title: Expression data from primary human bronchial epithelial basal cells from smokers non-COPD and COPD knocked down for SNAI2

first: Pierre

last: de la Grange

summary:
Bronchial epithelial basal cells express high levels of SNAI2 and in order to identify the genes downstream of SNAI2, we performed a knockdown approach with shRNA specific of SNAI2
We used microarrays to compare the effect of SNAI2 knockdown versus a non-targetting sequences and identified genes that are up- or down-regulated downstream of SNAI2

overall_design: Bronchial epithelial basal cells from smokers non-COPD and COPD, transduced by shRNA, either SNAI2 specific or non-targetting, were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Chams-Eddine

last: Brahim

first: Charlotte

last: Courageux

first: Ariane

last: Jolly

last: Leroy


title: RNA-seq analysis of archived skin from common bottlenose dolphin health assessments in the northern Gulf of Mexico

status: Public on May 04 2021

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

country: USA

institute: National Marine Mammal Foundation

type: Expression profiling by high throughput sequencing

summary: Archived skin samples collected during common bottlenose dolphin health assessments in Barataria Bay, LA from 2016 to 2017 were analyzed by RNA-seq to support and enhance the assessment of animal health.  The transcriptomic data were analyzed in conjunction with the substantial pool of health and environmental data collected during health assessments to investigate the utility of transcriptomic data in overall assessment of dolphin health and/or as markers of specific health concerns.

overall_design: Illumina based RNA-seq analyses were carried out on RNA extracts of skin from 28 archived samples using the Tursiops truncatus NIST Tur_tru v1 genome as a guide.  Samples were collected in Barataria Bay, LA during 2016 and 2017.

middle: S

first: Lori

middle: H

last: Schwacke


title: Effect of LSD1 knockdown on histone H3K4 methylation in HEL human erythroleukemia cell line.

city: Kumamoto

first: Kensaku

last: Kohrogi

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Department of Medical Cell Biology

country: Japan

institute: Kumamoto University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To understand the role of LSD1 in regulating histone H3K4 methylation status, ChIP-seq analyse of mono- and di-methylated H3K4 in LSD1-KD HEL cells were performed. The analyses revealed demethylation of H3K4me1 and H3K4me2 by LSD1 at regulatory regions including CEBPA gene enhancer.

overall_design: Examination of histone H3K4 methylation in HEL

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: Osteocytes as main responders to Low Intensity Pulsed Ultrasound for the treatment of fracture healing

status: Public on May 03 2021

city: Sapporo

first: Mari

last: Sato

address: Kita13 Nishi7 KIta ku

institute: Hokkaido University

summary: Skeletal tissue is known to respond to mechanical stress. Ultrasound stimulation is one of mechanical stress and low intensity pulsed ultrasound (LIPUS) devices have been clinically utilized to promote the fracture healing. However, it is still not clear which skeletal cells, especially osteocytes or osteoblasts, mainly respond to LIPUS stimulation and how they contribute to fracture healing. To examine that, we utilized medaka known to have bones without embedded osteocytes and zebrafish known to have bones with embedded osteocytes as an in vivo model. Interestingly, fracture healing was accelerated by ultrasound stimulation in zebrafish but not in medaka. To examine the molecular events induced by LIPUS stimulation in osteocyte, we performed RNA-sequencing with the murine long bone osteocyte Y4 (MLO-Y4) cell line exposed to LIPUS. 179 genes reacted to LIPUS stimulation and functional cluster analysis defined that several molecular signatures related in immunity, secretion and transcription. Especially, most of isolated transcription related genes were modulated by LIPUS also in vivo experiments using zebrafish. Target genes analysis showed that inflammatory response and bone formation in fracture healing could be transcriptionally regulated in osteocytes by LIPUS stimulation. Among these transcription genes, early growth response (Egr) 1,2, JunB, Forkhead box Q1 (FoxQ1) and nuclear factor of activated T cells (NFAT) c1 were not altered by LIPUS in medaka unlike zebrafish suggesting that these genes would be key transcriptional regulator of LIPUS-dependent fracture healing through osteocytes. In this study, we revealed bone-equipped osteocytes is necessary for LIPUS-induced promotion of fracture healing through the transcriptional control of target genes presumably to activate neighboring cells involved in fracture healing event.

overall_design: Examining the effects of low-intensity pulsed ultrasound (LIPUS) stimulation on MLO-Y4 cells.

first: Tatsuya

last: Shimizu

first: Naomasa

last: Fujita


title: Enterocyte–ILC1 crosstalk drives innate IFN-g-mediated control of Cryptosporidium

city: Philadelphia

first: Boris

last: Striepen

state: Pennsylvania

address: 380 S University Ave, Room H344

department: Pathobiology

institute: University of Pennsylvania

summary: Cryptosporidium infects enterocytes, but their contribution to parasite control is not well understood. Early resistance to Cryptosporidium is dependent on the production of IFN gamma. Loss of STAT1 in enterocytes, but not dendritic cells or macrophages, antagonized early parasite control. Moreover, transcriptional profiling of enterocytes from infected mice revealed the induction of an IFN gamma signature that included multiple genes (IDO, GBP, IRG) associated with control of intracellular pathogens.

overall_design: Two-three biological replicates were analyzed for each of 3 conditions (uninfected vs infected for 3 or 5 days)

first: Jodi

last: Gullicksrud

first: Chris

last: Hunter


title: Smalltalk in the big ocean - signaling molecules and DNA elicit chemotactic and genetic regulatory effects in surface associated Rhodobacteraceae

city: Oldenburg

first: Laura

last: Wolter

state: Deutschland

address: Carl-von-Ossietzky str. 9-11

department: Institute for Chemistry and Biology of the Marine Environment

country: Germany

institute: Carl-von-Ossietzky University Oldenburg

summary: Transcriptional response of wildtype Phaeobacter inhibens to several secondary metabolites (AHLs, TDA) and eDNA

overall_design: Samples from three independent cultures were treated with tested substance, DMSO control or left untreated.

first: Jürgen

last: Tomasch

first: Maren

last: Scharfe

first: Sujatha

last: Srinivas

first: David

middle: N

last: Torres

first: Matthias

last: Wietz

first: Irene

last: Wagner-Döbler

first: Thorsten

last: Brinkhoff


title: Expression data from human HCC tissues

city: chengdou

first: ji

middle: hong

last: jie

address: 37 Guoxue Road, Chengdu, China

country: China

institute: West China Hospital

summary:
The expression profiles of twenty paired human liver cancer and adjacent non-tumor tissues
We used microarrays to detail the changes of gene expression  in human HCC and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Tumor specimens of HBV-associated HCC were collected from HCC patients who underwent curative resection for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain differential gene in liver cancer and adjacent non-tumor tissues. To that end, we hand-selected twenty paired human liver cancer and adjacent non-tumor tissues:  cancer tissues: A8958, A8962, A8966, A8968, A8972, A8974, A8976, A8980, A8984, A8986, A8988, A8990, A8996, A9000, A9002,  A9004, A9006, A9008, A9359, A9361;    adjacent non-tumor tissues: A8959, A8963, A8967, A8969, A8973, A8975, A8977, A8981, A8985, A8987, A8989, A8991, A8997, A9001, A9003, A9005, A9007, A9009, A9360, A9362.

first: Yujun

last: Shi

first: Hongjie

last: JI


title: Targeting microRNA-mediated gene repression limits the adipogenic conversion of skeletal muscle mesenchymal stromal cells

status: Public on May 01 2021

city: El Cerrito

first: Christapher

last: Morrissey

state: CA

address: 7447 seaview Pl

institute: DNAnexus

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Concomitant Nrf2 and beta-catenin activation in hepatocellular cancer subset

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: In the current study, we want to explore the crosstalk between NFE2L2 and beta-catenin.

overall_design: We co-deliver T41A beta-catenin/G31A NFE2L2 mutant (MODEL1), T41A beta-catenin/T80K NFE2L2 (MODEL2) into 6-8 weeks old FVB mice hepatocytes via hydrodynamic tail vein injection(HDTVI) with the sleeping beauty transposon/transposase system, separately. The control group NFE2L2WT/ T41A beta-catenin injected mice are normal in gross image and H&E test at 14 weeks post injection. Meanwhile, T80K NFE2L2/T41A beta-catenin and G31A NFE2L2/T41A beta-catenin group has HCC tumor, and G31A NFE2L2/T41A beta-catenin HCC developed faster than the other HCC group.

first: Junyan

last: Tao

first: Yaketrina

last: Krutsenko

first: Sucha

last: Singh

first: Minakshi

last: Poddar

first: Aaron

last: Bell

first: Michael

last: Oertel

first: Aatur

last: Singhi

first: Silvia

first: Satdarshan

middle: P

last: Monga


title: Genome-wide occupancy of LSD1 in HEL human erythroleukemia cell line.

first: Kensaku

last: Kohrogi

summary: We examined the genome-wide distribution of LSD1 bound regions in HEL cells bya ChIP-seq analysis. We found that GATA family transcription factors co-operate with LSD1 to regulate metabolic genes. We also found that LSD1 binds to and represses CEBPA gene enhancer, resulting in the suppression of myeloid cell properties.

overall_design: Examination of LSD1 / DNA interaction in HEL. Two biological replicates were analyzed.

