_design: Studying the chromatin accessibility changes that occurred upon knocking down of PC4(PC4 KD) compared to shNS cells and the effect of PC4 phosphorylation on the chromatin accessibility upon expressing Flag tagged PC4, PM-PC4 and MTP5 in the PC4 KD background.

first: Pallabi

last: Mustafi

first: Madavan

last: Vasudevan

first: Tapas

last: Kundu


title: Liver-specific deletion of Pten and atypical E2Fs in 16-weeks old mice.

city: Utrecht

first: Bart

last: Westendorp

address: Uppsalalaan 8

department: Molecular Health Sciences

country: Netherlands

institute: Utrecht University

type: Expression profiling by high throughput sequencing

summary: RNA-sequencing analysis of liver gene expression after combinatorial liver-specific deletion of tumor suppressor genes in a mouse fatty liver disease and liver cancer model. Gene expression was determined at 16 weeks of age, before onset of liver tumor formation. Aim was to study how loss of atypical E2F transcription repressors affected gene expression in Pten-mutant livers.

overall_design: Gene expression was analyzed in four Alb-Cre-E2f7 E2f8 Pten conditional triple knockout livers, four Alb-Cre-E2f7 E2f8 conditional double knockout liver tumors, four Alb-Cre_Pten conditional single knockout livers, and four age-matched wild-type mice. All livers were harvested from 16-week old mice.


title: Somatic Cell Fate Maintenance in Mouse Fetal Testes via Autocrine/Paracrine Regulation of anti-Müllerian hormone and Activin B

city: RTP

first: Humphrey

last: Yao

state: NC

address: 111 TW Alexander Dr.

department: DIR

country: USA

institute: NIEHS

summary: Fate determination and maintenance of fetal testes in most mammals occur cell autonomously as a result of the action of key transcription factors in Sertoli cell. In the mouse testis AMH and Activin B are required for the maintenance of Sertoli cell fate. In the absence of both AMH and Activin B (in the global dKO) Sertoli cells at the testis poles transdifferentiate into granulosa cells by embryonic day 15.5.

overall_design: Control testis (Amh+/+; Inhbb+/+), Control ovaries (Amh+/+; Inhbb+/+) and dKO  (Amh-/-; Inhbb-/-) testis at E15.5

first: Karina

last: Rodriguez

middle: H


title: transcriptome profiles of differentiated wt1-SAM brown adipocytes treated with different LNAs and stimulated with isoproterenol

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Cold and nutrient activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via uncoupled respiration and secretion of endocrine factors thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to inter- scapular brown adipose tissue (iBAT) function in high fat diet (HFD) and cold stressed mice. We focused on Gm15551 which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis and downregulated by β-adrenergic activation in mature adipocytes. Albeit we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551.

overall_design: polyA RNA profiles of brown adipocytes (wt1-SAM) differentiated for 7 days, reverse transfected with different anti sense oligonucleotides at day 4 of differentiation and stimulated for 24 h with isoproterenol before harvesting were generated by deep sequencing in triplicate.

first: Christoph

middle: A

last: Engelhard

first: Chien

last: Huang

first: Sajjad

last: Khani

first: Petr

last: Kasparek

last: Procházka

last: Rozman

first: David

middle: P

last: Reguera

first: Radislav

last: Sedláček

first: Jan-Wilhelm


title: iBAT polyA RNA profiles of wild type C57BL/6N-ΔGm15551 mice exposed to cold.

overall_design: PolyA RNA profiles of interscapular brown adipose tissue (iBAT) from 12-week old  ∆Gm15551 and wild type litter mate mice housed at 4°C for 24 h.


title: RNA-sequencing of 3T3-L1 preadipocytes and adipocytes

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

overall_design: Examination of 6 samples derived from 3T3-L1 preadipocytes and adipocytes

first: Jeu

last: Park

first: A

middle: Y

first: Yoon

middle: J

first: Jae

middle: B


title: Transcriptome profiling of muscle from control, mdx and Sirt6 knockout on mdx background mice

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: In this study, Pax7-Cre mediated inactivation of Sirt6 in mdx mice resulted in profound improvement of the mdx phenotype at the functional level. To study the underlying molecular mechanisms we performed RNA-seq of muscles from control, mdx and Sirt6mKO/mdx mice.

overall_design: RNA-seq analysis of muscle from control (wild type), mdx and Sirt6mKO/mdx mice

first: Angelina

last: Georgieva

first: Stefan

last: Günther


title: The gene regulation landscape of MTAP in lung adenocarcinoma

city: Taipei

first: Wen-Hsin

last: Chang

address: 7F, No.2, Syu-jhou Road

country: Taiwan

institute: National Taiwan University

summary:
MTAP is an enzyme and found deleted in various cancers, but its role in lung adenoacrcinoma is still unclear. This study sought to investigate the effects of MTAP on the biological behavior and global gene expression profiles in lung adenocacinoma cells.
We used expression microarrays to identify the global gene alterations in lung adenocacinoma cell line, CL1-5 cells after ectopically expressing V5-tagged MTAP gene.

overall_design: Ectopically expressing V5-tagged MTAP gene and control vector (pcDNA3.1/V5-His-TOPO) in low MTAP-expressing lung cancer cell line, CL1-5.

first: Sung-Liang

last: Yu


title: Transcriptome profiling of muscle stem cells from control, mdx and Sirt6 knockout on mdx background mice

summary: In this study, Pax7-Cre mediated inactivation of Sirt6 in mdx mice resulted in profound improvement of the mdx phenotype at the functional level. To study the underlying molecular mechanisms we performed RNA-seq of MuSCs from control, mdx and Sirt6mKO/mdx mice.

overall_design: RNA-seq analysis of MuSCs from control (wild type), mdx and Sirt6mKO/mdx mice


title: RNA seq on two primary pancreatic cancer cell lines (cancer-collagen1 knockout cell line and control pancreatic cancer cell line)

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

summary: RNA sequencing analysis on two primary pancreatic cancer cell lines from transgenic mice: (1) cancer-collagen1 knockout cell line from KPPC;Col1pdxKO cancer-collagen1 knockout tumor and (2) control pancreatic cancer cell line from KPPC tumor

overall_design: Two primary pancreatic cancer cell lines were established from pancreatic tumors of transgenic mice with indicated genotypes, cultured, and extracted for RNA seq: (1) cancer-collagen1 knockout cell line from KPPC;Col1pdxKO cancer-collagen1 knockout tumor and (2) control pancreatic cancer cell line from KPPC tumor.


title: Transcriptional down-regulation of major histocompatibility complex as a possible pathogenesis for Meniere's disease

status: Public on May 11 2022

city: Yangsan

first: Jae-Hwan

last: Choi

address: Kumo-ro 20, Beomo-ri, Mulgum-eup

department: Neurology

institute: Pusan National University Yangsan Hospital

summary: This study aimed to determine the underlying pathogenesis of Meniere's disease (MD) using transcriptome analysis

overall_design: Total RNAs were extracted from peripheral blood mononuclear cells of 9 patients with MD and 9 normal controls. Using the Affymetrix Human Clariom S Assay, the differentially expressed genes (DEGs) between MD and normal control samples were screened by the cut-off criteria (|fold changes| > 2 and adjusted p-value < 0.05). Functional enrichment analysis for DEGs was performed using Gene Ontology (GO).

first: Kwang-Dong


title: Transcriptomic profilling of Mex3a+ cells in colon adenomas compared to LGR5

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Transcriptomic data related to 4 different subpopulations found in Mex3a Ki/+ Lgr5 Gfp in APCflfl adenomas in untreated animals. Adenomas where induced with 3%DSS and a single shot of 8mg/kg of Tamoxifen. The populations are refered as Mex3a + Lgr5, Mex3a- Lgr5+ Mex3a+ Lgr5- and Mex3a- Lgr5- according to the flow cytometry profile. Cells were isolated using FACsARIA (BD)

overall_design: 3 biological replicates (mouse) of 4 different population. Each replicate represent a pool of different colon adenomas.

last: Stephan-Otto Attolini

first: Adrian

last: Álvarez-Varela


title: Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling [cytokine cultures]

city: Berkeley

first: David

last: DeTomaso

state: CA

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

summary: RNA-sequencing of in vitro differentiated T cells cultured with varying cytokine conditions: IL-12, IL-12+IL-21, IL-1b+IL-6+IL-23, and TGFb+IL-6

overall_design: Naive T cells were isolated from reporter mice for IL-23R that carry an IRES-eGFP in the Il23r locus. Naive T cells (CD44lowCD62LhiCD4+CD25-) were isolated from heterozygous mice (Il23r wt/eGFP) by fluoresence-activated cell sorting (FACS) and then cultured for 5 days with full medium containing the aforementioned cytokine conditions.  Cells were then sorted based on eGFP expression before rna-sequencing.  The reporter allele (Il23reGFP) represents a functional KO of IL23r combined with eGFP through an IRES element.  Therefore, GFP was used as a indicator for IL23r expression in cells.

first: Mathias

last: Pawlak

first: Alexandra

last: Schnell

first: Gerd

last: Meyer zur Hoerste

first: Youjin

last: Lee

first: Jackson

last: Nyman

first: Danielle

last: Dionne

first: Brianna

last: Regan

first: Vasundhara

last: Singh

first: Toni

last: Delorey

first: Chao

last: Wang

first: Antonia

last: Wallrapp

first: Patrick

last: Burkett

first: Samantha

last: Riesenfeld

first: Ana

middle: C

last: Anderson

first: Aviv

last: Regev

first: Ramnik

last: Xavier

first: Nir

last: Yosef

first: Vijay

last: Kuchroo


title: Nupr1 controls the threshold of quiescent hematopoietic stem cells through p53 signaling pathway

city: Guangzhou

first: Tongjie

address: No.190 Kaiyuan Road

country: China

institute: Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

summary: RNAseq were performed to analyze the transcriptomic differences between wild type HSCs and Nupr1-/- HSCs.

overall_design: RNAseq: Four wild type HSCs samples from four wild type mice and Nupr1-/- HSCs samples from four Nupr1-/- mice.

