title: Estrogen-induced lncRNA, LINC02568, promotes estrogen receptor-positive breast cancer development and drug resistance through both in trans- and in cis-mechanisms

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

summary: Estrogen and estrogen receptor (ER) signaling play critical roles in the development of ER-positive breast cancer, and endocrine therapy is the frontline treatment for ER-positive breast cancer patients. However, the primary and acquired resistance to endocrine therapy including tamoxifen and fulvestrant remains as the major challenge in the clinic. Here, we identified an estrogen-induced lncRNA, LINC02568, through transcriptomic analysis, which is highly expressed in ER-positive breast cancer. LINC02568 is functional important in ER-positive breast cancer cell growth in vitro and tumorigenesis in vivo as well as endocrine therapy resistance. Mechanically, we demonstrated that LINC02568 regulates, in trans, estrogen/ERα-induced gene transcriptional activation by sponging miR-1233-5p to stabilize ESR1 mRNA in the cytoplasm. Meanwhile, LINC02568 contributes to tumor-specific pH homeostasis in breast cancer cells by regulating CA12 in cis in the nucleus. The dual functions of LINC02568 together contribute to breast cancer cell growth and tumorigenesis as well as endocrine therapy resistance. Antisense oligonucleotides (ASO) targeting LINC02568 significantly inhibits ER-positive breast cancer cell growth in vitro and tumorigenesis in vivo as well as resensitize tamoxifen-resistant cells to tamoxifen. Furthermore, combination treatment with ASO targeting LINC02568 and tamoxifen exhibits synergistic effect on tumor growth. Taken together, our findings revealed dual mechanisms of LINC02568 in regulating ERα signaling and pH homeostasis in ER-positive breast cancer, and indicated that targeting LINC02568 might represent a potential therapeutic avenue in clinic.

overall_design: RNA-seq performed in this study was designed to understand the molechular mechanisms undyling LINC02568 in estrogen-induced gene transcriptional activation.

first: Wen

first: Xue

last: Chen


title: MYC confers vulnerability to dual inhibition of CDK12 and CDK13 in high-risk Group 3 medulloblastoma

status: Public on Sep 13 2023

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

type: Expression profiling by high throughput sequencing

summary: To investigate the effect of CDK12/13 inhibition and MYC over-expression on gene expression of high-risk Group 3 medulloblastoma cells, we established D341 cells treated or not with 100 nM THZ531 for 6 hours and silenced (siMYC) or not (siCtrl) for MYC expression for 48 hrs, respectively.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THZ531- or DMSO-treated and siMYC or siCtrl D341 cells. Each sample has 3 biological repeats.

first: Consuelo

last: Pitolli

first: Alberto

last: Marini

first: Marika

last: Guerra

first: Marco

last: Pieraccioli

first: Veronica

last: Marabitti

first: Francesca

last: Nazio

first: Fernando

last: Palluzzi

first: Luciano

last: Giacò

first: Francesco

last: Cecconi

first: Gianpiero

last: Tamburrini

first: Claudio

last: Sette

first: Vittoria

last: Pagliarini


title: Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array based on comparison with the individual samples

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

summary: The pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K array are lacking. A previous study demonstrated that the methylation levels obtained from individual samples were accurately replicated using pooled samples but did not address epigenome-wide association study (EWAS) statistics. The DNA quantification method, which is important for the homogeneous mixing of DNA in the pooled sample method, has since become fluorescence-based, and additional factors need to be considered including the resolution of batch effects of microarray chips and the heterogeneity of the cellular proportions from which the DNA samples are derived. In this study, four pooled samples were created from 44 individual samples, and EWAS statistics for differentially methylated positions (DMPs) and regions (DMRs) were conducted for individual samples and compared with the statistics obtained from the pooled samples.