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: Analysis of the effect of clofarabine treatment on gene expression in K562 cells using mRNA sequencing

status: Public on May 02 2021

city: Ithaca

first: Yimon

last: Aye

state: NY

address: 259 East Ave.

department: Department of Chemistry and Chemical Biology

institute: Cornell University

summary: Clofarabine blocks the progression of cell cycle at the G1-S boundary. It induces upregulation of cyclin E and downregulation of histones and several other cell cycle related genes.

overall_design: We compared the differential mRNA expression in clofarabine treated cells and DMSO treated cells

first: Aye

last: Yimon

first: Fu

last: Yuan


title: Highly conserved sperm function-related transcripts across three species: human, rat and mouse.

city: Providence

first: Susan

last: Hall

state: RI

address: Box G-E5

institute: Brown University

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: mRNA sequences were analyzed in mouse, rat and human sperm samples to identify sperm transcriptomic similarities across species that could be used as biomarkers to predict male reproductive toxicity in animal models. Semen specimens were collected from men aged 18 to 55 years with proven fertility. Rat and mouse semen specimens were collected via needle punctures of the cauda epididymides. Sperm RNAs were extracted using an optimized sperm RNA isolation protocol and subjected to polyA-purified mRNA-sequencing.

first: Enrica

last: Bianchi

first: Kim

last: Boekelheide

first: Kathleen

last: Hwang


title: Transcriptome analysis of the ΔYGP1 strain compared to its parental strain

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

summary: We sought to understand the change in the global gene expression profile of the ΔYGP1 strain in comparison with the BGL-6_Kl parental strain. The transcriptome analysis revealed the change in expression of genes involved in cell wall structure, biogenesis, and integrity that might contribute to the improvement of the BGL display efficiency phenotype.

overall_design: RNA samples from two biological replicates of each yeast strain were prepared from 48-h cultured cells since it was the initial time point that the BGL activity on yeast cells of the BGL/ygp1Δ and BGL-6_Kl strains became apparently different.

first: Surisa

last: Suwannarangsee

first: Salisa

last: Charoensri


title: Comparing the miRNA transcriptome of FAPs cultured in basal medium (BM) and adipogenic differentiation medium (ADM)

first: Christapher

last: Morrissey

summary: FAPs isolated by FACS from wildtype mice were grown in culure and then placed in BM or ADM for 24 hours to assess the miRNA transcriptomic changes

overall_design: FACS isolated FAPs from wildtype (WT) mice were cultured in growth medium (GM) until ~80% confliuent. The cells were then switched to BM or ADM and maintained for 24 hours, at which time small RNAs were isolarted uisng the miRVana Kit. Small RNA libraries were then prepared with the Illumina TruSeq Small RNA Sample Prep kit. An additional size selection for barcoded miRNAs at band size of 147bp was completed on a TBE PAGE gel. Libraries were sequenced on an Illumina MiSeq system at the Stanford Functional Genomics Center (SFGC).

first: Michael

last: Wosczyna

first: Thomas

middle: A

last: Rando


title: Immunological Biomarkers of Fatal COVID-19: A Study of 868 Patients

city: New York

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

summary: Information on the immunopathobiology of coronavirus disease 2019 (COVID-19) is rapidly increasing; however, there remains a need to identify immune features predictive of fatal outcome. This large-scale study characterized immune responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection using multidimensional flow cytometry, with the aim of identifying high-risk immune biomarkers. Holistic and unbiased analyses of 17 immune cell-types were conducted on 1,075 peripheral blood samples obtained from 868 COVID-19 patients and on samples from 24 patients presenting with non-SARS-CoV-2 infections and 36 healthy donors. Immune profiles of COVID-19 patients were significantly different from those of age-matched healthy donors but generally similar to those of patients with non-SARS-CoV-2 infections. Unsupervised clustering analysis revealed three immunotypes during SARS-CoV-2 infection; immunotype 1 (14% of patients) was characterized by significantly lower percentages of all immune cell-types except neutrophils and circulating plasma cells, and was significantly associated with severe disease. Reduced B-cell percentage was most strongly associated with risk of death. On multivariate analysis incorporating age and comorbidities, B-cell and non-classical monocyte percentages were independent prognostic factors for survival in training (n=513) and validation (n=355) cohorts. Therefore, reduced percentages of B-cells and non-classical monocytes are high-risk immune biomarkers for risk-stratification of COVID-19 patients.

overall_design: Six cell immune populations sorted from 4 healthy donors

first: Esperanza

last: Martín-Sánchez

first: Juan-José

last: Garcés

first: Catarina

last: Maia

first: Susana

last: Inogés

first: Ascensión

last: López-Díaz de Cerio

first: Francisco

last: Carmona-Torre

first: Marta

last: Marín

first: Félix

last: Alegre

first: Elvira

last: Molano

first: Mirian

last: Fernandez-Alonso

first: Cristina

last: Perez

first: Cirino

last: Botta

first: Aintzane

last: Zabaleta

first: Ana-Belen

last: Alcaide

first: Manuel

middle: F

last: Landecho

last: Rua

first: Teresa

last: Pérez

first: Laura

last: Blanco

first: Sarai

last: Sarvide

first: Amaia

last: Vilas-Zornoza

first: Diego

last: Alignani

last: Moreno

first: Iñigo

last: Pineda

first: Miguel

last: Sogbe

first: Josepmaria

last: Argemi

first: Bruno

last: Paiva

first: José-Ramón

last: Yuste


title: A stress-responsive miRNA regulates BMP signaling to maintain tissue homeostasis

city: Bloomington

first: Nick

last: Sokol

state: IN

address: 1001 E 3rd Street, Biology Building

institute: Indiana University

summary: Adult organisms must sense, respond, and adapt to environmental fluctuations. In high-turnover tissues such as the intestine, these adaptive responses require rapid changes in gene expression that, in turn, likely involve post-transcriptional gene control. However, intestinal tissue specific microRNA mediated regulatory pathways remain unexplored. Here we report the role of an intestinal specific microRNA, miR-958, that non-cell autonomously regulates stem cell numbers during tissue homeostasis and regeneration in the Drosophila adult midgut. We identify its downstream target cabut, the Drosophila ortholog of mammalian KLF10/11 transcription factors, which mediates this miR-958 function by promoting paracrine enterocyte-to-stem cell BMP signaling. We also show that mature miR-958 levels transiently decrease in response to stress, and that this decrease is required for proper stem cell expansion during tissue regeneration. In summary, we have identified a novel post-transcriptional mechanism that modulates BMP signaling activity within Drosophila adult intestinal tissue both during normal homeostasis as well as tissue regeneration to regulate intestinal stem cell numbers.

overall_design: We compared microRNA read counts in small RNA libraries prepared from intestinal tissue and remaining "carcass" tissue from wildtype adult male Drosophila melanogaster. Analysis compared three intstinal samples to two carcass samples.

first: Sromana

last: Mukherjee

first: Kasun

last: Buddika

first: Nicholas


title: BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome [RNA-seq]

city: Oxford

first: Nadezda

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A monoubiquitylation (H2AK119ub1), which is enriched at Polycomb-repressed gene promoters but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we found that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive genome-wide accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 preferentially counteracts Ser5 phosphorylation on the C-terminal domain of RNA polymerase II at gene regulatory elements and causes reductions in transcription and transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes, which leads to their derepression, providing a potential molecular rationale for why the BAP1 ortholog in Drosophila has been characterized as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Mouse embryonic stem cells in which BAP1 or PRC1 catalytic activity can be conditionally removed, individually or in combination, were profiled for gene expression using spike-in calibrated nuclear RNA-seq.

first: Neil

last: Blackledge

first: Robert

middle: J

last: Klose


title: Transcriptome analysis of periodontal tissue response after immediate replantation and delayed replantation

city: Seoul

first: Yunhyeong

last: Kim

address: kyunghee daero 23

country: South Korea

institute: KYH

summary:
Objective: This study aimed to identify the transcriptome profiles from periodontal tissues of replanted teeth and evaluate the functional differences of transcriptomes between immediate replantation and delayed replantation in a rat teeth avulsion animal model.
Background: In dental avulsion, the prognosis of replanted teeth is hardly favorable in delayed replantation. After tooth replantation, complex inflammatory responses occur to return homeostasis in periodontal tissue. Various types of cytokines are produced in inflammatory microenvironment and these cytokines determine the periodontal tissue responses.
Methods: Maxillary first molars of Sprague–Dawley rats were extracted and exposed to dry environment, then replanted. The animals were divided into two groups according to extra–oral time: immediate replantation group (dry for 5 min) and delayed replantation (dry for 60 min). Either 3 or 7 days after replantation, the animals were sacrificed. The palatal gingival tissues were harvested for mRNA–sequencing. Hallmark gene set enrichment analysis were performed to predict the function of transcriptomes. Normalized enrichment score (NES) was generated to determine the functional differences between the groups.
Results: Hallmark gene sets enriched in delayed replantation at 3 days were oxidative phosphorylation (NES=2.82, q < 0.001) and TNF–α signaling via NF–κB pathway (NES= 1.52, q=0.034). At 7 days, TNF–α signaling via NF–κB pathway (NES=–1.82, q=0.002), angiogenesis (NES=–1.66, q =0.01), and TGF–β signaling pathway (NES=–1.46, q=0.051) were negatively highlighted in delayed replantation compared to immediate replantation.
Conclusions: Transcriptome profiles were significantly different between immediate replantation and delayed replantation. The responses of periodontal tissues were associated with TNF–α signaling via NF–κB pathway. However, the enrichment score of this pathway were changed with time–dependent manner between immediate replantation and delayed replantation.

overall_design: Maxillary first molars of Sprague–Dawley rats were extracted and exposed to dry environment, then replanted. The animals were divided into two groups according to extra–oral time: immediate replantation group (IR; dry for 5 min) and delayed replantation (DR; dry for 60 min). Either 3 or 7 days after replantation, the animals were sacrificed.

first: Yong

middle: K

last: Chae

first: Ok

last: Nam

first: Sung

middle: C

last: Choi


title: BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome [ATAC-seq]

overall_design: Mouse embryonic stem cells in which BAP1 can be conditionally removed were profiled for chromatin accessibility using spike-in calibrated ATAC-seq.


title: Comparing the transcriptome of cultured miR-206 KO FAPs and wildtype (WT) FAPs

first: Christapher

last: Morrissey

summary: FAPs isolated by FACS from miR-206 KO mice and WT mice were grown in culure and then placed in basal medium (BM) for 48 hours to assess the transcriptomic changes

overall_design: FAPs were isolated from miR-206 KO and WT mice by FACS and grown in culture with growth medium (GM) until ~90% confliuent. The cells were then switched to BM and maintained for 48 hours, at which time total RNA was isolated. This RNA was delivered to the Stanford Functional Genomics Center for library preparation and sequencing. Two replicates per condition were completed.

first: Michael

last: Wosczyna

first: Thomas

last: Rando


title: The role of MacroH2A1.2 in cancer (ChIP-Seq)

city: Singapore

first: Azhar

middle: B

last: Ali

address: 14 Medical Drive MD6 #11-01

department: CSI Singapore

country: Singapore

institute: National University of Singapore

summary: MacroH2A1.2 is a histone variant from H2A family. Expression of macroH2A1.2 is found to be dysregulated in cancer especially lung cancer. However, the role of macroH2A1.2 in lung cancer remains relatively unknown. Our study showed that macroH2A1.2 stabilized FASN expression, increased fatty acid production and hence improved OXPHO activity. As a result, the cancer cells with higher macroH2A1.2 expression were more respiratory active and metastatic.