first: Yong

last: Dong

first: Qitong

last: Weng

first: Jinyong


title: Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling [cd160 knockout ex-vivo]

first: David

last: DeTomaso

summary: RNA-sequencing of wild-type and cd160 knockout CD4 T cells utilized in a T cell transfer colitis model

overall_design: Naïve CD4+ CD45RBhigh T cells were FACS sorted from CD160 knockout and wildtype littermate controls and transferred into Rag1-/- recipient mice for the induction of T cell transfer colitis. At peak of disease, CD4+ T cells were sorted from the colons for bulk RNA-seq.

first: Mathias

last: Pawlak

first: Alexandra

last: Schnell

first: Gerd

last: Meyer zur Hoerste

first: Youjin

last: Lee

first: Jackson

first: Danielle


title: circ_0000045 promotes proliferation, migration, and invasion of head and neck squamous cell carcinomas via binding with HSP70 and MAPK signaling activation

first: li

middle: hao

last: yuan

address: International Biotech Island

institute: Forevergen Biosciences Co.,Ltd

type: Non-coding RNA profiling by high throughput sequencing

summary:
Objective: Head and neck squamous cell carcinoma (HNSCC) is one severe malignancy driven by complex cellular and signaling mechanisms. However, the roles of circular RNAs (circRNAs) in HNSCC’s development remains poorly understood. Therefore, this study investigated the functions of differentially expressed circRNAs in regulating HNSCC cell functions.
Methods: Differentially expressed circRNAs were characterized through RNA sequencing in HNSCC tissues. CircRNA’s identity was then confirmed using RT-PCR and Sanger’s sequencing. Next, expression levels of circRNA and mRNA were detected by qRT-PCR, after which protein abundances were measured by Western blotting. Subsequently, the proliferation, migration, and invasion of HNSCC cells was assessed by MTS, wound healing, and Transwell system, respectively, followed by identification of circRNA-binding proteins in HNSCC cells by circRNA pull-down, coupled with mass spectrometry.
Results: Great alterations in circRNA profiles were detected in HNSCC tissues, including the elevated expression of circ_0000045. As observed, silencing of circ_0000045 effectively repressed the proliferation, migration, and invasion of HNSCC cell lines (FaDu and SCC-9). Contrarily, circ_0000045’s overexpression promoted the proliferation, migration, and invasion in FaDu and SCC-9 cells. Results also showed that circ_0000045 was associated with multiple RNA-binding proteins in HNSCC cells, such as HSP70. Moreover, circ_0000045 knockdown enhanced HSP70 expression and promoted JNK2 and P38’s expression in HNSCC cells, which were oppositely regulated by circ_0000045’s overexpression.
Conclusion: The high expression of circ_0000045; therefore, promoted cell proliferation, migration, and invasion during HNSCC’s development through association with HSP70 protein to activate mitogen-activated protein kinase signaling.

overall_design: circular RNA profiles of oral tongue squamous cell carcinoma/corresponding adjacent non-cancerous tongue tissue samples

first: Ronghao

last: Sun

first: Yuqiu

last: Zhou

first: Yongcong

last: Cai

first: Chunyan

last: Shui

first: Xu

first: Jingqiang

last: Zhu


title: Effects of cadmium and ifg-1 mutant on gene expression and mRNA splicing

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

country: Canada

institute: University of Saskatchewan

summary: Splicing of pre-mRNA is an essential process for all eukaryotic dividing cells. Pre-mRNA splicing can be influenced by environmental factors and RNA splicing defects are implicated in numerous human diseases. To understand the genetic mechanism of RNA splicing regulation under environmental stress, we performed a genome-wide RNAi screen in C. elegans and identified suppression of protein synthesis leads to strong protection against cadmium-induced RNA splicing defects. Using a mutant with partial loss of function to the C. elegans ifg-1 gene (eIF4G), we performed RNA-sequencing and found that the levels of cadmium-induced alternative splicing observed in the wildtype is highly reduced in the ifg-1 mutant. Transcriptome analysis revealed ifg-1 mutant moderately up-regulate > 80 genes involved in RNA splicing regulation and depletion of core RNA splicing regulators abolish the ifg-1 long-lived phenotype. A secondary RNAi screen revealed depletion of sma-2 and sma-3 suppresses ifg-1’s protection against stress-induced RNA splicing protection, potentially via transcription of ifg-1 up-regulated RNA splicing regulating genes. Lastly, depletion of sma-2 and sma-3 reduces ifg-1’s long-lived phenotype. Our results propose a model where translation suppression via ifg-1 increases RNA splicing fidelity under stress by upregulating RNA splicing regulatory genes via the sma-2/3 pathway that contributes to its longevity phenotype.

overall_design: Total RNA was prepared from gravid young adult Caenorhabditis elegans with three biological replicates per group and sent to NovoGene for PE150 sequencing. Sequencing library were constructured with oligo-dT enrichment. Gene expression data were analyzed by DEGSeq with Alternative splicing data analyzed by rMATS.


title: Effect of all-trans retinoic acid (ATRA) treatment on hyperoxia-treated A549 lung adenocarcinoma cells

city: Middletown

first: Nikolaos

last: Tsotakos

state: PENNSYLVANIA

address: 777 W Harrisburg Pike

institute: Penn State Harrisburg

summary:
To investigate the effects of ATRA on hyperoxia-induced inflammatory responses in A549 lung adenocarcinoma cells, we exposed A549 cells (both ATRA- and control-treated) to hyperoxia.
We then performed gene expression profiling analysis using data obtained by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 cells pre-treated with ATRA and exposed to hyperoxia.

first: Zissis

last: Chroneos


title: Next Generation Sequencing-based Quantitative Analysis of female whole body transcriptomes from mock-infected control (sucrose fed) vs Pseudomonas entomophila (P.e)  orally infected flies

city: Calgary

first: Savraj

last: Grewal

state: Alberta

address: 3330 Hospital Drive

institute: University of Calgary

summary:
Purpose: The goal of this RNA-Seq is to analyze the whole-body transcriptomes from mock-infected bvs oral P.e. infected flies to identify differentially expressed genes
Abstract from associated manuscript: When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden but also to alter host physiology and behaviour to promote infection tolerance, and they are mediated through alterations in host gene expression. Here, we have used transcriptome profiling to examine gene expression changes induced by enteric infection with the gram-negative bacteria Pseudomonas entomophila (P.e) in adult female Drosophila. We find that infection induces a strong upregulation of metabolic gene expression, including gut and fat body-enriched genes involved in lipid transport, lipolysis, and beta-oxidation, as well as glucose and amino acid metabolism genes. Furthermore, we find that the classic innate immune deficiency (Imd)/Relish/NF-KappaB pathway is not required for, and in some cases limits, these infection-mediated increase in metabolic gene expression. We also see that enteric infection with P.e. down regulates the expression of many transcription factors and cell-cell signaling molecules, particularly those previously shown to be involved in gut-to-brain and neuronal signaling. Moreover, as with the metabolic genes, these changes occurred largely independent of the Imd pathway. Together, our study identifies many metabolic, signaling and transcription factor gene expression changes that may contribute to organismal physiological and behavioural responses to enteric pathogen infection.
Results: RNA Seq differential expression analysis identified a significant (p<0.05,> 1.5 fold expression) change in 2835transcripts, with 1602 transcripts showing reduced expression levels and 1233 transcripts with elevated expression levels.

overall_design: For each condition (mock -infected vs P.e. infected) there were 6 independent biological samples, each consisting of total RNA extracted from 5 adult female flies. The sucrose fed condition is the control and the 6 samples are labelled W-Sucrose 1-6; the infected samples are labelled W-Pe 1-6.


title: FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [FMRP-CLIP]

city: New York

first: Caryn

last: Hale

state: New York

address: 1230 York Avenue

institute: Rockefeller University

summary: We report cell-type and compartment-specific TRAP-seq, RNAseq, FMRP-CLIP, and PAPERCLIP from CA1 hippocampal neurons.  We use TRAP-seq and PAPERCLIP data to precisely define the dendritic transcriptome, including mRNAs that harbor APA and AS events that are differentially localized.  Further, we use FMRP-CLIP in order to define mRNAs that undergo compartment-specific regulation by FMRP.

overall_design: Cell-type and compartment-specific TRAP-seq, RNAseq, FMRP-CLIP, and PAPERCLIP from mouse microdissected CA1.

first: Robert

last: Darnell

first: Thomas

last: Carroll


title: Effect of early-life plane of nutrition on the hepatic transcriptional profile  in heifer calves

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The objective of this study was to examine changes in hepatic gene expression of heifer calves offered varying planes of nutrition during early life. At approximately 3 weeks of age (19 ± 5 days of age) Angus X Holstein-Friesian heifer calves  were offered a high (HP, n=15) or moderate plane of nutrition (MP, n=15) to achieve  target growth rates of 1.2 kg/d and 0.5 kg/d, respectively. After 18 weeks of differential feeding all calves were euthanized and the liver of each calf recovered. RNA was extracted and subsequently subjected to RNAseq analysis. A total of 591 genes were identified as significantly differentially expressed between HP and MP calves. Differentially expressed genes were involved in biological pathways and processes including those related to metabolism (amino acid, vitamin and mineral metabolism) as well as those involved in organ growth and development.

overall_design: 30 liver RNA samples were analyzed in total. 15 samples were derived from calves fed the High plane of nutrition (HP, n=15) and 15 samples were derived from the claves fed the Moderate plane of nutrition (MP, n=15). Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase, the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks. All samples were collected at the same time-point (21 weeks of age) all differentially expressed genes reported were up- or down-regulated in HP calves compared to MP calves.

first: Colin

last: Byrne

first: Alan

last: Kelly

first: David

last: Kenny


title: Next Generation Sequencing of CD8+ cells from Wild Type and miR-144/451 knockout mice

city: Yangzhou

first: Zhijie

last: Lin

state: Jiangsu

address: 136 Jiangyang road

department: Department of Immunology

institute: Yangzhou University

summary: To investigate the function miR-144/451 on the function of CD8+ cells, we sorted the CD8a+ cells from wild type and miR-144/451 knockout mice, and  then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD8a+ cells frim wild type and miR-144/451 knockour mice.


title: FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [PAPERCLIP]


title: Vitamin D deficiency during development permanently alters liver cell composition and function.