overall_design: Bisulfite-converted pooled blood DNA were hybridized into the Illumina Infinium Methylation EPIC Kit array

first: Akemi

last: Tomoda


title: Gene expression and splicing profiles across models of TTDN1 deficiency

city: St Louis

first: Sridhar

last: Nonavinkere Srivatsan

address: 660 S Eucild Ave

country: USA

institute: WashU School Of Medicine

summary: The molecular networks disrupted in Non-photosensitive trichothiodystrophy (NP-TTD) are largely uncharacterized. NP-TTD is linked to mutations in the gene encoding TTDN1, an uncharacterized protein thought to have functions in splicing or trasncription . The goals of this study are to identify splicing and gene expression defects occuring in multiple models of TTDN1 deficiency, including U2OS and Hela-S cell lines, as well as in cortical tissue from TTDN1 deficient mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profiles from WT and TTDN1 -/- U2OS and HeLa-S cell lines, as well as from 8 week old wild-type (WT) and knockout (KO) mice were generated by deep sequencing, in triplicate (cell lines) or in quintuplicate (mice), using Illumina Novaseq 6000 2x150bp. The sequence reads that passed quality filters were used to determine differential gene expression, gene length, splicing differences, and lariat identification between KO and WT samples.

first: Brittany

middle: A

last: Townley

first: Nima

last: Mosammaparast


title: Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1

city: Washington

first: Natalia

last: Soriano-Sarabia

state: DC

address: 2300 I St. NW

department: Microbiology Immunology and tropical Medicine

institute: George Washington University

summary: Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy 1. Current research efforts to cure HIV-1 infection include “shock and kill” strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells 2. However, the modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy 3,4. Aminobisphosphonates that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies 5. Here, we show the use of aminobisphosphonates as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that aminobisphosphonates induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin. RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further of alendronate-mediated latency reversal and activation of immune effector cells.Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of aminobisphosphonates to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.

overall_design:
Resting CD4 (rCD4) T cells were magnetically isolated from peripheral blood mononuclear cells (PMBC) from virally suppressed people living with HIV. All participants provided informed consent under an IRB approved study protocol. Cells were exposed to 2.5ug/mL pamidronate for six hours and plated untreated cells were used as a control. Cells were then harvested, pelleted and stored at -80. RNA was isolated using the automated KingFisher (Thermofisher Scientific, Waltham, MA). All RNA samples were assayed for integrity, concentration, and fragment size on a TapeStation system (Agilent, Inc. Santa Clara, CA).
Gene expression profiles from rCD4T cells were generated by RNA-sequencing using an Illumina HiSeq. Library was constructed using Truseq RNA Exome library construction following the steps: Fragmenting RNA, Synthesizing 1st Strand cDNA, Synthesizing 2nd Strand cDNA, Adenylating 3' Ends, Ligating Adaptors, Enriching DNA fragments, Hybridizing Probes to library, capturing Hybridized Probes, performing a 2nd Hybridization, performing a 2nd capture, Clean-up of captured library was performed via AMPure XP Beads followed by amplification of the enriched library, and a final clean-up of amplified enriched library using AMPureXP beads. Libraries were prepared on an Agilent Bravo Automated Liquid Handling System. Indexed libraries were prepared and run on HiSeq4000 to generated paired end 75 base pair reads which generated approximately 90 million reads per sample library with a target of greater than 90% mapped reads.

first: Marta

last: Sanz

first: Ann Marie

middle: K

last: Weideman

first: Adam

middle: R

last: Ward

first: Matthew

middle: L

last: Clohosey

first: Susana

last: Garcia-Recio

first: Sara

last: Selitsky

first: Brendan

middle: T

last: Mann

first: Marie

last: Iannone

first: Chloe

middle: P

last: Whitworth

first: Alisha

last: Chitrakar

first: Carolina

last: Garrido

first: Jennifer

last: Kirchherr

last: Coffey

first: Yi-Hsuan

last: Tsai

first: Shahryar

last: Samir

first: Yinyan

last: Xu

first: Dennis

last: Copertino

last: Bosque

first: Brad

last: Jones

first: Joel

middle: S

last: Parker

first: Michael

middle: G

last: Hudgens

first: Nilu

last: Goonetilleke


title: G4-dependent DNA loops regulate gene expression [RNA-seq]