overall_design: MacroH2A1.2 is overexpressed stably in the PC-9 cells. RNA expression in the macroH2A1.2 overexpressed PC-9 is profiled by RNA-seq and compared with vector transfected PC-9.

first: Chee

middle: W

last: Fhu

first: Jun

middle: T

last: Teo

first: Chan-shuo

last: Wu

first: Yaw

last: Lim

first: Tan

middle: M

last: Chin

first: Boon

last: Goh

first: Daniel

middle: G

last: Tenen


title: Photosensitivity and c-GAS-dependent type I IFN activation in lupus patients with TREX1 deficiency

city: Dresden

first: Claudia

last: Günther

address: Fetscherstr. 74

department: Klinik und Poliklinik für Dermatologie

institute: Universitätsklinikum Carl Gustav Carus

summary: High throughput screening comparing gene expression in human wildtype and patient (TREX1-mutated) fibroblasts, Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: RNA sequencing of transcripts isolated out of native and 8h post UV-irradiated cell (fibroblast) samples

first: Nicole

last: Berndt


title: The role of MacroH2A1.2 in cancer (RNA-Seq)

summary: MacroH2A1.2 is a histone variant from H2A family. Expression of macroH2A1.2 is found to be dysregulated in cancer especially lung cancer. However, the role of macroH2A1.2 in lung cancer remains relatively unknown. Our study showed that macroH2A1.2 stabilized FASN expression, increased fatty acid production and hence improved rate of mitochondria respiration. As a result, the cancer cells with higher macroH2A1.2 expression were more metastatic.


title: Bulk RNA-Seq comparing the transcriptome of pancreatic acinar cells in the presence or absence of pancreatitis

city: Woluwe Saint-Lambert

first: Mohamad

last: Assi

state: Brussels

address: 75 Hippocrate Avenue

country: Belgium

institute: de Duve Institute

summary: ElastaseCreER/ROSAYFP mice were treated or not with Cerulein to induce pancreatitis

overall_design: Using our mouse model we sorted pancreatic acinar cells and compared their transcriptomes in 2 conditions: 1) WT and 4) WT+Cerulein

first: Patrick

last: Jacquemin


title: Bulk RNA-Seq comparing pancreatic acinar cells based on their expression levels of KRAS protein (Citrine-KRAS fusion)

summary: We developped new mouse models to detect endogenous KRAS protein expression pattern via a Citrine-KRAS (Cit-K) fusion construction

overall_design: Using our mouse model we sorted pancreatic acinar cells based on their expression levels of Cit-K. We compared the transcriptiome of Cit-K-Pos (KRAS-Pos) vs Cit-K-Neg/Low (KRAS-Neg/Low) cells


title: Alteration of the whole skin gene expression as a result of Flg deficiency

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

summary: Defects of filaggrin (FLG) compromise epidermal barrier function and represent an important known genetic risk factor for atopic dermatitis (AD), but also for systemic atopy, including allergic sensitization and asthma. A loss of epidermal barrier integrity can provide a significant stress for the cells in both the epidermis as well as the underlying dermal layer of the skin, either due to the increased moisture evaporation from the skin or increased penetration of the antigens and microflora into the lower layers. This analysis was therefore designed to understand the effect of this loss of barrier integrity on the total skin transcriptional profile.

overall_design: Total shaved back skin tissue samples were collected from 8 week old Flg-deficient mice and wt ctrls  Total RNA was isolated using the RNeasy Mini Kit+ (Qiagen). mRNA libraries were prepared using a SMART protocol and subjected to deep sequencing on an Illumina NextSeq 500.

first: Lina

last: Muhandes


title: miR-206 pulldowns in FAPs to idenfity transcript targets

first: Christapher

last: Morrissey

summary: Biotin labelled miR-206 mimics ('06") and miR-Control mimics ("NC") were used to indentify putative miRNA transcript targets in FAPs form skeletal muscle

overall_design: FAPs were isolated from wildtype (WT) mouse skeletal muscle and grown to ~80% confluency, transfected with mimics for 24 hours, then maintained for 48 hours in basal medium (BM), at which time miRNA-transcript pulldowns were performed. Libraries were made with transcripts that were pulled down and these were sequenced to identify miR-206 targets. Two replicates per condition were completed.


title: Repeat elements analysis of  Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblasts using RNA-Seq

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: RNA sequencing of  Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblasts. Total RNA was sequenced to analyse noncoding transcripts and repeats

overall_design: RNA-Seq was performed on total RNA from 6 samples (WT and KO with three biological replicates each)

first: Xin

last: Xie

first: Syed

middle: R

last: Mahmood


title: Long non-coding RNA H19 promotes the progression of pancreatic cancer by APOBEC3G and both are inhibited by sulforaphane

first: Yiqiao

last: Luo

address: Im Neuenheimer Feld 365

institute: Section Surgical Research

summary: Long non-coding RNA H19

overall_design: mRNA was isolated by the use of the RNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions with lipotransfected NC or siH19. Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).

first: Bin

last: Yan

first: Li

last: Liu

first: Libo

last: Yin

first: Huihui

last: Ji

first: Xuefeng

last: An

first: Jury

last: Gladkich

first: Zhimin

last: Qi

first: Carolina

last: De La Torre

first: Ingrid

last: Herr


title: EZH2 deficiency induced gene expression change in CRCs

city: shanghai

first: Yongfeng

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

summary: Knockdown of EZH2 in colorectal cancer cells by lentivirus-mediated shRNA, and use total RNA for sequencing analysis after determining the efficiency of EZH2 knockdown in order to analyze the gene expression affected by EZH2.

overall_design: Genome-wide expression profiling of CRCs with or without EZH2.


title: Genome-wide ChIP-Seq maps of REST distribution in Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblast

summary: β-actin is a crucial component of several chromatin remodeling complexes which control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes. While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can affect the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2 in a dosage-dependent manner. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversable changes in 3D genome architecture. Our findings support a novel role for β-actin levels in shaping the chromatin landscape during development and differentiation.

overall_design: ChIP-Seq was performed on 8 samples (WT, KO, WT_input and KO_input with two biological replicates each)

first: Nadine

last: Hosny ElSaid

first: Kristin

last: Gunsalus


title: RNA-Seq analysis of WT and PCD8 RNAi-21 mutant in response to light.

city: beijing

first: Zhou

middle: wen

last: bin

address: 12 Zhongguancun South Street

institute: Chinese Academy of Agricultural Sciences

summary: We report the RNAi-21 had some genes with suppressed transcript levels (mainly involved in photosynthesis, oxidative phosphorylatio,amino acid, carbohydrate and cell wall components metabolism).  In contrast, the genes were stronger expressed compared to WT were mainly involved in plant hormone signal transduction and MAPK signaling pathway after 2 hours of exposure.

overall_design: Analysis of differentially expressed genes between WT and RNAi-21 in the dark, 0.5 and 2 h of light,respectively.

first: Shanshan

last: shi

first: Xi

last: Li

first: Rudan

last: Geng


title: Repetitive mild closed head injury in adolescent mice is associated with impaired proteostasis, neuroinflammation, and tauopathy

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: Repetitive mild traumatic brain injury (mTBI) in children and adolescents leads to acute and chronic neurological sequelae and is linked by epidemiological data to later life neurodegenerative disease.  However, the biological mechanisms connecting early life mTBI to neurodegeneration remain unknown.  Using an adolescent mouse repetitive closed head injury (CHI) model that induces progressive cognitive impairment in the absence of overt histopathology, we examined transcriptional and translational changes in neurons isolated from sham and injured brain in the chronic phase after injury.  At 14 months, single nuclei RNA sequencing of cortical brain tissue identified disruption of genes associated with neuronal proteostasis in injured mice. Western blot analysis of neurons isolated by immunopanning showed evidence of inflammasome activation, accumulation of misfolded, hyperphosphorylated Tau, and changes in expression of proteins suggestive of impaired translation. Compared to injured wild type, injured interleukin-1 receptor 1 knockout mice, which are protected from post-injury cognitive deficits, had reduced microgliosis and decreased accumulation of pro-interleukin-1 beta and misfolded tau in cortex and cerebellum at six months. Taken together, our findings provide evidence for neuronal inflammasome activation and impaired proteostasis as key mechanisms linking repetitive mTBI in adolescence to later life neurological dysfunction and neurodegeneration.

overall_design: Single-cell RNA-seq of mouse cortex from mice exposed to mild repetitive brain injury and controls


title: Bulk RNA-Seq comparing pancreatic acinar cells expressing  KRASG12D in the presence or absence of pancreatitis

first: Mohamad

last: Assi

summary: ElastaseCreER-LSLKRASG12D/ROSA26YFP mice were treated or not with Cerulein to induce pancreatitis

overall_design: Using our mouse model we sorted pancreatic acinar cells and compared their transcriptomes in 2 conditions:  1) KRASG12D and 2) KRASG12D+Cerulein

first: Patrick

last: Jacquemin


title: Modulation of  PSF binding property at RNA level by small molecule treatment in prostate cancer

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and androgen receptor (AR) downstream signalings promote prostate cancer cell proliferation. PSF is a RNA binding protein which is involved in AR signaling.To investigate the effect of samll molecule, No.10-3, on the RNA binding ability of PSF, we performed RNA immunoprecipitation (RIP) sequence analysis in AR positive prostate cancer cell line long term androgen deprivation (LTAD) cells to explore the differences of PSF function to associate with RNAs in prostate cancer cells.