status: Public on May 10 2022

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

summary: Vitamin D, a fat-soluble vitamin, plays a critical role in calcium homeostasis, the immune system, and normal development. Many epidemiological cohort studies globally have found high prevalence rates of vitamin D deficiency and insufficiency, recognized as an important health issue that needs to be solved. In particular, reproductive age and pregnant women low in vitamin D status may confer risks of diseases like obesity on their offspring. While observational studies have suggested associations between prenatal vitamin D deficiency and metabolic phenotypes in offspring, not yet determined is whether prenatal vitamin D deficiency permanently alters the development of the liver, a major metabolic organ. We tested the histopathology and the transcriptomic profiles of livers from male C57BL/6J mice exposed to prenatal vitamin D deficiency through a maternal dietary intervention model. We found that prenatal vitamin D deficiency increases the prevalence of histopathological changes in the liver, and alters its gene expression profile. Cell subtype proportion analysis showed that the liver of prenatal vitamin D deficiency alters non-parenchymal cells of the liver, specifically macrophages, a subset of endothelial cells, and dendritic cells. Our results indicate the long-term memory of prenatal vitamin D deficiency exposure in the adult liver, a potential contributor to offspring health risks.

overall_design: Liver RNA profiles of 16 weeks old prenatal vitamin D deficiency or sufficiency exposed mice

first: Kassidy

last: Lundy

first: John

last: Greally

first: Grace

last: Essilfie-Bondzie

first: Josephine

last: Olivier

first: Reanna

last: Doña-Termine


title: Activation of inflammatory pathways in transcriptome from patients affected by limb girdle muscular dystrophy D2 (LGMDD2)

city: Majadahonda

first: Francisco

last: Díez-Fuertes

address: Carretera Majadahonda - Pozuelo Km 2.2

institute: Instituto de Salud Carlos III

summary: LGMDD2 is a rare form of muscular dystrophy characterized by a heterozygous deletion within the TNPO3 gen, firstly reported in a large Spanish family in 2001. TNPO3-wildtype is involved in the nuclear import of the essential splicing factors, a function altered in the mutated protein. Our group has shown that both TNPO3-wildtype and TNPO3-mutated proteins are translated in these patients. Besides its role in LGMDD2 disease, TNPO3 is also a HIV-1 co-factor but the mechanism underlying its antiviral action is still controversial. In an attempt to connect both LGMDD2 disease and HIV-1 infection, we demonstrated that PBMCs from LGMDD2 patients are refractory to in vitro HIV-1 infection due to a deficient viral integration subsequent to a deficient transport of the splicing factor CPSF6, due to TNPO3 mutation. The accumulation of HIV-1 capsid and retrotranscribed DNA in the cytosol may trigger anti-HIV inflammatory responses, therefore enhancing the blockade of HIV-1 replication. Further characterization of the crosstalk between HIV-1 infection and LGMDD2 disease may contribute to a better understanding of cellular alterations occurring in subjects living with LGMDD2. To this regard, here we show a high-throughput transcriptome profiling of PBMCs from LGMDD2 patients compared to their non-affected relatives. The differentially expressed genes were up-regulated and included G protein-coupled receptor binding chemokines, zinc ion binding proteins and metalloendopeptidases. The functional annotation showed an enrichment in immune response and inflammation pathways including IL-17, TNF, NOD-like receptor, TLR receptor, and NF-κβ signaling pathways, which are also known to be altered during HIV-1 infection. In summary, a holistic perspective of cellular changes occurring during LGMDD2 pathology is shown here providing new factors in this muscular dystrophy that may be considered in the design of new therapeutic strategies.

overall_design: mRNA profiles of PMBCs collected from individuals affected by limb girdle muscular dystrophy D2 (LGMDD2) compared with their non-affected relatives

first: Sara

last: Rodríguez-Mora

first: José

last: Alcamí


title: SRSF3-mediated regulation of N6-methyladenosine modification-related lncRNA ANRIL splicing in promotion of pancreatic cancer resistance to gemcitabine II

city: Fuzhou

first: Zu-wei

last: Wang

address: No. 134, East Street, Fuzhou, 350001, Fujian Province, PR China

institute: Fujian provincial hospital

summary: Serine/arginine-rich splicing factor 3 (SRSF3) functions to regulate mRNA alternative splicing, a molecular mechanism to process more than 90% of the protein-coding genes and provides an essential source for the biological versatility and targeting of SRSF3 could be a novel approach for cancer therapy. This study identify that SRSF3 expression was upregulated in pancreatic cancer tissues and associated with drug resistance and poor prognosis. Thus, we found that SRSF3 regulated ANRIL splicing and modified m6A modification of ANRIL in pancreatic cancer cells. More importantly, we demonstrated that the m6A methylation on lncRNA-ANRIL was essential for splicing process. Meanwhile, we also found that the different isoforms of ANRIL were differentially expressed in drug-resistant pancreatic cancer cell lines, and SRSF3 promotes gemcitabine resistance by regulating the expression of ANRIL-208. In addition, ANRIL-208 regulated pancreatic cancer cell chemoresistance by forming a complex with Ring1b and EZH2 and enhanced DNA homologous recombination repair (HR) capacity. In conclusion, the current study first established the link among SRSF3, m6A modification, lncRNA splicing, and DNA HR repair in pancreatic cancer, and first demonstrated that abnormal alternative splicing and m6A modification are closely related to chemotherapy resistance in pancreatic cancer.

overall_design: 6 samples; triplicates

first: Zu-Wei

first: Jing-Jing

last: Pan

first: Jian-Fei

last: Hu

first: Shi

last: Chen


title: Exercise-Induced Engagement of the IL-15/IL15Rα axis Promotes Anti Tumor Immunity

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: The advent of immune checkpoint blockade has improved patient outcomes, providing durable disease control by reversing localized tumor-mediated immune-suppression and promoting anti-tumor immunity. Despite successes in melanoma and lung cancer, these therapies have largely failed in pancreatic ductal adenocarcinoma (PDA); a ‘cold’ tumor with the highest mortality rate among all major cancers. PDA is uniquely characterized by multiple intra-pancreatic tumor- and stroma-induced mechanisms of immune-suppression, and there remains a great need to explore creative approaches to improve anti-tumor immune responses in this disease. Herein, we show routine aerobic exercise provides tumor-protective benefits in murine PDA through modulation of both systemic and intra-tumoral immunity. Reversing immune-suppressive properties of both myeloid  and T cell populations, we found the anti-tumor benefits of exercise require CD8 T cell activation and expansion in the tumor. Specifically, we report the sub-population of IL15Ra+ CD8 T cells is required for exercise-induced tumor protection and anti-tumor immunity, both of which are abrogated in the context IL-15 blockade. We further show that exercise-induced increases in intra-tumoral T cells are governed by adrenergic signaling and S1P-gradient dependent lymphocyte migration. Finally, we found that combination with aerobic exercise sensitizes pancreatic tumors to anti-PD-1 therapy. Overall, our work highlights the unique mechanisms governing exercise-induced tumor protection in PDA,  and uncovers the importance of the interplay between systemic and intra-tumoral immunity to develop innovative strategies to reverse immune-suppression in this devastating disease.

overall_design: In this work, we set out to peform unibased analysis of the tumor immune microenvironment in pancretic cancer tumors in response to aerobic exercise. All live leukocytes in control and exercised tumors were isolated and were assessed for changes in the relative proportion of specific immune populations or changes to the transcriptional phenotype within each immune cell subset. Differences in the immune cell infiltrates of control and exercised mice would be used to inform mechanistic insights for exercise-induced tumor protection in pancreatic cancer.

first: Emma

last: Kurz

first: Carolina

last: Alcantara Hirsch

first: Tanner

last: Dalton

first: Sorin

last: Alberto Shadoloey

first: Emily

last: Vucic

first: Rafael

last: Winograd

first: Dafna

last: Bar-Sagi


title: SRSF3-mediated regulation of N6-methyladenosine modification-related lncRNA ANRIL splicing in promotion of pancreatic cancer resistance to gemcitabine I


title: SRSF3-mediated regulation of N6-methyladenosine modification-related lncRNA ANRIL splicing in promotion of pancreatic cancer resistance to gemcitabine

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

sample_organism:
Homo
Homo sapiens

platform_organism:
Homo
Homo sapiens

overall_design: Refer to individual Series


title: Differential modulation of nuclear receptor LRH-1 through targeting buried and surface regions of the binding pocket

city: Atlanta

first: Michael

middle: Lee

last: Cato

state: GA

address: 1510 Clifton Rd. NE

department: Biochemistry

institute: Emory University

summary: Liver receptor homolog-1 (LRH-1) is a phospholipid-sensing nuclear receptor that has shown promise as a target for alleviating intestinal inflammation and disease states characterized by metabolic dysregulation in the liver. LRH-1 contains an unusually large ligand binding pocket but generating synthetic modulators has been challenging. Leveraging a hexahydropentalene (6HP) core, we have had recent success in generating potent and efficacious agonists through two distinct strategies. We targeted residues deep within the pocket to enhance compound binding, while residues at the mouth of the pocket were targeted to mimic interactions made by endogenous phospholipids. Here, we unite these two designs into one hybrid molecule to synthesize the most potent LRH-1 agonist to date. Through a combination of global transcriptomic, biochemical, and structural studies, we show that selective modulation can be driven through contacting deep vs. surface polar regions in the pocket. While deep pocket contacts convey high-affinity, contacts with the pocket mouth dominate allostery and provide a phospholipid-like transcriptional response in cultured cells.

overall_design: Examination of compound-mediated effects on transcriptome of HepG2 cells.

last: Lee Cato

first: Eric

last: Ortlund


title: Circadian change of genes expressed in mice epidermis

city: Sakyo-ku

first: Hitoshi

last: Okamura

state: Kyoto

address: Yoshida-Konoe-cho

department: Division of Physiology and Neurobiology

country: Japan

institute: Kyoto University Graduate School of Medicine

summary:
Circadian rhythms are known to observed in all organs in mice. Skin is composed of epidermis, dermis, and subcutaneous tissue. Daily changes of epidermal genes are examined in mice.
The epidermis acts as a primary barriers of the external pathogens invading into the organism. Gene expression profiles identified many bioactive substances showed daily rhythms including clock genes.