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: University of California Riverside

summary: RNAPII is mainly responsible for mRNA transcription and plays a vital role in gene expression. In light of the above results showing that cellular G4s are highly correlated with RNAPII-mediated DNA loops, we performed the RNA-seq to evaluate how G4-dependent long-range DNA interactions modulate gene expression. We revealed  that PDS treatment modulates the expression of not only genes with G4 in their promoters, but also those with promoters being connected with distal G4 through RNAPII-linked long-range DNA interactions.

overall_design: We performed RNA-seq with or without PDS treatment. Two biological replicates were done for each experiments.

first: Jun

last: Yuan


title: G-quadruplex DNA contributes to RNA polymerase II-mediated 3D chromatin architecture [HiChIP]

summary: High-order chromatin organization plays an important role in biological processes and disease development. Previous studies revealed a widespread occurrence of guanine quadruplex (G4) structures in the human genome, with enrichment in gene regulatory regions, especially in promoters. However, it remains unclear if G4 structures contribute to RNA polymerase II (RNAPII)-mediated long-range DNA interactions and transcription activity. In this study, we conducted an intuitive overlapping analysis of previously published data of RNAPII ChIA-PET (chromatin interaction analysis with paired-end tag) and BG4 ChIP-seq (chromatin immunoprecipitation followed by sequencing with the use of a G4 structure-specific antibody). We observed a strong positive correlation between RNAPII-mediated DNA loops and G4 structures in chromatin. Additionally, our RNAPII HiChIP-seq (in situ Hi-C followed by ChIP-seq) results showed that treatment of HepG2 cells with pyridostatin (PDS), a small-molecule G4-stabilization ligand, could diminish RNAPII-linked long-range DNA contacts, with more pronounced decreases being observed for those contacts involving G4 structure loci.

overall_design: We performed the HiChIP for POLR2A with or without PDS treatment. At least two replicates were done for each experiments.


title: Neutrophils Resist Ferroptosis and Promote Breast Cancer Metastasis through Aconitate Decarboxylase 1

city: Notre Dame

first: Yun

last: Zhao

state: Indiana

address: 100 Galvin Life Science Center

institute: University of Notre Dame

summary: Lung metastasis is the principal cause of breast cancer-related mortality. Neutrophils have emerged as an important component of the tumor microenvironment (TME), supporting tumor proliferation and mediating immunosuppression. Here, we show that aconitate decarboxylase 1 (Acod1) is highly expressed in tumor-infiltrating neutrophils and promotes breast cancer lung metastasis by supporting neutrophil survival in the TME. Acod1 expression is regulated by tumor-derived granulocyte-macrophage colony-stimulating factor (GM-CSF) through the JAK/STAT signaling pathway and CCAAT/enhancer-binding protein beta (C/EBPβ) transcription factor activity. Acod1 loss in tumor-infiltrating neutrophils leads to ferroptosis-like cell death, resulting in decreased frequency of neutrophils in the TME. Mechanistically, itaconate, the product of Acod1, activates nuclear factor erythroid 2-related factor 2 (Nrf2), resulting in upregulated antioxidant responses and decreased lipid-reactive oxygen species. Genetical deletion of Acod1 in neutrophils suppresses lung metastasis of breast cancer in mouse models by decreasing neutrophil-lymphocyte ratio and elevating cytotoxic T cell response. Importantly, genetic targeting of Acod1 enhances the anti-tumor efficacy of immune checkpoint blockade.  Overall, our findings reveal a mechanism of how immunosuppressive neutrophils survive in the harsh TME and support Acod1-targeting approaches for cancer treatment.