overall_design: RIP sequence analysis of PSF in prostate cancer cells


title: The role of MacroH2A1.2 in cancer

first: Azhar

last: Ali

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

overall_design: Refer to individual Series


title: Hyperexcitable arousal circuits cause sleep instability during aging

city: Stanford

first: Justus

last: Kebschull

address: 327 Campus Drive

institute: Stanford University

summary: 10X single nucleus RNAseq of hyprcretin neurons from lateral hypothalamus in young and aged mice

overall_design: single cell analysis of young and aged hcrt neurons in male and female mice

first: Shi-Bin

first: Luis

last: de Lecea


title: Expression data of human endometrial stromal cells after miR-371a-3p mimic transfection

city: Nottingham

first: Dimitra

last: Makri

state: Nottinghamshire

address: Room E/D 1615, D Floor, East Block Division of Child Health, Obstetrics and Gynaecology Queen's Medical Centre

department: Obstetrics and Gynaecology

institute: University of Nottingham

summary:
Members of the miR-371 cluster are of the earliest de novo synthesized by embryos and have important actions in mammalian reproduction. MiR-371a is secreted by embryos at the peri-implantation period and its release has been previously associated with poor embryo quality and lower implantation rates in women undergoing IVF. Here we investigated the potential biological role of miR-371a release in regards to embryonic implantation, and specifically the molecular effects that this miRNA exerts on the cells of the endometrial lining.
Gene expression changes in endometrial cells upon miR-371a addition were therefore identified using large-scale genomic plattform that covers the whole human genome (Affymetrix).

overall_design: Human endometrial stromal cells were transfected with a miR-371a-3p mimic, to identify transcriptomic changes that might result from miR-371a regulation. Total RNA was extracted, purified, and sent for transcriptomic profliling using the Clariom S human assay (Affymetrix). The genomic data were processed with Partek and online bioinformatics tools to identify any related pathways to implantation.

first: Walid

middle: E

last: Maalouf


title: Effects of PSF inhibitors on gene expression profile in prostate cancer cells [microarray]

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. Although initially hormone-deprovation therapy is effective to inhibit cancer progression, most of cancers relapse as castration-resistant prostate cancer (CRPC). PSF is one of RNA binding proteins associated with prostate cancer progression. In this study, we examined the effect of small molecule treatment interacting with PSF in CRPC cells.
In order to investigate the effect of small molecule interacting with PSF cells, we analyzed gene expression profile in AR-positive prostate cancer cell line LNCaP and CRPC model cell derived from LNCaP cells.We treated LNCaP cells with vehicle or dihydrotestosterone (DHT) for 24 h. LTAD cells were treated with siControl or siPSF (10 nM) for 48 h. LTAD cells were treated with vehicle or small molecule interacting with PSF (No.10-3) for 48 h.

overall_design: Global analysis of gene expression changes in prostate cancer cells after treatmet with siRNA targeting PSF or small molecule interacting with PSF using microarray.


title: Effects of PSF inhibitors on histone acetylation and gene expression profile in prostate cancer cells


title: SATB1 promotion of trophoblast stem cell renewal

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

summary: Trophoblast stem (TS) cell renewal and differentiation are essential processes in placentation. Here, we have identified the mechanism/targets of chromatin organizer/transcription factor called special AT-rich binding protein 1 (SATB1) action on TS cell renewal by RNA-seq analysis in Rcho-1 TS cells expressing Satb1 shRNAs.

overall_design: Rcho-1 TS cells transduced with control shRNAs were used as controls. Cells transduced with two different shRNAs targeting Satb1 were used as treatment. RNA-seq was performed in TS cells at 4 days (acute) and 10 days (chronic) after transduction.

first: Kaiyu

last: Kubota

first: Michael

last: Soares


title: Histological and single cell transcriptomic analysis of human retinal organoid models of Leber Congenital Amaurosis identifies endoplasmic reticulum stress as a common degenerative pathway

city: Baltimore

first: Alyssa

last: Kallman

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University, School of Medicine

summary: This study utilized human stem cell derived retinal organoids to characterize two models of Leber Congenital Amaurosis.  Using CRISPR/Cas9, we generated CRB1 and RPGRIP1 KO cell lines and differentiated WT and KO lines into retinal organoids.  Single cell capture was performed using Dropseq at days 70, 90, 120, 150, 190, and 225 of differentiation.  We report upregulation of DDIT3 in both KO organoids relative to WT and confirm DDIT3 induction at the protein level by immunohistochemistry.  These results indicate that these genetically different models of disease converge on endoplasmic reticulum stress and DDIT3 induction as a shared degenerative pathway.  Therapeutic targeting of ER stress could help alleviate the degenerative phenotype in cases where diseased photorececeptors suffer ER stress.

overall_design: single cell RNAseq of wild type, RPGRIP1 KO, and CRB1 KO human retinal organoids at days 70, 90, 120, 150, 190, and 225

first: Don

last: Zack


title: Effects of PSF inhibitors on histone acetylation in prostate cancer cells [ChIP-seq]

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. Although initially hormone-deprovation therapy is effective to inhibit cancer progression, most of cancers relapse as castration-resistant prostate cancer (CRPC). PSF is one of RNA binding proteins associated with prostate cancer progression. In this study, we examined the effect of small molecule treatment interacting with PSF on the histone acetylation status in CRPC cells.

overall_design: In order to investigate the effect of small molecule interacting with PSF cells, we analyzed histone acetylation by Chromatin immunoprecipitation (ChIP)-sequence in AR-positive prostate cancer cell line LNCaP and CRPC model cell derived from LNCaP cells.We treated LNCaP cells with vehicle or dihydrotestosterone (DHT) for 24 h. LTAD cells were treated with siControl or siPSF (10 nM) for 48 h. LTAD cells were treated with vehicle or small molecule interacting with PSF (No.10-3) for 48 h.


title: The major and minor spliceosome interact to regulate alternative splicing [PBMCs]

city: Storrs

first: Rahul

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Mutations in minor spliceosome components are linked to diseases such as Roifman syndrome, Lowry-Wood syndrome, and early-onset cerebellar ataxia (EOCA). Here we report that besides increased minor intron retention, Roifman syndrome and EOCA can also be characterized by elevated alternative splicing (AS) around minor introns. Consistent with the idea that the assembly/activity of the minor spliceosome informs AS in minor intron-containing genes (MIGs), inhibition of all minor spliceosome snRNAs led to upregulated AS. Notably, alternatively spliced MIG isoforms were bound to polysomes in the U11-null dorsal telencephalon, which suggested that aberrant MIG protein expression could contribute to disease pathogenesis. In agreement, expression of an aberrant isoform of the MIG Dctn3 by in utero electroporation, affected radial glial cell divisions. Finally, we show that AS around minor introns is executed by the major spliceosome and is regulated by U11-59K of the minor spliceosome, which forms exon-bridging interactions with proteins of the major spliceosome. Overall, we extend the exon-definition model to MIGs and postulate that disruptions of exon-bridging interactions might contribute to disease severity and pathogenesis.

overall_design: Sequencing of total RNA from PBMCs of individuals with mutation in RNU4ATAC (Roifman syndrome and Lowry-Wood syndrome) and their heterozygous parents and unrelated healthy controls

first: Anouk

last: Olthof


title: The major and minor spliceosome interact to regulate alternative splicing


title: ChIP-seq for E4BP4 in the liver from transgenic mouse with liver specific E4BP4 overexpression

city: Ube

first: Akihiko

last: Taguchi

state: Yamaguchi

address: 1-1-1 minamikogushi

institute: Yamaguchi University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the effects of liver-specific E4BP4 overexpression under mouse albumin promoter on the liver glucose and lipid metabolism.
Methods: We generated transgenic mice (TG) with liver-specific E4BP4 overexpression, and harvested two livers with one TG mouse each. After cervical dislocation, mouse liver was perfused with a buffer containing Hanks' balanced salt solution, and cross-inked for 30 minutes with 2mM DSG and for 10 minutes with 1% formaldehyde by perfusion, followed by frozen at -80C. Then, Liver was homogenated by gentleMACS Dissociators. Nuclei were isolated and protein-DNA complexes were incubated with antibodies against two kinds of E4BP4 and immunoprecipitated with IgG paramagnetic beads.
Results: There were many significant peaks at the promoter/enhancer or intronic region of many genes.
Conclusions: E4BP4 possibly regulates the expression of some genes linked to lipid metabolism in the liver.

overall_design: ChIP-Seq in liver from transgenic mouse with liver specific E4BP4 overexpression

first: Yasuharu

last: Ohta

first: Yukio

last: Tanizawa


title: RNA-Seq analysis of wild-type and dmd1 anthers at tetrad stage

city: Beijing

first: lijun

last: Ren

address: No. 1 West Beichen Road, Chaoyang District

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Sciences

summary: Highly coordinated pollen wall patterning is essential for male reproductive development. However, the regulatory mechanisms involved in these processes remain poorly understood. Here, we report the identification of Defective Microspore Development1 (DMD1), which encodes a nuclear-localized protein possessing transactivation activity. DMD1 is preferentially expressed in the tapetum and microspores during postmeiotic anther development. Mutations in DMD1 cause a male sterile phenotype with impaired microspore cell integrity. The mutants display abnormal callose degradation, and primexine thickening is inhibited in the newly released microspores. The expression levels of several genes associated with callose degradation and primexine formation are down-regulated in dmd1 anthers. Moreover, irregular Ubisch body morphology and discontinuous endexine is observed in dmd1, and the baculum is completely absent. DMD1 interacts with Tapetum Degeneration Retardation (TDR), a basic helix-loop-helix transcription factor required for exine formation. Taken together, our results suggest that DMD1 is responsible for microspore cell integrity, primexine formation, and exine pattern formation during rice microspore development, and is a potential approach for manipulating male fertility in hybrid rice breeding.

overall_design: Three biological replicates of wild-type and dmd1 anthers from the tetrad stage to the early microspore stage were sampled for total RNA isolation

first: Lijun

first: Tingting

last: Zhao

first: Lei

last: Zhang

first: Guijie

last: Du

first: Yi

last: Shen

first: Ding

last: Tang

first: Yafei

last: Li

first: Qiong

last: Luo

first: Zhukuan

last: Cheng


title: Expression profiles of skeletal muscle from transgenic mouse with liver specific overexpression

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the effects of liver-specific E4BP4 overexpression under mouse albumin promoter on the muscle glucose and lipid metabolism.
Methods: We generated transgenic mice (TG) with liver-specific E4BP4 overexpression. Gasrocnemius muscles were isolated at Zeitgeber Time (ZT) 0 or 12 from transgenic mice and WT littermates, and total RNA was extracted. Muscle RNA profiles were generated by deep sequencing for four groups with three mouse samples each.
Results: There were no significant differences between WT and transgenic mice at both ZT0 and 12.
Conclusions:  Muscle metabolism was not  altered at the transcription level by liver specific overexpression of  E4BP4.