overall_design: Lazer dissected epidermis from 6 time points of WT or Cry-null mice in the constant dark (DD) enviroment were subjected to gene expression analysis.

first: Yasuko

last: Santo

first: Hiroyuki

last: Yamada


title: Disentangaling the gene expression programs controlled by ciliary and cytosolic cAMP signaling

city: Bonn

first: Jan

middle: N.

last: Hansen

address: Venusberg Campus 1

institute: University of Bonn

summary: Primary cilia are tiny membrane protrusions emanating from the surface of almost all mammalian cell types. Recently, a picture has emerged of the primary cilium functioning as a cellular antenna that senses extracellular stimuli via receptors, locally processes the signal using cilia-specific signalling pathways, and transduces this information into a cellular response. Components of the cyclic AMP (cAMP) signalling cascade have been proposed to be part of the ciliary signalling pathways. We aimed to shed light on whether ciliary cAMP signaling controls gene expression, and if yes, which gene expression program is particularly targeted by ciliary cAMP signaling. To this end, we targeted an optogenetic tool to increase cAMP levels (bPAC) to the primary cilium in murine, kidney-derived inner medullary collecting duct (mIMCD-3) cells (mIMCD-3 cilia-bPAC cells). As controls, we used cells were bPAC is targeted to the cytosol (mIMCD-3 cyto-bPAC cells) and wild-type cells (mIMCD-3 WT cells). We increased cAMP levels by light stimulation and next analysed gene expression using bulk RNA-sequencing. As an additional control, we also included WT cells treated with the compound Forskolin, which targets endogeneous adenylyl cyclases and thus, in principle, is believed to increase cAMP levels in both compartments, cilium and cell soma.

overall_design: The whole experiment including all conditions was performed four times independently. The experimentID characteristics links conditions from the same experiment day.

middle: N

last: Kraut

first: Heidi

last: Theis

first: Anna-Dorothee

last: Drews

first: Elena

last: De-Domenico

first: Kristian

last: Händler

first: Dagmar

last: Wachten


title: Apolipoprotein E4 Is Associated with a Distinct Transcriptomic Profile of Hippocampal Neurons and Attenuates Their Maturation In Vitro

first: Alireza

last: Khodadadi-Jamayran

summary: The APOE gene is diversified by three alleles e2, e3, and e4 encoding corresponding apolipoprotein (apo) E isoforms. The e4 allele promotes age-related cognitive decline, risk of Alzheimer’s disease (AD), and the rate of AD dementia progression. ApoE is produced by astrocytes as high-density lipoprotein-like particles and these are internalized by neurons upon binding to neuron-expressed apoE receptors. ApoE isoforms differentially engage neuronal plasticity through poorly understood mechanisms. We examined here the effects of native apoE lipoproteins produced by immortalized astrocytes homozygous for e2, e3, and e4 alleles on the maturation and the transcriptomic profile of primary hippocampal neurons. Control neurons were grown in the presence of conditioned media from Apoe-/- astrocytes. ApoE2 and apoE3 significantly increase the dendritic arbor branching, the combined neurite length, and the total arbor surface of the hippocampal neurons, while apoE4 fails to produce similar effects and even significantly reduces the combined neurite length compared to the control. ApoE lipoproteins show no systemic effect on dendritic spine density, yet apoE2 and apoE3 increase the mature spines fraction, while apoE4 increases the immature spine fraction. This is associated with opposing effects of apoE2 or apoE3 and apoE4 on the expression of NR1 NMDA receptor subunit and PSD95. There are 1,062 genes differentially expressed across neurons cultured in the presence of apoE lipoproteins compared to the control. KEGG enrichment and gene ontology analyses show common for apoE2 and apoE3 activation of genes involved in neurite branching, and synaptic signaling. In contrast, apoE4 cultured neurons show upregulation of genes related to the glycolipid metabolism, which are involved in dendritic spine turnover and those which are usually silent in neurons and are related to cell cycle and DNA repair. In conclusion our work reveals that lipoprotein particles comprised of various apoE isoforms differentially regulate neuronal development through interaction with neuronal transcriptome. ApoE4 produces a functionally distinct transcriptomic profile, which is associated with attenuated neuronal development. Differential regulation of neuronal transcriptome by apoE isoforms is a newly identified biological mechanism, which has both implication in the development and aging of the CNS.

overall_design: RNA seq profiles of primary cultures of hippocampal neurons incubated with conditioned media from immortalized astrocytes homozygous for apoE2, apoE3, and apoE4 or Apoe-/- (control).

first: Jenny

middle: R

last: Diaz

first: Martin

last: Sadowski


title: Constitutive loss of DNMT3A causes morbid obesity through misregulation of adipogenesis

city: Houston

first: Margaret

last: Goodell

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

summary: DNA Methyltransferase 3A (DNMT3A) is an important facilitator of differentiation of both embryonic and hematopoietic stem cells. Heterozygous germline mutations in DNMT3A lead to Tatton-Brown-Rahman Syndrome (TBRS), characterized by obesity and excessive height. While DNMT3A is known to impact feeding behavior via the hypothalamus, here we investigated a role in adipocyte progenitors utilizing heterozygous knockout mice that recapitulate cardinal TBRS phenotypes. These mice become morbidly obese due to adipocyte enlargement and tissue expansion. Adipose tissue in these mice exhibited defects in preadipocyte maturation and precocious activation of inflammatory gene networks, including interleukin-6 signaling. Adipocyte progenitor cell lines lacking DNMT3A exhibited aberrant differentiation. Furthermore, mice in which Dnmt3a was specifically ablated in adipocyte progenitors showed enlarged fat depots and increased progenitor numbers, partly recapitulating the TBRS obesity phenotypes. Loss of DNMT3A led to constitutive DNA hypomethylation, such that the DNA methylation landscape of young adipocyte progenitors resemble that of older wild-type mice. Together, our results demonstrate that DNMT3A coordinates both the central and local control of energy storage required to maintain normal weight and prevent inflammatory obesity.

overall_design: Samples are extracted from WT and DNMT3A-HET mouse models age matched littermates were used in all experiments

first: Ayala

last: Tovy

first: Jaime

last: Reyes


title: Dopamine and GPCR-mediated modulation of DN1 clock neurons gates the circadian timing of sleep

status: Public on May 09 2022

city: Waltham

first: Matthias

last: Schlichting

state: MA

address: 450 South St. MS 008

institute: Brandeis University

summary: The metronome-like circadian regulation of sleep timing must still adapt to an uncertain environment. Recent studies in Drosophila indicate that neuromodulation not only plays a key role in clock neuron synchronization but also affects interactions between the clock network and brain sleep centers. We show here that the targets of neuromodulators, G-Protein Coupled Receptors (GPCRs), are highly enriched in the fly brain circadian clock network. Single cell sequencing indicates that they are not only enriched, but they are also differentially expressed and contribute to clock neuron identity. We generated a comprehensive guide library to mutagenize individual GPCRs in specific neurons and verified the strategy by introducing a targeted sequencing approach. Combined with a behavioral screen, the mutagenesis strategy revealed a novel role of dopamine in sleep regulation by identifying two dopamine receptors and a clock neuron subpopulation that gate the timing of sleep.

overall_design: GFP-labeled neurons (nSyb>GFP) and GFP-labeled clock neurons (clk856>GFP) were FACS sorted and SmartSeq2 libraries were prepared at ZT2 and ZT14. 2 Repeats each.

first: Michael

last: Rosbash


title: EED is required for Mouse Primordial Germ Cell Differentiation in the Embryonic Gonad

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary: Development of Primordial germ cells (PGCs) is required for reproduction. During PGC development in mammals, major epigenetic remodeling occurs which is hypothesized to establish an epigenetic landscape for sex-specific germ cell differentiation and gametogenesis. In order to address the role of Embryonic Ectoderm Development (EED) and Histone 3 lysine 27 trimethylation (H3K27me3) in this process, we created a conditional deletion in EED and show that EED is essential for regulating the timing of sex-specific PGC differentiation in both ovaries and testes, as well as X chromosome dosage decompensation in testes. Integrating chromatin and whole genome bisulfite sequencing of epiblast and PGCs, we identified a poised repressive signature of H3K27me3/DNA methylation which we propose is established in the epiblast where EED and DNMT1 interact. Thus, EED joins DNMT1 in regulating the timing of sex-specific PGC differentiation during the critical window when the gonadal niche cells specialize into an ovary or testis.

overall_design: Examination of Transcription and DNA methylation in control and PGC-specific EED conditional knockout primordial germ cells

first: Matthew

last: Lowe

first: Ming-Ren

last: Yen

first: Fei-Man

last: Hsu

first: Linzi

last: Hosohama

first: Zhongxun

last: Hu

first: Tsotne

last: Chitiashvili

first: Timothy

last: Hunt

first: Isaac

last: Gorgy

last: Bernard

first: Sissy

last: Wamaitha

first: Amander

middle: Ｔ

last: Clark


title: Gene expression profiling of Tumor and liver infiltrating NK cells from patients with Hepatocellular Carcinoma

city: Parma

first: ALESSANDRA

last: ZECCA

state: Parma

address: Via gramsci, 14

country: Italy

institute: University of Parma

summary: Natural Killer (NK) cells play a central role in cell-mediated immune response to cancer. In previous studies number and function of NK-cells have been shown to be positively correlated with HCC outcome. In this study, we have performed a genetic expression analysis comparing mRNA expression by NK cells from tumor samples derived from HCC patients to NK cells infiltrating the liver counterpart and to NK cells in the normal liver as controls.  The bioinformatic analysis has been completed by an immunophenotypic study, functional analysis and metabolic assessment of the infiltrating NK cells. It is known that NK cells may present functional defects in HCC patients however previous studies have not systematically address the molecular mechanisms associated with these defects by an unbiased genetic expression study. We have identified altered cellular pathways and hypothesized possible mechanisms that could be targeted for restoring an immune-protective NK cell response.