overall_design: Drop-seq of purified neutrophils from blood and tumor of Py7160-bearing mice

first: Zhao

last: Yun

first: Lu

last: Xin


title: SFKs overexpression suffices to change the gene expression landscape in unstimulated BJAB cells

city: Patras

first: Athanasios

middle: Nasir

last: Shaukat

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

summary: Whole transcriptome sequencing of untreated BJAB cells, and BJAB cells after inducing the ectopic expression of Lck or Lyn

overall_design: Whole transcriptome sequencing on the Ion torrent S5 platform

middle: N

first: Constantinos

last: Stathopoulos

first: Adamantia

last: Kouvela

first: Vassiliki

last: Stamatopoulou

first: Vasileios

last: Morfos

first: Kyriakos

last: Konnaris

first: Nikolaos

last: Koutras

first: Konstantina

last: Nika


title: Pregnancy Outcomes in Mouse Dams Exposed to Arsenic: The Role of CYR61 m6A Modification

city: hefei

first: yaping

middle: Ya

last: Song

address: No. 81, Meishan Road, Hefei City

department: department of toxicology

country: China

institute: Anhui Medical University School of Public Health

summary:
This study aimed to investigate the effects of gestational As exposure on placental and fetal development, and its underlying mechanisms.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different placental tissue

overall_design: Comparative gene expression profiling analysis of RNA-seq data to find the key regulatory molecule

first: Ya-Ping

first: De-Xiang

last: Xu


title: RNASeq data from OMP-52M51 acute treated T-ALL PDX mice

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

summary: We recently demonstrated that a human Notch1-specific neutralizing antibody (OMP-52M51) was very effective in T-ALL patient derived xenografts (PDX) bearing NOTCH1/FBW7 mutations. To evaluate the transcriptomic downstream effects of anti-NOTCH1 therapy, we perform RNA-Seq analysis in leukemia cells derived from PDTALL46 PDX mice after an acute treatment with control Ab or OMP-52M51.

overall_design: Cells from spleens of control (Ctrl Ab) or  OMP-52M51 antiboby acute treated mice were recovered for RNA extraction and RNASEq analysis. Each sample derived from a different mouse (4 mice/group).

first: Sonia

last: Minuzzo


title: Shigella induces epigenetic reprogramming of zebrafish neutrophils

city: London

first: Serge

last: Mostowy

address: Keppel Street, Bloomsbury

country: United Kingdom

institute: LSHTM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Trained immunity is a long-term memory of innate immune cells, generating an improved response upon re-infection. Shigella is an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae we demonstrate that after Shigella priming neutrophils are more efficient at bacterial clearance. We observe that Shigella-induced protection is non-specific and long-lasting, and is unlike training by BCG and β-glucan. Analysis of histone ChIP-seq on primed neutrophils revealed that Shigella training deposits the active H3K4me3 mark on promoter regions of 1612 genes, significantly changing the epigenetic landscape of neutrophils towards enhanced microbial recognition and mitochondrial ROS production. Finally, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K4me3 in zebrafish neutrophils

first: Margarida

middle: C

last: Gomes

first: Dominik

last: Brokatzky

first: Magdalena

last: Bielecka

first: Fiona

last: Wardle


title: NFE2L3 Drives Hepatocellular Carcinoma Proliferation via Regulating the Proteasome-Dependent Degradation of ISGylation p53 through interaction with TRIM25.

city: Nanchong

first: Yongang

last: Ren

state: Sichuan

address: No. 55 Dongshun Road, Gaoping District, Nanchong, Sichuan

institute: North Sichuan Medical College

summary:
To investigate the function of NFE2L3 and NFE2L3△C(557-694aa) in the regulation of hepatocellular carcinoma proliferation, we established HepG2 cell lines in which the target gene has been over express by lentiviruses.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells at three-time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cell derivatives (lvNC, lvNFE2L3, and lvNFE2L3△C(557-694aa)).

first: Ren

last: Yonggang

first: Yang

last: Jing


title: Single-cell transcriptomic analysis of human and mouse oligodendrocyte precursor cells