overall_design: Muscle mRNA profiles of 8-week old wild type mice and transgenic mice with  liver-specific E4BP4 overexpression


title: The major and minor spliceosome interact to regulate alternative splicing [HEK293 cells]

overall_design: Sequencing of nascent RNA from HEK293 cells electroporated with antisense morpholino oligonucleotides against U12 snRNA, U4atac snRNA, U6atac snRNA and U2 snRNA


title: Analysis of microRNAs expression in four head and neck cancer cell lines

city: Shenyang

first: Pai

last: Pang

state: Liaoning

address: No. 117 Nanjing Bei Jie, Heping, Shenyang, Liaoning 110002, P.R. China

institute: China Medical University

summary:
MicroRNA expression in two pair of  head and neck squamous cell carcinoma cell lines were analyzed. 4A/4B and 37A/37B cells were from two different head and neck squamous cell carcinoma patients.
A cells were from patients' primary focus. B cells were from patients' lymph node metastasis. B cells have higher migratory and invasive abilities and CCR7 expression levels than A cell.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Four cell samples: 4A, 4B, 37A, 37B were analyzed.


title: Next-generation sequencing quantitative analysis of the transcriptome of intrahepatic cholangiocarcinoma cell line treated with or without anlotinib.

city: Shanghai

first: Fei

last: Song

state: Shanghai

address: 180 Fenglin Road Shanghai China

institute: Zhongshan Hospital

summary: To examine the potential mechanism of anlotinib to inhibit intrahepatic cholangiocarcinoma, we used RNA-seq to analyze the effect of anlotinib treatment on the transcriptome changes of intrahepatic cholangiocarcinoma cell lines HCCC9810 and RBE. HCCC9810 and RBE cells were treated with DMSO or anlotinib at 5 μM for 24 hours, and then subjected to total RNA isolation and deep sequencing. We used Venn diagrams of RNA-seq results of HCCC9810 and RBE cells treated with anlotinib to indicate genes that were up- or down-regulated (adjusted P value <0.05, fold = 2.0). There are 420 genes in both groups (Figure 4A, 273 genes up-regulated and 147 genes down-regulated). In summary, the above sequencing results were analyzed by bioinformatics, and it was concluded that by inactivating the VEGF / PI3K / AKT signaling pathway and through cell cycle arrest, anlotinib treatment inhibited the proliferation and invasion of tumor cells and promoted Apoptosis.

overall_design: Intrahepatic cholangiocarcinoma cell lines (HCCC9810, RBE) in two groups were examined for changes in transcriptomics at anlotinib (24 hours after 5 μM concentration treatment). There were three biological replicates in each group.，3 treatment vs 3 control

first: Bo

last: Hu

first: Xin-Rong

last: Yang


title: The  ETS  inhibitors  YK-4-279  and  TK-216  have  anti-tumor  activity  in  lymphomas  and  interfere  with  SPIB  in  activated  B  cell-like  type  diffuse  large  B  cell  lymphoma

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: TMD8 and U2932 were treated with YK-4-279 for 4 and 8 hours.

overall_design: Identifing genes modulated by the YK-4-279 in human lymphoma cell lines

first: Luciano

last: Cascione


title: miRNA expression profile of mantle tissues for pearl oyster, Pinctada fucata

first: Xuejing

last: Zhu

address: Tsinghua University, Haidian District Beijing

department: School of Life Sciences

institute: Tsinghua University

summary: To elucidate the modulatory participation of miRNAs in mollusk biomineralization, we have employed high-throughput sequencing to identify miRNAs of pearl oyster, Pinctada fucata. Our study focused on the miRNA expression profile of the mantle, an organ responsible for shell formation of the oyster. The pearl oysters were cultured in the tank with the maintaining conditions of temperature 19 ℃, PH 8.1 and salinity 33‰ in recirculating seawater.

overall_design: Live and healthy adult pearl oysters P. fucata (shell length 5-6cm and wet weight 30-40g) were obtained from Zhanjiang Pearl Farm (Guangdong, China). Prior to use, the oysters were cultured at controlled temperature 19 ℃, PH 8.1 and salinity 33‰ in tanks with aerated artificial seawater for 2 weeks. They were fed with spirulina powder every day. Samples from ten individuals were pooled together to obtain one biological replicate. Total RNA of the mantle tissues was extracted, and fragments of 18-30nt were isolated to generate the small RNA library.

first: Rongqing


title: Comparing the Transcriptomes of Wild Type and Zp3-Cre mediated Mtor-Oocyte-Conditional Knockout (CKO) Mouse Metaphase II oocytes by RNA-Seq Analysis

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary:
The goal of this study is to identify the differentially expressed genes in Zp3-Cre mediated Mtor oocyte-specific knockout (CKO) Metaphase II (MII) oocytes by comparing the transcriptomes of Wild-Type (WT) and CKO Mouse MII oocytes via RNA-Seq Analysis.
Methods: mRNA profiles of 3 sets of super-ovulated MII oocytes collected from 24-day old WT- and Mtor CKO female mice were generated by deep sequencing using an Illumina Hiseq2500 platform with 41bp single read. All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.8b). Reads aligned to genes are counted by cufflinks (v2.1.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.

overall_design: mRNA profiles of super-ovulated MII oocytes from 24-day old WT- and Mtor Oo-cKO female mice were generated by deep sequencing, in triplicate, using Illumina Hiseq2500


title: RNA-Seq of whole kidneys of Six2Cre+TFAP2Afl/flTFAP2Bfl/WT mice and control littermates

city: Charlestown

first: Alexander

last: Marneros

address: 13th Street

institute: Massachusetts General Hospital

summary: RNA-Seq of kidneys lacking the gene TFAP2A in the nephron and that are heterozygous for TFAP2B

overall_design: 4 whole kidneys of Six2Cre+TFAP2Afl/flTFAP2Bfl/WT mice and control littermates were used for RNA-Seq


title: Next Generation Sequencing facilitated analysis of gene expression differences in the subthalamic nucleus (STN) between Parkinson's and Normal post-mortem human brains

city: Auckland

first: Xi

middle: Hua

last: Wu

state: Auckland

address: 85 Park Road, Grafton

department: Centre for Brain Research

country: New Zealand

institute: University of Auckland

summary: Parkinson’s disease (PD) is a progressive neurodegenerative movement disorder with the characteristic feature of extensive death of dopaminergic neurons in the substantia nigra. The global decrease in dopamine levels within the basal ganglia leads to the emergence of distinctive pathophysiology in multiple signalling midbrain regions. The subthalamic nucleus (STN) is one of the critical basal ganglia nuclei affected, which displays elevated excitatory activation in PD and contributes to the cardinal hypokinetic motor symptoms. In order to better understand the role of the STN in PD, we have investigated the human STN transcriptome in seven PD and nine neurologically normal post-mortem brains. Differential gene expression analysis conducted between PD and normal brains yielded 159 genes with changes in expression, 128 up-regulated and 31 down-regulated, in the PD STN. Collectively, the up-regulated genes showed enrichment in multiple cellular processes including neuroinflammation, immune response, regulation of cell death and blood vessel homeostasis. Conversely, the down-regulated genes showed profound dysregulation of dopamine biosynthetic and metabolic processes. The differential transcription of a subset of genes identified in the transcriptome analysis was then further validated using the Nanostring nCounter system, confirming expression differences in 21 of 26 assessed genes. Furthermore, the transcription factor MafF, which showed the largest fold change from both RNA-seq and nanostring was demonstrated to be induced under pro-inflammatory conditions. Although the STN constitutes one of the brain regions that shows minimal neurodegeneration in PD, our differential gene expression data suggest that this structure is fundamentally altered in PD.

overall_design: RNA-seq analysis of the human subthalamic nucleus in 16 cases, 9 controls and 7 PD

middle: H

first: Suzanne

last: Reid

first: Henry

last: Waldvogel


title: RNA-seq analysis of Huh7 cells based on PANK1 knockdown

status: Public on Apr 30 2021

city: Changsha

first: yuan

middle: yu

last: zi

address: Changsha Xiangya Road

institute: Xiangya hospital

summary:
Purpose: Analysis of the regulatory network involved in PANK1 in liver cancer cells .
Methods: mRNA profiles of Huh7-shPANK1 and Huh7-shNC group  were generated by deep sequencing,  using Illumina Novaseq platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets.
Results: We identified 681 differential genes, of which 441 were up-regulated and 240 were down-regulated. In GO enrichment analysis, the biological process is mainly in the cell ions homeostasis and the molecular function is mainly in the defense response to virus、defense response to other organism and receptor ligand activity. KEGG analysis shows that differential genes are enriched in Systemic lupus erythematosus , Alcoholism and influenza A pathways.
Conclusion: Based on RNA-seq analysis, the regulatory network involved in PANK1 in liver cancer is depicted.

first: Yuyuan

last: Zi

first: Yuezhen

last: Deng

first: Lunquan

last: Sun


title: RNA-seq analysis of HT8 cells based on PPDPF knockdown

summary:
Purpose: Analysis of the regulatory network involved in PPDPF in colon cancer cells.
Methods: mRNA profiles of HT8-cas1 and HT8 group were generated by deep sequencing,  using Illumina Novaseq platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets.
Results: We identified 3233 differential genes, of which 1877 were up-regulated and 1356 were down-regulated. In GO enrichment analysis,the biological process is mainly in the cell ions homeostasis and the molecular function is mainly in viral life cycle,response to virus,neutrophil activation, and the transmembrane signaling receptor activity. KEGG analysis shows that differential genes are enriched in Epstein-Barr virus infection ,Glutathione metabolism and Proteasome pathways.
Conclusion: Based on RNA-seq analysis, the regulatory network involved in PPDPF in colon cancer .

overall_design: mRNA profiles of HT8-cas1 and HT8 group

first: Liyu

last: Liu


title: SET1B facilitates activation of the hypoxia response through site-specific histone methylation [ChIP-seq_2]