overall_design: Liver and tumor-infiltrating lymphocytes from 11 patients with HCC arising in Hepatitis C virus (HCV) infection and 6 patients undergoing liver resection for colorectal metastasis as control were stained with appropriate fluorescent antibodies, in order to distinguish NK-cells. RNA was purified from sorted NK-cells and  amplified. cDNA was labeled and hybridized to Agilent microarrays.

first: Alessandra

last: Zecca

first: Valeria

last: Barili

first: Elisabetta

last: Cariani

first: Gabriele

last: Missale


title: Genome-wide analysis of fasting induced gene expression in the mouse hypothalamus

city: Concord

first: Eirini

last: Vagena

address: 2331 Saint George Dr

institute: UCSF

summary: This study utilized AgRP+/- and AgRP-/- mice either under fed or 30h fasted conditions, to reveal genes that are regulated by fasting and AgRP.

overall_design: Total RNA obtained from hypothalamic samples of AgRP+/- or AgRP-/- male mice fed either ad libitum or under 30h fasted conditions.

first: Allison

middle: W

last: Xu


title: Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells (RNA-Seq 1)

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

summary: Pancreatic ductal adenocarcinomas (PDACs) are composed of a mixture of highly heterogeneous cancer cells with distinct gene expression programs and functional properties, ranging from well-differentiated (low-grade) epithelial cells forming pseudo-glandular structures, to undifferentiated (high-grade) quasi-mesenchymal cells. Low-grade, differentiated PDAC cells are characterized by the constitutive expression of many Interferon (IFN)-stimulated genes (ISGs) but the mechanistic bases and the functional implications of this property are unknown. Here we show that constitutive ISG expression as well as responsiveness to IFN stimulation depend on the maintenance of high expression levels of the transcription factor IRF1 (Interferon Regulatory Factor 1) by epithelial lineage-determining transcription factors. IRF1-dependent gene expression provides differentiated PDAC cells with a range of distinctive properties related to antigen presentation and processing and maintenance of epithelial identity, as well as a distinctive metabolic program in which both mitochondrial respiration and fatty acid synthesis are directly suppressed

overall_design: Total RNA from human pancreatic ductal adenocarcinoma cell lines was processed for multiparallel sequencing. Experiments were carried out in genome edited clonal CFPAC1 cells (3 pools of IRF1-deleted CRISPR-Cas9 clones and 3 pools of WT  clones) and in low grade and high grade PDAC cell lines (CFPAC1, CAPAN1, MiaPaCa2, PANC1) untreated and treated with 1000 U/ml of hIFNbeta for 2 hours (3 replicates each).

last: Alfarano

first: Matteo

last: Audano

first: Marta

last: Milan

first: Pierluigi

last: Di Chiaro

first: Sara

last: Polletti

first: Giuseppe

last: Diaferia

first: Nico

last: Mitro

first: Gioacchino

last: Natoli


title: Prx1Cre;Rosa26-tdTomato  single cell RNA-sequencing of muscle resident non-myogenic mesenchymal cells

city: Durham

first: Matthew

middle: J.

last: Hilton

address: 450 Research Drive, LSRC B321C

institute: DUKE UNIVERSITY SCHOOL OF MEDICINE

summary: In order to assess the descendants of lateral plate mesoderm within the muscle interstitium, we utilized Prrx1Cre;Rosa26-tdTomato P21 tdTomato+ FACS sorted muscle interstitial cells

overall_design: 10X Genomics Single cell RNA-sequencing of muscle resident non-myogenic mesenchymal cells

first: Abigail

last: Leinroth

first: Anthony

last: Mirando

first: Douglas

last: Rouse

first: Yoshihiko

last: Kobayashi

first: Purushothama

last: Tata

first: Helen

last: Rueckert

first: Yihan

last: Liao

first: Jason

middle: T

last: Long

first: Joe

last: Chakkalakal


title: Investigating the role of aging and lung fibrosis in Endothelial Cells with ATAC sequencing

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: In order to elucidate the contribute of the pulmonary vasculature to lung fibrosis, we injured young and aged mice with bleomycine, to create a model of resolving versus persistent lung fibrosis. The animals were sacrificed 30 days after the injury (time point in which we observed a divergent resolving vs persistent lung fibrosis in young vs aged mice).

overall_design: Freshly isolated lung endothelial cells from young and aged mice either sham or after bleomycin were subjected to ATACseq analysis. A widespresd reduction in chromatin accessibility was found in aged lung endothelial cells, either sham or after bleomycin administration, compared to young endothelial cells.

first: Nunzia

last: Caporarello

first: Giovanni

last: Ligresti

first: Daniel

last: Tschumperlin


title: Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells (ChIP-Seq)

first: Chiara

last: Balestrieri

overall_design: Chromatin from human pancreatic ductal adenocarcinoma cell lines was immunoprecipitated with various transcription factors and histone modification targeting antibodies and subjected to multiparallel sequencing. Experiments were carried out in unmodified and genome edited clonal CFPAC1 cells.

first: Gabriele

last: Alfarano

first: Matteo

last: Audano

first: Marta

last: Milan

first: Pierluigi

last: Di Chiaro

first: Sara

last: Polletti

first: Giuseppe

last: Diaferia


title: Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells (ChIP-Seq 2)


title: Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells (RNA-Seq 2)

overall_design: Total RNA from human pancreatic ductal adenocarcinoma cell lines was processed for multiparallel sequencing. Experiments were carried out  in low grade and high grade PDAC cell lines (CFPAC1, CAPAN1, MiaPaCa2, PANC1) untreated and treated with 1000 U/ml of hIFNbeta for 2 hours (3 replicates each).

first: Nico

last: Mitro

first: Gioacchino

last: Natoli


title: Knowk-down of EWSR1-FLI1 in Ewing sarcoma cell lines (RNA-seq)

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

summary: EWSR1-FLI1 is a chimeric transcription factor resulting from the pathognomonic translocation present in Ewing sarcoma cells. Here, we silenced EWSR1-FLI1 in different Ewing sarcoma cell lines. RNA from SKNMC, TC71 and MHH-ES1 cells was extracted 96h post transfection (siCT or siEWSR1-FLI1) or prior doxycycline (day 0) and 7 days after inducing silencing of EWSR1-FLI1 with doxycycline in ASP14 cells. RNA-seq was performed for all conditions.

first: Didier

last: Surdez

first: Sakina

last: Zaidi

first: Sandrine

last: Grossetête


title: Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells (ATAC-Seq)

overall_design: Native chromatin from human pancreatic ductal adenocarcinoma cell lines was tagmented in order to identify accessible sites  and subjected to multiparallel sequencing. Experiments were carried out in  genome edited clonal CFPAC1 cells and their respective control clones.


title: Single-cell RNA-seq of CD8 T cells sorted from one sample of seropositive rheumatoid arthritis synovial fluid

status: Public on May 08 2022

city: Boston

first: Anna Helena

last: Jonsson

address: 60 Fenwood Road

department: Dept of Medicine/Division of Rheumatology, Inflammation, and Immunity

institute: Brigham and Women's Hospital/Harvard Medical School

summary: We used FACS to sort CD8 T cells from synovial fluid mononuclear cells from one patient with seropositive rheumatoid arthritis

overall_design:
SFMCs were thawed, stained with MR1 tetramers and surface antibodies, and CD8 T cells (Propoidium Iodide- CD3+ CD14- CD19- MR1 tetramer- CD8α+ CD4- cells) isolated by FACS. Single-cell RNA-seq was then performed by 10X Genomics technology.
***Please note that FASTQ files will be uploaded to dbGaP since these are human patient samples****

first: Michael

last: Brenner

first: Anna

middle: H


title: Research of EGR2 binding sites in Ewing cell line by CHIP-seq experiment

summary: Identification of  EGR2 binding site, H3K27Ac, H3K4me3 and EWSR1-FLI1 in Ewing cell line

overall_design: POE shEGR2_4#22 clone harboring a doxycycline-inducible shRNA against EGR2 overexpressed HA-EGR2

first: Wietske

last: van der ent

first: Karine

last: Laud-Duval


title: Pooled single-cell RNA-seq data from T cells from human synovial tissue

summary: T cells from several separate single-cell RNAseq datasets from human RA synovial tissue were combined into one dataset. The dataset includes both previously published and new data.

overall_design:
Cryopreserved human synovial tissue samples from patients with rheumatoid arthritis or osteoarthritis were disaggregated and processed for single-cell RNAseq.
***Please note that FASTQ files (for the new RA samples) will be uploaded to dbGaP since these are human patient samples****
***Please note that raw data for the published synovial tissue samples from RA patients [amp] is  available on dbGaP under accession number phs001457.v1.p1.

first: Kevin

last: Wei


title: Effect of T cell supernatants or cytokines on synovial fibroblasts

summary:
To investigate the effects of soluble factors produced by synovial CD8 T cells, we stimulated human rheumatoid arthritis (RA) synovial fibroblasts with supernatants from synovial fluid CD8 T cells, blood CD8 T cells, or synovial fluid CD4 T cells stimulated with anti-CD3/CD28 antibody-coated beads.
For comparison, we stimulated RA synovial fibroblasts with recombinant TNF or interferon-gamma or T cell supernatants pre-incubated with TNF-blocking antibodies.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for rheumatoid arthritis synovial fibroblasts treated with supernatants from stimulated CD4 or CD8 T cell populations or with recombinant cytokines
***Please note that FASTQ files will be uploaded to dbGaP since these are human patient samples****


title: RNA-seq analysis on osteoclasts and periosteal stem cells from control and Prmt5 f/d Ctsk-Cre mice

status: Public on May 07 2022

city: Tokyo

first: Masayuki

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

institute: The University of Tokyo

summary: To gain insights into the role of Prmt5 in osteoclasts and periosteal stem cells , we performed RNA sequencing (RNA-seq) on osteoclasts and periosteal stem cells from control and Prmt5 f/d Ctsk-Cre mice

overall_design: RNA-seq analysis on osteoclasts  and periosteal stem cells  collected from control (n=3) and Prmt5 f/d Ctsk-Cre mice (n=3)


title: 3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_OVCA429shGRHL]