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: We report single cell gene expression analysis of human fetal and mouse postnatal oligodendrocyte precursor cells

overall_design: Examination of oligodendrocyte precursor cells isolated from healthy human embronic cortex and wildtype mouse forebrain based on PDGFRa protein expression

first: Hiroko

last: Nobuta


title: RNA sequencing of B-cell acute lymphoblastic leukemia-derived mesenchymal stem cells cultured alone and co-culture with leukemia cells

city: Guiyang

first: Chengyun

last: Pan

state: Guizhou

address: No. 28, Guiyi Street, Yunyan District

institute: Affiliated Hospital of Guizhou Medical University

summary: To explore the possible differences in gene expression profiles between MSCs cultured alone and MSCs in leukemia niches

overall_design: Bone marrow mesenchymal stem cells (BM-MSCs) was isolated from bone marrow aspirates of B-cell acute lymphoblastic leukemia (B-ALL) patients and the ficoll gradient centrifugation was conducted for BM-MSCs separation. MSCs cultured alone for 72 h (n=3) and MSCs co-cultured with Nalm-6 cell lines for 72 h (n=3) were collected, respectively. Then RNA sequencing analyses were performed on these BM-MSCs and the gene expression profiles of BM-MSCs in the two groups were compared.

first: Ping

last: Liu

first: Tianzhen

last: Hu

first: Jishi

last: Wang


title: Spatial transcriptomic analysis of human oligodendrocyte development across gestational weeks 10 to 24

summary: We report human oligodendrocyte development across gestational weeks 10 to 24 using spatial transcriptomics

overall_design: Examination of healthy human brain cortex from gestational week 10 to 24


title: Characterization of a novel 3D-FN-silk breast cancer model

city: Stockholm

first: Caterina

last: Collodet

state: Stockholm

address: Roslagstullsbacken 21

department: Protein technology

country: Sweden

institute: KTH

summary: To offer a robust and highly characterized three-dimensional (3D) model for anti-cancer drug discovery and basic research, we developed a 3D system in which the immortalized breast cancer cell lines MCF-7 and MDA-MB-231 were grown in recombinantly produced spider silk functionalized with the cell adhesion motif from fibronectin (FN-silk). The aim of this study is to evaluate whole-transcriptome changes driven by growth in such 3D model.

overall_design: The expression profiling was generated using two immortalized breast cancer cell lines (MCF-7 and MDA-MB-231) cultured in two-dimensional (2D) or three-dimensional (3D) conditions for seven days. As a baseline control condition, cells obtained from canonical 2D culture on tissue-culture-treated flask on the day of the 3D scaffold creation (day 0) were used. For each condition, three replicates originating from independent experiments were considered as biological replicates. 18 samples were produced and analyzed.

first: Collodet

last: Caterina

first: My

last: Hedhammar

first: Johan

last: Hartman

first: Xinsong

last: Chen


title: Effects of overexpression of IFI6 in bone marrow mesenchymal stem cells on gene expression profiles of acute lymphoblastic leukemia cells

summary: We explored the effects of high expression of interferon-inducible protein 6 in bone marrow mesenchymal stem cells on the gene expression profiles of acute lymphoblastic leukemia cells.

overall_design: The human acute lymphoblastic leukemia (ALL) cell lines RS4;11 were obtained from the Laboratory of Hematopoietic Stem Cell Transplantation Center of Guizhou Province and were cultured in an RPMI-1640 medium. Bone marrow mesenchymal stem cells (BM-MSCs) were isolated from bone marrow aspirates of ALL patients and were cultured in the complete medium of adult BM-MSCs (Saiye, Shanghai, China). RS4;11 cell lines (n=3) co-cultured with MSCs transfected with empty vector (EV) or MSCs transfected with interferon-inducible protein 6 (IFI6) overexpression clone lentiviral particle (LV-IFI6) for 72 h were collected, respectively. Then RNA sequencing analyses were performed on RS4;11 cell lines in the two groups.