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Hypoxia-inducible transcription factors (HIFs) are fundamental to the cellular adaptation to low oxygen levels but how they interact with chromatin and efficiently activate their target genes is unclear. Using genome-wide mutagenesis in human cancer cells, we define genes required for HIF transcriptional activation, and identify a requirement for the Histone 3 lysine 4 (H3K4) methyltransferase SET1B. Loss of SET1B leads to a selective reduction in HIF transcriptional activity in hypoxia, with SET1B driving expression of genes involved in angiogenesis rather than glycolysis, resulting in impaired tumour establishment in SET1B deficient xenografts.  Mechanistically, we show that SET1B is itself oxygen regulated, accumulates on chromatin in hypoxia, and is recruited to HIF target genes through HIF-1a. Accordingly, we show that the hypoxic induction of H3K4me3 at specific HIF targets is both HIF and SET1B dependent, and when impaired, decreases promotor acetylation and gene expression. Together, these findings reveal SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.

overall_design: We used ChIP-seq to determine HIF-1alpha, HIF-2alpha and HIF-1beta binding across the genome in control HeLa cells incubated in 1% oxygen  for 6 hr

first: James

last: Nathan

first: Olivia

last: Lombardi

first: Brian

last: Ortmann


title: SET1B facilitates activation of the hypoxia response through site-specific histone methylation

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

overall_design: Refer to individual Series


title: Effect of Aging on Mitochondrial Energetics in the Human Atria

city: Milwaukee

first: Arshad

last: Jahangir

state: WI

address: 2801 Kinnic Kinnic River Parkway, Suite 777

department: Cardiology

institute: Advocate Aurora Health

summary:
Energy production in myocardial cells occurs mainly in the mitochondrion. Although alterations in mitochondrial functions in the senescent heart have been documented, the molecular bases for the aging-associated decline in energy metabolism in the human heart are not fully understood.
The purpose of our study was to identify aging-related transcriptional changes in genes coding for mitochondrial proteins involved in substrate metabolism, oxidative phosphorylation system (OXPHOS), and the tricarboxylic acid (TCA) cycle, and to correlate these with the functional changes in the OXPHOS in human atrial appendage tissue from adult and aged patients free of atrial pathologies.

overall_design: We examined transcription profiles of genes coding for mitochondrial proteins in atrial tissue from aged (> 65 years old) and comorbidities-matched adult (< 65 years old) patients with preserved left ventricular function using high throughput microarray (Human Genome U133 Plus 2.0 arrays) and verified by RT-PCR.

first: Claudia

last: Preston


title: Transcriptomic analysis of mouse brain tissue treated by 5-ALA-mediated photodynamic therapy

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

institute: Henan University

summary: We report the application of 5-ALA ( 5-Aminolevulinic acid)-mediated photodynamic therapy on mouse brain  tissue, and further explored the impact of PDT on nervous system.

overall_design: Examination of transcriptome levels in mouse brain tissue treated with PDT.

first: Bingyang

last: Shi


title: Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Upon competence‐inducing nutrient‐limited conditions, only part of the Bacillus subtilis population becomes competent. Here, we separated the two subpopulations by fluorescence‐assisted cell sorting (FACS). Using RNA‐seq, we confirmed the previously described ComK regulon. We also found for the first time significantly downregulated genes in the competent subpopulation. The downregulated genes are not under direct control by ComK but have higher levels of corresponding antisense RNAs in the competent subpopulation. During competence, cell division and replication are halted. By investigating the proteome during competence, we found higher levels of the regulators of cell division, MinD and Noc. The exonucleases SbcC and SbcD were also primarily regulated at the post‐transcriptional level. In the competent subpopulation, yhfW was newly identified as being highly upregulated. Its absence reduces the expression of comG, and has a modest, but statistically significant effect on the expression of comK. Although expression of yhfW is higher in the competent subpopulation, no ComK‐binding site is present in its promoter region. Mutants of yhfW have a small but significant defect in transformation. Metabolomic analyses revealed significant reductions in tricarboxylic acid (TCA) cycle metabolites and several amino acids in a ΔyhfW mutant. RNA‐seq analysis of ΔyhfW revealed higher expression of the NAD synthesis genes nadA, nadB and nadC.

overall_design: 6 samples 2 replicates

first: Mirjam

last: Boonstra

first: Marc

last: Schaffer

first: Joana

last: Sousa

first: Luiza

last: Morawska

first: Siger

last: Holsappel

first: Petra

last: Hildebrandt

first: Praveen

last: Sappa

first: Hermann

last: Rath

last: de Jong

first: Michael

last: Lalk

first: Ulrike

last: Mäder

first: Uwe

last: Völker

first: Oscar

middle: P

last: Kuipers


title: Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish

city: Utrecht

first: Jeroen

last: den Hertog

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: We developed a ptpn6 knock-out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings.

overall_design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages (mpeg) were sorted in 384 well plates.

last: Bakker

first: Maaike

last: Allers

first: Sasja

last: Blokzijl-Franke

first: Herman

last: Spaink


title: Genome-wide maps of 5hmC in control and Tet3 inactivated lung smooth muscle cells

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: To examine the influences for 5hmC enrichment on genome wide after Tet3 inactivation, we determined the enrichment profiles of 5hmC, the direct demethylated target of Tet3, by hMeDIP-seq with genomic DNA from control and Tet3 inactivated lung smooth muscle cells

overall_design: Examination of 5hmC genomic distribution of control and Tet3 inactivated lung smooth muscle cells

first: Fan

last: Wu


title: Glioblastoma cells acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion [WGS]

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

institute: University of Edinburgh

summary: Glioblastoma multiforme (GBM) is an aggressive brain tumour. Current immunotherapy approaches have been unsuccessful, highlighting the need to determine underlying mechanisms of immune evasion. Here, we developed syngeneic immunocompetent mouse models of GBM to explore this. GBM stem cells (GSCs) were serially transplanted through immunocompetent hosts, which uncovered an acquired capability to escape immune clearance through an enhanced immunosuppressive tumour microenvironment. Mechanistically, this was not elicited via genetic selection of tumour subclones, but through an epigenetic immunoediting process wherein stable transcriptional and epigenetic changes in GSCs are enforced following immune attack. These include activation of interferon signalling modules, myeloid-affiliated transcription factors and chemokines, which leads to increased recruitment of tumour-associated macrophages. Furthermore, we identify similar epigenetic and transcriptional signatures in human mesenchymal subtype GSCs. We conclude that epigenetic immunoediting may drive an acquired immune evasion program in the most aggressive mesenchymal GBM subtype by reshaping the tumour immune microenvironment.

overall_design: Whole genome sequencing for WT BL6,  engineered mouse neural stem cells (NPE, Nf1 -/-, Pten -/-, EGFRvIII), and tumour derived engineered mouse neural stem cells (NPE IE).

first: Benjamin

first: Leanne

last: Bradley

first: Steven

last: Pollard


title: Glioblastoma cells acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion [BiSulfite-seq]

type: Methylation profiling by high throughput sequencing

overall_design: WT BL6, and engineered mouse neural stem cells with common GBM driver mutations in double and triple combinations (NP, NPE), profiled by RRBS.


title: Glioblastoma cells acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion


title: Bat3 regulates T cell terminal differentiation in an mTORC2-dependent manner

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

institute: Broad Institute of MIT and Harvard

summary: Human leukocyte antigen B (HLA-B)-associated transcript 3 (Bat3), also called Bcl-2-associated athanogene 6 (BAG6), is a multifunctional adapter protein that was previously shown to bind to the cytoplasmic tail of the checkpoint inhibitor Tim-3 and inhibit its downstream signaling pathway.  Using mouse genetic models, we now demonstrate that deficiency of Bat3 selectively in T cells elicits a profound exhaustion phenotype and dampens autoreactive T cell-mediated neuroinflammation. Mechanistically, Bat3 acts as a critical mTORC2 inhibitor to suppress Akt function. As a result, Bat3 deficiency leads to increased Akt activity, and FOXO1 phosphorylation, indirectly promoting Prdm1. Transcriptional analysis of myelin antigen-specific CNS-infiltrating Bat3 deficient CD4 T cells revealed upregulation of dysfunction-associated genes concomitant with downregulation of genes associated with T cell effector function. Genes upregulated in Bat3cko T cells were significantly enriched for Prdm1(BLIMP1) and exhaustion gene signatures suggesting the absence of Bat3 can trigger T cell dysfunction even under highly inflammatory autoimmune conditions. Taken together, in this paper we identify a novel mechanism by which Bat3 not only directly suppresses Tim-3 signaling, but also plays a critical role in controlling the mTORC2-Akt-Blimp-1 pathway thereby suppressing the induction of the co-inhibitory module and preventing terminal differentiation and dysfunction of T cells.

overall_design: RNA-Seq comparision of Bat3cKO and Tim3cKO CNS-infiltrating Th1 cells from mice undergoing EAE.

first: Chen

last: Zhu

first: Karen

middle: O

last: Dixon

first: Vijay

last: Kuchroo


title: Glioblastoma cells acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion [RNA-seq]

overall_design: WT BL6, and engineered mouse neural stem cells with common GBM driver mutations in single, double and triple combinations, profiled by RNA-seq in triplicate.


title: Genome wide expression change by RNF31 knocking down in MCF-7 cells

city: Shenzhen

first: Juntao

last: Xu

state: Guangdong

address: Yuehai Subdistrict, Nanshan District

institute: Philrivers

summary: We aim to the investigate the role of RNF31 in breast cancer progression. MCF-7 cells were used as the model and RNF31 was silenced by siRNA.

overall_design: The MCF-7 cells were treated with 50nM stramble siRNA and siRCF31. After 48 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: Jian


title: LKB1 inactivation initiates a chromatin remodeling cascade to drive metastatic progression

city: STANFORD

first: Jeffrey

middle: Michael

last: Granja

state: CA

address: 279 Campus Drive W

department: Genetics

institute: Stanford University

summary: Metastasis is the leading cause of cancer-related deaths, enabling cancer cells to expand to secondary tumor sites and compromise systemic organ function1. Given that primary tumors and metastases often share the same constellation of functional driver mutations2–4, the mechanisms driving their distinct phenotypes are unclear. Here, we show that inactivation of a frequently mutated tumor suppressor gene, liver kinase B1 (LKB1), has evolving effects throughout lung cancer progression, differentially re-programming the epigenetic landscape of early-stage primary tumors compared to late-stage metastases. By integrating genome-scale CRISPR/Cas9 screening with bulk and single-cell multi-omic analyses, we unexpectedly identify LKB1 as a master regulator of chromatin state in lung adenocarcinoma primary tumors. Using an in vivo model of metastatic progression, we further reveal that loss of LKB1 activates the early endoderm transcription factor SOX17 in metastases and metastatic-like sub-populations of cancer cells within primary tumors. SOX17 expression is both necessary and sufficient to drive a second wave of epigenetic changes in LKB1-deficient cells that enhances metastatic ability. Overall, our study demonstrates how the downstream effects of an individual driver mutation can change throughout cancer development, with implications for stage-specific therapeutic resistance mechanisms and the gene regulatory underpinnings of metastatic evolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk ATAC-seq and bulk RNA-seq was performed on immortalized cell lines and murine lung adenocarcinoma primary tumors and metastases following gene perturbations and/or different treatment conditions. Single-cell ATAC-seq was performed on murine lung adenocarcinoma primary tumors of different genotypes. Genome-wide CRISPR screen was performed on immortalized cell lines of two different genotypes.