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Background   The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests that regulation of EMT may occur at a higher order of three-dimensional  genome level.  Results  We perform Hi-C analysis and combine ChIP-seq data across cancer cell lines representing different EMT states. We demonstrate that the epithelial and mesenchymal genes are regulated distinctively. We find that EMT genes are regulated within their topologically associated domains (TADs), with only a subset of mesenchymal genes being influenced by A/B compartment switches, indicating topological remodelling is required in the transcriptional regulation of these genes. At the TAD level, epithelial and mesenchymal genes are associated with different regulatory trajectories. The epithelial gene-residing TADs are enriched with H3K27me3 marks in the mesenchymal-like states. The mesenchymal gene-residing TADs , which do not show enrichment of H3K27me3 in epithelial-like states, exhibit increased interaction frequencies with regulatory elements in the mesenchymal-like states.  Conclusions  We propose a novel workflow coupling immunofluorescence and dielectrophoresis to unravel EMT heterogeneity at single-cell resolution. The predicted three-dimensional structures of chromosome 10, harboring Vimentin, identify cell clusters of different states. Our results pioneer a novel avenue to decipher the complexities underlying the regulation of EMT and may infer the barriers of plasticity in the 3D genome context.

overall_design: single-cell Hi-C seq profiling of OVCA429 shGRHL2 Tet-inducible, an ovarian cancer cell line.

first: Qing

last: Pang

first: Ruby

last: Huang


title: The long non-coding antisense RNA JHDM1D-AS1 regulates inflammatory responses in human monocytes

city: Amsterdam

first: Brendon

middle: P.

last: Scicluna

address: Meibergdreef 9

institute: Amsterdam UMC Locatie AMC

summary: Monocytes are key players in innate immunity, with their ability to regulate inflammatory responses and combat invading pathogens. There is a growing body of evidence indicating that long non-coding RNA (lncRNA) participate in various cellular biological processes, including the innate immune response. The immunoregulatory properties of numerous lncRNAs discovered in monocytes remain largely unexplored. In this study, we used RNA sequencing data of circulatory blood monocytes obtained from sepsis patients to identify the elevated antisense lncRNA JHMD1D-AS1, relative to healthy participants. We subsequently demonstrated that in both circulatory blood monocytes and monocyte-derived macrophages exposed to TLR-agonists, JHMD1D-AS1 expression was induced in a temporal specific manner. Using small interfering RNA (siRNA) electroporation to render monocytes deficient of JHDM1D-AS1 and over-expression experiments, we revealed a role for lncRNA JHDM1D-AS1 in cell development, as well as in restraining pro-inflammatory gene expression. Altogether, these findings identify antisense lncRNA JHDM1D-AS1 as a potential repressor of the inflammatory response in human primary monocytes and macrophages.

overall_design: THP1-MD2-CD14 cells expressing ectopic JHDM1D-AS1 (n=4) or empty vector control (n=4), treated with 100ng/ml LPS (n=4) or not (n=4) (medium control) for 2 or 6 hours.

first: Erik

last: Malmstrom

first: Tom

last: van der Poll

first: Hina

last: Khan


title: Effect of the p38 mitogen-activated protein kinase signaling cascade on radiation biodosimetry

status: Public on May 06 2022

city: New York

first: Constantinos

last: Broustas

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

summary: Radiation biodosimetry based on transcriptomic analysis of peripheral blood is a valuable tool to detect radiation exposure after a radiological/nuclear event and obtain useful biological information that could predict tissue and organismal injury. However, confounding factors, including inflammation, can potentially obscure the predictive power of the method. The mitogen-activated protein kinase (MAPK) p38 is normally regulated by the MAP3K-MAP2K pathway in mammalian cells. Members of the p38 MAPK family respond to pro-inflammatory signals and environmental stresses. However, in T cells there is an alternative pathway for p38MAPK activation. This pathway has been shown to play an important role in antigen-receptor-activated T cells and participate in immune and inflammatory responses. Radiation is known to induce a pro-inflammatory response. To examine the role of p38MAPK in response to radiation, we used two mouse models expressing either a p38αMAPK dominant negative (DN) mutation that would be expected to globally suppress p38MAPK signaling or a double knock-in (DKI) mutant, which would be expected to inhibit specifically T cell receptor activation. We exposed wild-type and p38MAPK mutant mice to 7 Gy x-rays and 24 h later we isolated whole blood and performed genome microarray and gene ontology analysis. Comparison between the two mutants (DN, DKI) suggest that the alternative p38MAPK pathway may have wider functions in the response to radiation exposure beyond its well established role as a downstream effector of activated T-cell receptor. Among the differentially enriched pathways, irradiation leads to a significant overrepresentation of pathways associated with morbidity and mortality as well as organismal cell death. In contrast, these pathways were significantly underrepresented in p38MAPKDN and p38MAPKDKI mutant mice, implying that p38MAPK suppression protects mice from the deleterious effects of radiation. Furthermore, radiation exposure resulted in an enrichment of a small number of phagocytosis-related pathways; however, considerably more phagocytosis-related pathways were overrepresented in the p38MAPK mutant mice, implying that p38MAPK signaling, normally, restricts phagocytosis of apoptotic cells after radiation and may, thus, contribute to persistent inflammation. Finally, despite the significant changes in gene expression, we were still able to identify a panel of genes that could accurately distinguish between irradiated and control mice, irrespective of p38MAPK status.

overall_design: Radiation induced gene expression in  blood from p38WT, p38DKI, and p38DN mice was measured 24 h after 7 Gy of x-rays. Five independent experiments were performed at each p38 genotype and treatment.

middle: G


title: 3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_PEO1HEYA8]

overall_design: single-cell Hi-C seq profiling of ovarian cancer cell line PEO1 and HEYA8.


title: Genetic evidence that uptake of the fluorescent analog 2NBDG occurs independently of known glucose transporters

city: Tucson

first: Deepta

last: Bhattacharya

state: AZ

address: 1656 East Mabel St

department: Immunobiology

institute: University of Arizona

summary: RNA-sequencing was performed to examine for compensatory upregulation of Slc2 transporters in Slc2a1 gRNA- or Slc2a1, Slc2a3, Slc2a5, Slc2a6, and Slc2a8 gRNA-transduced 5TGM1 cells relative to a control (Rosa26) gRNA transduced 5TGM1-Cas9 cell line. Abstract: The fluorescent derivative of glucose, 2-Deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)-amino]-D-glucose (2NBDG), is a widely used surrogate reagent to visualize glucose uptake in live cells at single cell resolution. Using a model of CRISPR-Cas9 gene editing in 5TGM1 myeloma cells, we demonstrate that ablation of the glucose transporter gene Slc2a1 abrogates radioactive glucose uptake but has no effect on the magnitude or kinetics of 2NBDG import. Extracellular 2NBDG, but not NBD-fructose was transported by plasma cells into the cytoplasm suggesting a specific mechanism that is unlinked to glucose import and that of chemically similar compounds. Competing glucose in media or pharmacological inhibition of GLUT1 did not have any effect on 2NBDG uptake. RNA-Seq analysis of primary plasma cells and the 5TGM1 myeloma cell line revealed expression of other candidate glucose transporters. Yet, deletion of these transporters individually or in combination with one another also had no impact on 2NBDG uptake. Ablation of the genes in the Slc29 and Slc35 families of nucleoside and nucleoside sugar transporters as well as the ATP-binding cassette (ABC) transporter family also failed to impact 2NBDG import. Thus, cellular uptake of 2NBDG is promoted by an unknown mechanism and is not a faithful indicator of glucose transport.

overall_design: RNA-sequencing of control (Rosa26) gRNA, Slc2a1 gRNA, and Slc2a1, Slc2a3, Slc2a5, Slc2a6, and Slc2a8 gRNA transduced 5TGM1-Cas9 cells

first: Lucas

last: D'Souza


title: 3D genome organization in the epithelial-mesenchymal transition spectrum

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

overall_design: Refer to individual Series


title: Non-productive infection of glial cells with SARS-CoV-2 in hamster organotypic cerebellar slice cultures

city: Winnipeg

first: Jessy

middle: Andrew

last: Slota

state: Manitoba

address: 1015 Arlington St.

department: One Health Division

institute: National Microbiology Laboratory; Public Health Agency of Canada

summary: The numerous neurological syndromes associated with COVID-19 implicate an effect of viral pathogenesis on neuronal function, yet reports of direct SARS-CoV-2 infection in the brain are conflicting. We used a well-established organotypic brain slice culture to determine the permissivity of hamster brain tissues to SARS-CoV-2 infection. We found levels of live virus waned after inoculation and observed no evidence of cell-to-cell spread, indicating that SARS-CoV-2 infection was non-productive. Nonetheless, we identified a small number of infected cells with glial phenotypes; yet no evidence of viral infection or replication was observed in neurons. Our data corroborates several clinical studies that have assessed patients with COVID-19 and their association with neurological involvement.

overall_design: Comparative transcriptional analysis of RNAseq data from hamster organotypic cerebellar slice cultures inoculated with SARS-CoV-2 or Mock infection treatment

first: Lise

last: Lamoureux

first: Babu

last: Sajesh

middle: A

first: Sarah

last: Medina

first: Matthew

last: Mayor

first: Kathy

middle: L

last: Frost

first: Bryce

last: Warner

last: Manguiat

first: Heidi

last: Wood

first: Darwyn

last: Kobasa

first: Stephanie

last: Booth


title: Expression data from human Duodenal Organ Chips

first: Don

last: Ingber

state: Massachusetts

address: 3 Blackfan Circle, CLSB 5th Floor

institute: Wyss Institute for Biologically Inspired Engineering at Harvard University

summary: Environmental Enteric Dysfunction (EED) is a chronic inflammatory condition of the intestine characterized by villus blunting, compromised intestinal barrier function, and reduced nutrient absorption. Here, we show that key genotypic and phenotypic features of EED-associated intestinal injury can be reconstituted in a human intestine-on-a-chip (Intestine Chip) microfluidic culture device lined by organoid-derived intestinal epithelial cells from EED patients and cultured in nutrient deficient medium lacking niacinamide and tryptophan (-N/-T). Exposure of EED Intestine Chips to -N/-T deficiencies resulted in transcriptional changes similar to those seen in clinical EED patient samples including congruent changes in six of the top ten upregulated genes. Exposure of EED Intestine Chips or chips lined by healthy intestinal epithelium (healthy Intestine Chips) to -N/-T medium resulted in severe villus blunting and barrier dysfunction, as well as impairment of fatty acid uptake and amino acid transport.