first: Pierce

last: Sarah

first: Granja

last: Jeffrey


title: Effect of senktide administration on the embryo collected from superovulated cows

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

institute: Nagoya University

summary: To clarify the effect of intravenous senktide administration on the quality and developmental stage of collected embryo from superovulated cows, mRNA expression profiles of the embryo were investigated. Hierarchical cluster analysis with the expression levels of all genes was divided these cows into three clusters. First cluster was composed of control cows, second cluster contained senktide (30 nmol/min, 2h) treated cows and third cluster consisted of senktide (300 nmol/min, 2h) treated cows.

overall_design: At 48 h after the start of superovulated treatment, senktide solutions were intravenously infused (30 or 300 nmol/min) for 2 h in cows. All cows were inseminated with frozen–thawed semen 108 and 120 h after the start of superovulated treatment. On 7 days after the first artificial insemination, embryos were collected by nonsurgical uterine flushing. Then, the mRNA expression profiles of the embryo were investigated to clarify the effect of intravenous senktide administration on the quality and developmental stage of collected embryo from superovulated cows.

first: Sho

last: Nakamura

first: Shiori

last: Minabe

first: Satoshi

last: Ohkura

first: Koji

last: Kimura


title: Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [m6A-RIP-seq]

city: Shanghai

first: Huabing

last: Li

address: 280 Chongqing South Rd, Building #5-6th floor, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

summary: Total RNAs were isolated from WT_CON, KO_CON, WT_LPS and KO_LPS Raw 264.7 cells, subjected to standard m6A RIP protocol. The libraries were generated with IPed and Input RNAs and subjected to Sequencing. Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat , and gene expression levels were measured by Cufflinks.

overall_design: m6A modified RNAs were immunopriciptated and enriched with m6A speicifc antibody from WT_CON, KO_CON, WT_LPS and KO_LPS Raw 264.7 cells, and subjected to deep sequencing, in duplicate, using illumina HiSeq 2000.

first: Jiyu

last: Tong


title: Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation


title: Impact of Erlotinib incubation on primary human keratinocytes and fibroblasts

city: Bonn

first: Sarah

last: Kemski

address: Kurt-Georg-Kiesinger-Allee 3

department: Research

institute: Federal Institute for Drugs and Medical Devices

summary: We used next generation sequencing to analyze the effects of Erlotinib incubation on primary human keratinozytes and fibroblasts. We compared miRNA expression in cell lines more reactive to Erlotinib against cell lines less reactive to Erlotinib

overall_design: 12 primary human keratinocyt cell lines (6 sensitive and 6 insensitive) and 8 fibroblast cell lines (4 sensitive and 4 insensitive) were incubated with DMSO (0.05%) or Erlotinib (5 µM) for 2 h (keratinozytes) or 24 h (fibroblasts) and then stimulated with EGF (4 nM) for 5 min (DMSO, DMSO + EGF, Erlitinib + EGF). miRNA expression was compared between cell lines more reactive to Erlotinib and cell lines less reactive.

first: Catharina

last: Scholl

first: Michael

last: Steffens

first: Denna

last: Tabari

first: Tina

last: Wirtz

first: Tim

last: Nümm


first: Jeroen

last: den Hertog

summary: Loss of kdrl marks the shift from embryonic to adult HSPCs in zebrafish embryos

overall_design: CHTs (5dpf) were dissected and dissociated, using FACS sorting HSPCs were isolated and single cell RNA seq was performed.

first: Sasja

last: Blokzijl-Franke

first: Maja

last: Solman


title: Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [Amplicon-seq]

summary: Customized pooled RNA Binding Protein (RBP) CRISPR libraries were applied to macrophage cell line Raw 264.7 cells to identify RBPs that are critical for LPS activated TNFa production.sgRNAs that enriched in TNFa-low, TNFa-High and pre-sort populations were sequenced and significant enriched genes were retrieved with MAGeCK test subcommand.

overall_design: Examination of single guide RNAs (sgRNAs) enrichment in sorted cell populations based on TNFa expression


title: Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [RNA-seq]

summary: The involvement of m6A modification in macrophage activation has been validated in our study that the expression of TNF-α in Mettl3-depleted Raw 264.7 cells stimulated with LPS were markedly reduced in comparison to control cells. To further explore the biological effects of m6A deficiency macrophages, we performed RNA sequencing analysis of Mettl3-KO and WT control Raw 264.7 cells upon LPS treatment. The GO enrichment analysis documented that the downregulated transcripts in Mettl3-KO Raw 264.7 cells were enriched in innate immune response related to defense and external stimulus. Notably, transcripts of the downstream components of the TLR4 signaling pathway, such as proinflammatory cytokines (Tnf-α, Il-6, Il-1β, Il-18,and Il-23) and co-stimulation molecules (Cd86), were downregulated in Mettl3-deficient cells, suggesting that METTL3 has a critical function in controlling the innate immune response of Raw 264.7 macrophages.

overall_design: RNA samples from Mettl3-KO and WT control Raw 264.7 cells upon LPS treatment were collected, and then RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer's instructions (Illumina).

first: Yongbo

last: Liu


title: SET1B facilitates activation of the hypoxia response through site-specific histone methylation [ChIP-seq_1]

first: David

last: Mole

summary: Hypoxia-inducible transcription factors (HIFs) are fundamental to the cellular adaptation to low oxygen levels but how they interact with chromatin and efficiently activate their target genes is unclear. Using genome-wide mutagenesis in human cancer cells, we define genes required for HIF transcriptional activation, and identify a requirement for the Histone 3 lysine 4 (H3K4) methyltransferase SET1B. Loss of SET1B leads to a selective reduction in HIF transcriptional activity in hypoxia, with SET1B driving expression of genes involved in angiogenesis rather than glycolysis, resulting in impaired tumour establishment in SET1B deficient xenografts.  Mechanistically, we show that SET1B is itself oxygen regulated, accumulates on chromatin in hypoxia, and is recruited to HIF target genes through HIF-1a. Accordingly, we show that the hypoxic induction of H3K4me3 at specific HIF targets is both HIF and SET1B dependent, and when impaired, decreases promotor acetylation and gene expression. Together, these findings reveal SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.

overall_design: We used ChIP-seq to determine locus-specific changes in H3K4me3 levels across the genome in control, HIF1b or SET1B deficient HeLa cells incubated in 21% or 1% oxygen  for 6 hr

first: James

middle: A

last: Nathan

first: Brian

last: Ortmann


title: Multivalent histone and DNA engagement by the triple reader module of ZMYND8 directs the recruitment of a transcriptional network to genes to regulate gene expression

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

institute: Oxford University

summary: Elucidation of multivalent interactions involving both DNA and histone post-translational-modifications (PTMs) is essential for providing insight into complex biological functions. We report here the high resolution crystal structure of the N-terminal triple reader module (PHD-Bromo-PWWP) of ZMYND8, which forms a stable unit, capable of simultaneously recognizing histone PTMs and providing a charged platform for DNA interaction. Monte Carlo simulations provide a model whereby the reader module directly engages the core nucleosome particle, extracting the entire histone H3 tail and initiating contacts with the DNA super-coil structure. Systematic mutation of these interaction interfaces reveals cooperativity within the ensemble. Single domain disruption destroys the functional network of interactions initiated by ZMYND8, which impairs recruitment to sites of DNA damage and alters transcription. Taken together, our results establish an important role of the ZMYND8 multivalent reader module in nucleosome binding and chromatin function.

overall_design: Total RNA was extracted from (1) HEK293 T-Rex cells; (2) HEK293 cells stably expressing ZMYND8 following 24 h induction with 100 nM of doxycycline; (3) HEK293 cells stably expressing ZMYND8 mutant (N228F) following 24 h induction with 100 nM of doxycycline; (4) HEK293 T-Rex cells following 48 h treatment with 100 pmol of siRNA (CTRL);  (5) HEK293 T-Rex cells following 48 h treatment with 100 pmol of siZMYND8. Each condition was performed in biological triplicates.

first: Christine

last: Blancher


title: Hepatic transcriptomics of squalene in male Apoe-deficient mice on Western diet

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

summary: Background and Purpose: Squalene is the main hydrocarbon present in extra virgin olive oil and it has been reported to have anti-steatotic properties in different animal models. The aims of this study were to investigate its effects on liver transcriptomics in Male C57BL/6J Apoe-deficient mice. Experimental Approaches: Male C57BL/6J Apoe-deficient mice were fed a purified Western diet with or without squalene during 11 weeks and hepatic squalene content was assessed. Hepatic transcriptomic changes were studied and confirmed by RT-qPCR. Key Results: Squalene supplementation increased its hepatic content. The Cyp2b10 and Cyp2c55 gene expressions were significantly up-regulated by the squalene intake in all animal models, with independence of sex, sexual hormones, dietary fat content, genetic background and dose, and were strongly associated with antioxidant defense capacity and with lipid content and composition. Conclusions and Implications: hepatic squalene exerts its activity through overexpression of these cytochromes and their changes in virgin olive oil diets may be due to squalene.

overall_design: Two-condition experiment, livers of squalene-containing Western diet vs those Western diet fed mice.  Biological replicates: 4 hepatic RNA pools were prepared for control male mice receiving Western diets and another four for squalene-supplemented male Apoe-deficient mice on the same diet, each pool consisting of RNA from 2 or 3 animals.