overall_design: Microarray experiments were carried out using one healthy duodenal donor (n=3 biological replicates) and one EED doudenal donor (n=3 biological replicates) for each media type (complete and nutritionally depleted).

first: Amir

last: Bein

first: Cicely

last: Fadel


title: Circadian alignment of early onset caloric restriction promotes longevity in male C57BL/6J mice

city: Dallas

first: Victoria

last: Acosta

address: 6001 Forest Park Lane

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Caloric restriction (CR) prolongs lifespan, yet the mechanisms by which it does so remain poorly understood. Under CR, mice self-impose chronic cycles of 2-hour-feeding and 22-hour-fasting, raising the question whether calories, fasting, or time of day are causal. We show that 30%-CR is sufficient to extend lifespan 10%; however, a daily fasting interval and circadian-alignment of feeding act together to extend lifespan 35% in male C57BL/6J mice. These circadian effects of CR are independent of fasting duration and body weight. Aging induces widespread increases in gene expression associated with inflammation and decreases in expression of genes encoding components of metabolic pathways in liver from ad lib fed mice. CR at night ameliorates these aging-related changes. Thus, circadian interventions promote longevity and provide a perspective to further explore mechanisms of aging.

overall_design: mRNA-seq circadian profiles generated for C57BL/6J male mice fed under 6 different feeding conditions and collected at 6 and 19 months of age. Liver samples were collected every 4h during 2 days (12 timepoints x 2 biological replicates x 6 feeding conditions x 2 ages, total 288 samples).

last: Acosta-Rodríguez

first: Filipa

last: Rijo-Ferreira

first: Mariko

last: Izumo

first: Pin

last: Xu

first: Mary

last: Wight-Carter

first: Carla

middle: B

last: Green

first: Joseph

middle: S

last: Takahashi


title: Bulk RNA-seq of human synovial fluid CD8 T cells sorted by Granzyme B vs Granzyme K expression

first: Anna Helena

last: Jonsson

summary:
Cryopreserved synovial fluid mononuclear cells from three patients  with seropositive rheumatoid arthritis were thawed and stained for surface antibodies, then fixed and stained for intracellular granzyme K and granzyme B.
CD8 T cells with the following expression patterns were then isolated by FACS.

overall_design:
RNA was isolated from the sorted cell subsets using techniques adapted for fixed cells.
***Please note that FASTQ files will be uploaded to dbGaP since these are human patient samples****

first: Michael

last: Brenner

first: Anna


title: Cellular drivers of injury response and regeneration in the adult zebrafish heart

city: Berlin

first: Bo

last: Hu

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbueck-Center Berlin

summary: We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non-muscle cells. Based on spatiotemporal information, we systematically identified potential cellular regulators of cardiomyocyte regeneration, including several fibroblast-like cell types that express pro-regenerative factors. We used high-throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium, like the epicardium, gives rise to several distinct fibroblast cell types, and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process.

overall_design: Single cell RNA seq of uninjured and injured / wnt-inhibited and non-inhibited zebrafish hearts. CRISPR-based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.

first: Sara

last: Lelek

first: Bastiaan

last: Spanjaard

first: Mariana

last: Guedes Simões

first: Hananeh

last: Aliee

first: Ronny

last: Schäfer

first: Fabian

last: Theis

first: Daniela

last: Panáková

first: Jan

middle: P

last: Junker


title: Morphine alleviates pain after heart cryonjury in zebrafish without impeding regeneration

summary: Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish, similarly to higher vertebrates, also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not, however, take into account the adverse effects including pain that may potentially arise from these methodologies. Here, we assess the effect of two analgesics, lidocaine and morphine, followed after the heart cryoinjury in zebrafish. Monitoring swimming behaviour together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology, we show morphine, but not lidocaine, significantly improves animal welfare 6 hours post-cryoinjury, without impairing heart regeneration process. Altogether, morphine should be considered as the analgesic of choice to reduce post-surgical pain in adult zebrafish.

overall_design: Single cell RNAseq of morphine treated and untreated zebrafish heart samples at 3, 7 and 15 days post injury

first: Ahmed

middle: M

last: Alameldeen

first: Maciej

last: Czajkowski

first: Alexander

last: Meyer

first: Fabienne

last: Ferrara


title: In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIPmentation]

status: Public on May 05 2022

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: Vertebrate genomes organize into topologically associating domains (TADs), delimited by boundaries that insulate regulatory elements from non-target genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CTCF boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding sites (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors like CBS number and orientation. Combined deletions demonstrated that CBS cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops can be formed by non-canonically oriented sites, which suggests a loop interference mechanism. Further, we observe that insulation strength constitutes an effective modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.

overall_design: CTCF and Rad21 experiments in developing distal limbs of several homozygous mutants and WT mice at E11.5

first: Chiara

last: Anania

middle: D

first: Johanna

last: Jedamzick

first: Adriano

last: Bolondi

first: Giulia

last: Cova

first: Norbert

last: Brieske

first: Ralf

last: Kühn

first: Lars

last: Wittler

first: Francisca

last: Real

first: Darío

last: Lupiáñez


title: Inhibition of DYRK1A, via histone modification, promotes cardiomyocyte proliferation and heart repair after myocardial infarction [ChIP-Seq]

city: Chongqing

first: Cong

last: Lan

state: Chognqing

address: 10 Changjiangzhilu Road

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University

summary: To explore effect of DYRK1A silencing on H3K4me3 and H3K27ac modification of primary cultured cardiomyocytes isolated from 1-day-old SD rats

overall_design: Neonatal cardiomyocytes in primary culture were transfected with siRNA against DYRK1A (si-DYRK1A) or scramble siRNA (si-NC) and cultured for 48 h to prepare sample, and ChIP assay was performed with anti-H3K27ac or anti-H3K4me3 antibody. The purified DNA fragments were subjected to ChIP-sequencing.

first: Caiyu

last: Chen

first: Shuang

last: Qu

first: Nian

last: Cao

first: Hao

last: Luo

first: Cheng

last: Yu

last: Wang

first: Yuanzheng

last: Xue

first: Xuewei

last: Xia

first: Chao

last: Fan

first: Hongmei

last: Ren

first: Pedro

last: Jose

first: Zaicheng

last: Xu

first: Gengze

last: Wu

first: Chunyu

last: Zeng


title: Autologous SPEAR T-cell therapy in MAGE-A4 positive solid cancers: a Phase 1 trial of afamitresgene autoleucel in HLA-A*02 positive patients

city: Houston

first: David

last: Hong

state: Texas

address: Room FC8.3050, 1400 Holcombe Blvd.

department: Department of Investigational Cancer Therapeutics

institute: University of Texas M.D. Anderson Cancer Center

summary: Afamitresgene autoleucel, an HLA-restricted autologous specific peptide enhanced affinity receptor (SPEAR) T-cell therapy targeting MAGE-A4, was developed to treat HLA-A*02 positive patients with MAGE-A4 expressing solid tumors. A multicenter, dose-escalation, Phase 1 trial (NCT03132922) was conducted evaluating afamitresgene autoleucel in patients with relapsed or refractory (≥1 prior line of therapy) metastatic solid tumors. The primary endpoint was safety. The secondary endpoint was anti-tumor activity including overall response rate, best overall response, time to response, duration of response, duration of stable disease, progression-free survival and overall survival. Thirty-eight patients were treated with afamitresgene autoleucel across 9 tumor types, including 16 with synovial sarcoma (SS). Overall, afamitresgene autoleucel was well tolerated. The most common adverse events were cytopenias. Cytokine release syndrome occurred in 55% of all patients with severity grade ≤2 in 90% of reported cases. Overall response rate (ORR) was 24% and disease control rate (DCR) was 74% with objective responses in 7 patients with SS, 1 patient with non-small cell lung cancer, and 1 patient with head and neck squamous cell carcinoma. ORR in patients with SS, all prior treated with ifosfamide chemotherapy, was 44%, and DCR was 94%. Median progression-free survival and overall survival were 20.4 weeks (95% CI: 10.0, 52.1) and 58.1 weeks (95% CI: 36.3,-), respectively, for patients with SS and 12.3 weeks (95% CI: 10.857, 19.1) and 42.9 weeks (95% CI: 20.7, -), respectively, for the overall population. Translational findings demonstrated that afamitresgene autoleucel infiltrates into tumors, has an IFNγ-driven mechanism-of-action, and triggers adaptive immune responses. Overall, afamitresgene autoleucel has an acceptable safety profile with early and durable responses in HLA-A*02 positive patients with MAGE-A4 expressing solid tumors, especially in patients with metastatic SS. The recommended treatment regimen for Phase 2 evaluation involves lymphodepleting chemotherapy consisting of cyclophosphamide 600 mg/m2 x 3 days and fludarabine 30 mg/m2 x 4 days followed by afamitresgene autoleucel at a dose range of 1 to 10 billion transduced T-cells.

overall_design:
Expression of several gene groups and gene set enrichment analysis using NanoString PanCancer Immune Profiling panel was done.
Pre- and post-treatment biopsies from three Synovial sarcoma and a single ovarian tumor patients were compared.

first: Brian

last: Van Tine

first: Melissa

last: Johnson

first: Swethajit

last: Biswas

first: Cheryl

last: McAlpine

first: Anthony

middle: J

last: Olszanski

first: Jeffrey

last: Clarke

first: Dejka

last: Araujo

first: George

middle: R

last: Blumenschein

first: Partow

last: Kebriaei

first: Quan

last: Lin

first: Alex

last: Tipping

first: Joseph

last: Sanderson

first: Ruoxi

first: Trupti

last: Trivedi

first: Thejo

last: Annareddy

first: Jane

last: Bai

first: Stavros

last: Rafail

first: Amy

last: Sun

first: Lilliam

last: Fernandes

first: Jean-Marc

last: Navenot

first: Robyn

last: Broad

first: Martin

last: Isabelle

first: Revashnee

last: Naidoo

first: Natalie

last: Bath

first: Gareth

last: Betts

first: Zohar

last: Wolchinsky

first: Dzmitry

last: Batrakou

first: Erin

last: Van Winkle

first: Erica

last: Elefant

first: Armin

last: Ghobadi

first: Amanda

last: Cashen

first: Anne

last: Grand’Maison

first: Philip

last: McCarthy

first: Paula

last: Fracasso

first: Elliot

last: Norry

first: Dennis

last: Williams

first: Mihaela

last: Druta

last: Liebner

first: Kunle

last: Odunsi

first: Marcus

middle: O


title: PDGFRα-induced stromal maturation is required to restrain postnatal intestinal epithelial stemness and promote defense mechanisms.