first: Clara

last: Gabás-Rivera

first: Enrique

last: Jurado-Ruiz

first: Araceli

last: Sánchez-Ortiz

first: Eduardo

last: Romanos

first: Roberto

last: Martínez-Beamonte

first: María

last: Navarro

first: Joaquín

middle: C

last: Surra

first: Carmen

last: Arnal

middle: J

last: Rodríguez-Yoldi

first: Valentina

last: Ruiz-Gutiérrez

first: Jesús


title: Checkpoint-mediated DNA polymerase e exonuclease activity curbing counteracts resection-driven fork collapse

city: Madrid

first: Mohammed

last: Al Mamun

state: Madrid

address: Calle Ramiro de Maeztu, 9

department: Cell and Molecular Biology

institute: CIB-CSIC

summary: DNA polymerase epsilon (Pole) carries out leading strand synthesis with high fidelity owing to its exonuclease activity. Pole polymerase and exonuclease activities are in balance, due to partitioning of nascent strands between catalytic sites, so that net end resection occurs when synthesis is impaired. Stalling of chromosomal DNA synthesis activates replication checkpoint kinases, required to preserve the functional integrity of replication forks. We found that Pole is phosphorylated in a Rad53CHK1-dependent manner upon fork stalling, likely to limit Pole-driven nascent strand resection that causes replication fork collapse. In stress conditions Pole phosphorylation occurs on serine 430 of the Pol2 catalytic subunit. A S430 phosphomimic limits strand partitioning and exonucleolytic processivity, while non-phosphorylatable Pol2-S430A bypasses checkpoint regulation causing stalled fork resection and collapse. We propose that checkpoint kinases switch Pole to an exonuclease-safe mode by curbing active site partitioning thus preventing nascent strand resection and stabilizing stalled replication forks.

overall_design: Comparative Genome Sequencing (CGS) was carried out as decribed (Frattini et al., Mol Cell 2017). In brief, genomic DNA was extracted from cells arrested in G1 or after different times following release into S-phase in the presence of hydroxyurea (HU). Genomic DNA was sequenced, reads were mapped to the reference genome for each sample and S/G1 read number ratios were used to plot replication profiles along the S.cerevisiae genome.

first: Grazia

last: Pellicanò

first: Dolores

last: Jurado

first: Sara

last: Villa-Hernández

first: Xingyu

last: Yin

first: Michele

last: Giannattasio

first: Michael

last: Lanz

first: Marcus

last: Smolka

first: Joseph

last: Yeeles

first: Marco

last: Foiani

first: Katsuhiko

last: Shirahige

first: Miguel

last: García-Díaz

first: Rodrigo

last: Bermejo


title: Induction of stable human FOXP3+ Tregs by a parasite-derived TGF-β mimic

status: Public on Apr 29 2021

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

institute: Chiba University

summary:
Objectives. Immune homeostasis in the intestinal tract is tightly controlled by FOXP3+ regulatory T cells (Tregs), with loss of this Treg-mediated control linked to development of chronic conditions, such as inflammatory bowel disease (IBD). As a mechanism of immune evasion, several species of intestinal parasites strengthen intestinal Treg activity, leading to the notion that parasite-derived products could be harnessed and used as an immunoregulatory therapy for IBD. It has been previously demonstrated that the parasite Heligmosomoides polygyrus secretes a molecule (Hp-TGM) which mimics the ability of TGF-β to induce FOXP3 expression in CD4+ T cells. Our aim was to investigate whether Hp-TGM could induce human FOXP3+ Tregs as a potential therapeutic approach.
Methods. Human CD4+ T cells from healthy volunteers were expanded in the presence of Hp-TGM or mammalian TGF-β. The induction of Tregs was measured by flow cytometric detection of FOXP3 and other Treg markers, such as CTLA-4 and CD25. Epigenetic changes were detected using ChIP-Seq and pyrosequencing of FOXP3. Treg phenotype stability was assessed following inflammatory cytokine challenge and Treg function was assessed by cellular co-culture suppression assays and secreted cytokines measured by cytometric bead array.
Results. Hp-TGM efficiently induced FOXP3 expression (>60%), in addition to another Treg functional marker CTLA-4. Hp-TGM caused epigenetic modification of the FOXP3 loci to a greater extent than did TGF-β. Hp-TGM-induced Tregs also had superior suppressive function compared to TGF--induced Tregs, and retained their phenotype following exposure to inflammatory cytokines. Hp-TGM also induced a Treg phenotype in in vivo differentiated Th17 cells, indicating its potential to re-program memory cells to enhance immune tolerance.
Conclusion. These data indicate Hp-TGM has the potential to be used to generate stable human FOXP3+ Tregs to treat IBD.

overall_design: Examination of H3K27Ac in TGFbeta or TGM primed human CD4 T cells

first: Laura

last: Cook

first: Steven

middle: F

last: Ziegler

first: Megan

middle: K

last: Levings


title: Nanostring human miRNA panel: exosome fraction from peripheral blood of pancreatitis patients versus healthy

city: Gainesville

first: Rob

last: Maile

state: FL

department: Surgery

institute: University of Florida

summary:
827 human miRNA standard human panel
Plasma derived extracellular vesicles (EV)/exosomes can serve as markers of cell damage/disease but can also have therapeutic utility depending on the nature of their cargo, such as miRNA.  Currently there are challenges and lack of innovations regarding early diagnosis and therapeutic options within different aspects of management of patients suffering from chronic pancreatitis (CP). Use of exosomes as biomarkers for pancreatic health, and/or or as adjuvant therapy would make a difference in management of these patients. To explore the feasibility of this approach, we characterized the miRNA cargo of exosomes purified from CP patients, and compared it to those from healthy participants.
Methods:
EVs were isolated from plasma of 15 CP patients and 10 healthy controls. Nanoparticle Tracking Analysis was used to determine frequency and size while NanoString technology was used to characterize the miRNA cargo. Relevant clinical parameters were correlated with these EV/exosome characteristics.
Results:
~30 miRNA species were identified to have significantly (p<0.05) different expression in exosomes from individuals with CP compared to healthy individuals; ~40 miRNA were differentially expressed in exosomes from pre-diabetic versus non-diabetic CP patients. miR-579-3p, while exhibiting significantly lower (~16-fold) expression in exosomes from CP compared to healthy individuals and lower (~24-fold) in CP narcotic users compared to the less severe CP in non-users, is actually enriched (~32-fold) within exosomes in pre-diabetic CP patients compared to non-diabetic CP patients. A unique pattern was identified in female CP patients.
Conclusions:
These first of a kind data support the prospect of using a bioinformatics approach to assess pancreatic health,  and their therapeutic potential in CP patients.

overall_design: Two groups were enrolled: Group 1: patients diagnosed with chronic pancreatitis (CP1-11) and Group 2: normal healthy volunteers as a control (H1-10).  In Group 1, chronic pancreatitis was diagnosed by radiographic imaging, and/or decreased stool elastase levels, and/or genetic mutation of hereditary chronic pancreatitis along with correlative symptoms.

first: Robert

first: Chirag

last: Desai


title: ChIPseq experiments for chromatin modification in S.cerevisiae upon truncations of CTR9

city: Boston

first: Stephen

last: Buratowski

state: MA

address: 240 Longwood Avenue

department: BCMP

institute: Harvard Medical School

overall_design: Detection of global H3K36 di and tri- methylation, H3K4 di and tri metyhlation, total H3 and Rpb3 upon expression of WT CTR9, ΔΤ CTR9, ΔC CTR9 or ΔΤC CTR9 in S.cerevisiae

first: Steve

first: Adam

last: Volanakis


title: Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis

city: Orsay

first: Sanchari

last: Sircar

address: Batiment 630 Rue Noetzlin

country: France

summary: Previous studies in animals have shown that polycomb targets marked with H3K27me3 can establish interactions between them, forming a repressive chromatin hub (Lanzuolo et al., 2007; Cheutin and Cavalli, 2014). In plants few studies suggested that H3K27me3 may act directly or indirectly to regulate the interactivity of polycomb marked genes. However, several aspects of the molecular function of the H3K27me3 histone modification on the 3D chromatin architecture remained obscure. To decipher the impact of H3K27me3 levels on loop formation, we combined genetics, 3D epigenomics and transcriptomic approaches. By using the ref6 mutant, defective for a histone demethylase, that displays ectopic accumulation of H3K27me3, we demonstrated that H3K27me3 is important to trigger chromatin loop formation. Reciprocally, using clf mutant, a histone methyltransferase mutant that displays a strong reduction of H3K27me3 we found that a reduction of the H3K27me3 leads to the decrease of interactions inside the polycomb repressive domain. Surprisingly, we observed that regions losing H3K27me3 in clf establish new interactions with regions marked with the H3K9ac active histone modification, showing that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether our results demonstrate that the 3D organization of the genome is tightly linked to histone modifications that trigger the formation of chromatin domains associated with gene co-regulation, thereby allowing proper plant development and in which H3K27me3 is a key regulator of chromatin topology at global and local scales.

overall_design: H3K27me3 histone modification on the 3D chromatin architecture in Arabidopsis

first: Ying

last: Huang

last: Sicar

first: David

last: Latrasse

first: Moussa

last: Benhamed


title: Deconvoluting global cytokine signaling networks in natural killer cells [ATAC-Seq]

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Cytokine signaling via signal transducer and activator of transcription (STAT) proteins is crucial for optimal antiviral responses of natural killer (NK) cells. However, the pleiotropic effects of both cytokine and STAT signaling preclude the ability to precisely attribute molecular changes to either source. In this study, we employ a multi-“omics” approach to deconstruct and rebuild the complex interaction of three major STAT signaling pathways in NK cells. We uncover a global STAT4-STAT5 cooperative axis that is distinct and sometimes antagonistic to the STAT1 axis. We generate a network of STAT targets that highlights an integrated negative feedback loop, and demonstrate distinct STAT modes of epigenetic regulation. Finally, we identify shared signatures between mouse in vitro profiles and profiles from viral infection and humans, highlighting clinically translatable targets. Overall, we begin to unravel the intricate crosstalk between cytokine signaling pathways, and offer a valuable resource for improving cellular immunotherapy.

overall_design: ATAC-seq was performed on ex-vivo NK cells stimulated with various cytokine combinations.

middle: M

first: Joseph

last: Sun