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur


title: TRIM33 is an oncogenic transcriptional coactivator stabilizing AR from Skp2-mediated ubiquitin-proteasomal degradation in prostate cancer

city: Macau

first: Edwin

middle: Chong Wing

last: CHEUNG

state: Macau

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

institute: University of Macau


title: The landscape, properties, and determinants of transcriptional activation of endogenous transposable elements in grapevine (Vitis vinifera L.)

city: Lincoln

first: Christopher

last: Winefield

state: Canterbury

address: Ellesmere Junction Road/Springs Road

country: New Zealand

institute: Lincoln University

summary:
Background: Transcriptional activation of structurally autonomous transposable elements (TEs) is a precursor to both autonomous and non-autonomous transposition in host genomes. However, the identification of those transcribed TE loci that are competent autonomous elements, their genomic locations and the specific conditions under which these loci can contribute to mobilisation of both autonomous and non-autonomous elements remains largely unknown.
Results: A three-channel analysis pipeline was established to identified expressed TE loci. This pipeline is mainly comprised of three different existing tools (htseq-count, bedtools, and TEFingerprint) for mapped read quantification. Using Vitis vinifera embryogenic callus as a model, we exposed the callus to live cultures of an endemic grapevine yeast Hanseniaspora uvarum to determine the landscape and properties of expressed TE loci. In this system, only 1.7%-2.5% of total annotated TE loci were transcribed, of which 5%-10% of these were full-length (>90% length integrity). Collectively, these TE loci (including fragmented and structurally ‘autonomous’ loci) exhibited a significant tendency to be found within introns of expressed genes. This strong location bias towards expressed genes was also observed in Arabidopsis thaliana wild-type and ibm2, but not in ddm1. Moreover, in the grapevine model, differentially expressed TE loci tend to present similar expression pattern with co-localized differentially expressed genes. Nonetheless, utilizing Oxford Nanopore Technology (ONT) cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified full-length transcripts derived from structurally autonomous TE loci in our grapevine system, although the level of these transcripts was low.
Conclusions: Our observations in the two disparate plant model systems reveal the closely connected transcriptional relationship between TEs and co-localized genes when the epigenetic silencing system is not compromised. Furthermore, we found that the stress treatment alone was not sufficient to induce large scale full length transcription from structurally intact TE loci, a precursor for mobilisation of non-autonomous and autonomous elements.

overall_design: Time-series mRNA profiles of grapevine wild-type embryogenic callus subjected to mock treatment or mock plus continuous live yeast (Hanseniaspora uvarum) inoculation. A common time zero (T=0h) was used for all treatments

first: Chen

last: Ting-Hsuan

first: Winefield

last: Christopher


title: TRIM33 is an oncogenic transcriptional coactivator stabilizing AR from Skp2-mediated ubiquitin-proteasomal degradation in prostate cancer [RNA-Seq]

summary: Using a proteomics approach, we identified the Tripartite Motif Containing 33 (TRIM33) as a novel transcriptional coactivator of AR. We demonstrate TRIM33 facilitates the AR chromatin binding to directly regulate a transcription program that promotes PCa progression by protecting AR from Skp2-mediated ubiquitination and proteasomal degradation. We also show TRIM33 is essential for PCa tumor growth by avoiding cell cycle arrest and apoptosis, and TRIM33 knockdown sensitizes PCa cells to AR antagonists. In clinical analyses, we find TRIM33 is upregulated in multiple PCa patient cohorts. Finally, we uncover an AR-TRIM33 coactivated gene signature that is highly expressed in PCa tumors and predicts disease recurrence. Overall, our results reveal TRIM33 is an oncogenic AR coactivator in PCa and a potential therapeutic target for PCa treatment.

overall_design: RNA-seq following TRIM33 knockdown in LNCaP cells.

last: Cheung

first: Mi

last: Chen

first: Shreyas

last: Lingadahalli

first: Nitin

last: Narwade


title: YFP+ and YFP– stromal cells isolated from intestinal ulcers of indomethacin treated LTBRYFP mice

summary: After birth, the intestine undergoes major changes to shift from an immature proliferative state to a functional intestinal barrier. By combining inducible lineage tracing and transcriptomics in mouse models, we identify a pro-differentiation PDGFRαHigh intestinal stromal lineage originating from postnatal LTβR+ perivascular stromal progenitors. Genetic blockage of this lineage increased the intestinal stem cells pool while decreasing epithelial and immune maturation at weaning age, leading to reduced postnatal growth and dysregulated repair responses. Ablating PDGFRα in the LTβR stromal lineage demonstrates that PDGFRα has a major impact on the lineage fate and function, inducing a transcriptomic switch from pro-stemness genes such as Rspo3 and Grem1 to pro-differentiation factors including BMPs, retinoic acid and laminins, and on spatial organization within the crypt-villus and repair responses. Our results show that PDGFRα-induced transcriptomic switch in intestinal stromal cells is required in the first weeks after birth to coordinate postnatal intestinal maturation and function.

overall_design: CD45-CD31- stromal cells expressing YFP (YFP+) or not (YFP-) were isolated by FACS from the intestinal ulcers of indomethacin treated LTβRYFP mice to perform RNA sequencing

first: Lucie

last: Peduto

first: Jean-Marie

last: Jacob


title: Epigenetic reprogramming leads to down regulation of CD4 and functional changes in African green monkey memory CD4+ T cells

city: Bethesda

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

summary: African green monkeys (AGMs) are a natural host for a lentivirus related to human immunodeficiency virus, simian immunodeficiency virus. SIV-infected AGM rarely progress to AIDS despite robust viral replication. Though multiple mechanisms are involved, a primary component is their ability to downregulate CD4 expression on mature helper CD4+ T cells, rendering these cells resistant to infection by SIV. These CD8aa+ T cells retain functional characteristics of helper CD4+ T cells while simultaneously aquiring abilities of cytoxic CD8ab+ T cells. To determine mechanisms underlying functional differences between T cell subsets in AGMs, chromatin accessibility in purified populations was determined by ATACseq. Differences in chromatin accessibility alone were sufficient to cluster cells by subtype, and acceesibility at the CD4 locus reflected changes in CD4 expression. DNA methylation at the CD4 locus also correlated with inaccessible chromatin. By associating accessible regions with nearby genes, gene expression was found to correlate with accessibility changes. T cell and immune system activation pathways were identified when comparing regions that changed accessibility from CD4+ T cells to CD8aa+ T cells. Different transcription factor binding sites are revealed as chromatin accessibility changes, and these differences may elicit downstream changes in differentiation. This comprehensive description of the epigenetic landscape of AGM T cells identified genes and pathways that could have translational value in therapeutic approaches recapitulating the protective effects CD4 downregulation.

overall_design: This study involves ATAC-seq in 5 T cells populations from 10 separate african green monkeys, totalling 50 samples. Half of the monkeys have SIV and the other half do not.

first: Andrew

last: Rahmberg

first: Tovah

middle: E

last: Markowitz


title: YFP+PDGFRa+ and YFP+PDGFRa– stromal cells isolated from the small intestine of LTBRfloxedPDGFRa/YFP mice

overall_design: CD45-CD31- YFP+ stromal cells expressing PDGFRα (YFP+PDGFRα+) or not (YFP+PDGFRα-) were isolated by FACS from the small intestine of LTβRfloxPDGFRα/YFP mice to perform RNA sequencing


title: YFP+ and YFP– stromal cells isolated from the small intestine of LTBRYFP mice

overall_design: CD45-CD31- stromal cells expressing YFP (YFP+) or not (YFP-) were isolated by FACS from the small intestine of LTβRYFP mice to perform RNA sequencing


title: In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIP-seq]

first: Rafael

last: Acemel

overall_design: ChIP-seq against CTCF in mouse ES cells with various genotypes

first: Chiara

last: Anania

first: Johanna

last: Jedamzick

first: Adriano

last: Bolondi

first: Giulia

last: Cova

first: Norbert

last: Brieske

first: Ralf

last: Kühn

first: Lars

last: Wittler

first: Francisca

last: Real

first: Darío

last: Lupiáñez


title: Fine-tuning modulation of oxidation-mediated posttranslational control of Bradyrhizobium diazoefficiens FixK2 transcription factor

city: Granada

first: Socorro

last: Mesa

address: C/Profesor Albareda 1

department: Soil and Plant Microbiology

institute: CSIC

summary: Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) wild type and a C183D FixK2 encoding strain which were cultured under microoxic conditions (0.5% O2). For comparison, this work also includes the expression data samples GSM210246 to GSM210268, and samples GSM313727 to GSM313734 in GEO record number GSE12491. Keywords: CRP/FNR proteins, in vitro transcription, microoxia, posttranslational control, protein-DNA interaction, Rhizobia, transcriptomics

overall_design: Comparative transcriptional profiling of a C183D FixK2 encoding strain with wild type, both grown microoxically

first: S

last: Parejo

first: J

last: Cabrera

first: A

last: Jiménez-Leiva

first: L

last: Tomás-Gallardo

first: E

last: Bedmar

last: Gates


title: TRIM33 is an oncogenic transcriptional coactivator stabilizing AR from Skp2-mediated ubiquitin-proteasomal degradation in prostate cancer [ChIP-seq]

first: Edwin

last: CHEUNG

overall_design: ChIP-seq for TRIM33 and AR in LNCaP cells.

last: Cheung

first: Mi

last: Chen

first: Shreyas

last: Lingadahalli

first: Nitin

last: Narwade