title: Exploration of specific gene expression behind the intercellular heterogeneity of type 2 cytokine secretion activity of Group 2 innate lymphoid cell (ILC2) isolated from peripheral blood of severe asthma patients I

city: Bunkyo-ku

first: Yoshitaka

last: Shirasaki

state: Tokyo

address: Hongo 7-3-1

department: Graduate School of Pharmaceutical Science

institute: The University of Tokyo

summary:
To investigate the gene expression underlying the intercellular diversity in type 2 cytokine secretion activity of ILC2, we performed time-series measurements of type 2 cytokine secretion activity  of ILC2 from the peripheral blood of severe asthma patients after IL-33 stimulation .
Single cells were collected separately before stimulation and secretion-negative or -positive cells after stimulation, and performed RNA-seq on each cell for gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data of human peripheral blood ILC2.

first: Mai

last: Yamagishi

first: Yumiko

last: Tanaka

first: Kaede

last: Miyata

first: Sotaro

last: Uemura

first: Hiroki

last: Kabata

first: Takashi

last: Kamatani

first: Rie

last: Baba

first: Satomi

last: Irie

first: Koichi

last: Fukunaga

first: Kazuyo

last: Moro


title: Effect of paternal inorganic arsenic exposure on transcriptional profilings of F1-male liver in mouse

city: Hefei

first: Yanfeng

last: Xue

state: Anhui

address: Changjiang Western Road 130

institute: Anhui Agricultural University

summary: Adult male mice (F0) were exposed to 250 ppb inorganic arsenic (iAs) in drinking water before mating with unexposed female mice to generate male F1 offspring (iAsF1-M). Unexposed male mice were bred simultaneously to generate male controls (conF1-M). Both iAsF1-M and conF1-M mice drank normal water without iAs. Adult iAsF1-M and conF1-M mice were harvested to collect liver samples to do RNA-seq.

overall_design: Compare the differences in transcriptome profiles between the liver sample from iAsF1-M and conF1-M mice.

first: Yingyun

last: Gong

first: Fei

last: Peng

first: Zheng

last: Sun


title: The effects of Ring1A on gene expression profiles of lamina propria immune cells in DSS colitis  at single cell level

city: Shenzhen

first: Zhen

last: Wang

address: DaPeng

institute: AGIS

summary: immune cells in intestinal lamina propria play important roles in pathogenesis of DSS colitis. Here, we used single cell RNA sequencing (scRNA-seq) to reveale the intestinal immune landscape of DSS colitis and study the effects of Ring1A on intestinal immune cells.

overall_design: CD45+ immune cells in intestinal  lamina propria of WT  and Ring1AKO (Ring1A knockout) mice were sorted and conducted scRNA-seq

first: Peng


title: A Compendium of Syngeneic, Transplantable Pediatric High-Grade Glioma Models Reveals Subtype-Specific Therapeutic Vulnerabilities

status: Public on Sep 12 2023

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

summary: Pediatric high-grade gliomas (pHGG) are lethal, incurable brain tumors frequently driven by clonal mutations in histone genes. They often harbor a range of additional genetic alterations that correlate with different ages, anatomic locations, and tumor subtypes. We developed models representing 16 pHGG subtypes driven by different combinations of alterations targeted to specific brain regions. Tumors developed with varying latencies and cell lines derived from these models engrafted in syngeneic, immunocompetent mice with high penetrance. Targeted drug screening revealed unexpected selective vulnerabilities—H3.3G34R/PDGFRAC235Yto FGFR inhibition, H3.3K27M/PDGFRAWTto PDGFRA inhibition, and H3.3K27M/PDGFRAWTand H3.3K27M/PPM1DΔC/PIK3CAE545Kto combined inhibition of MEK and PIK3CA. Moreover, H3.3K27Mtumors with PIK3CA, NF1, and FGFR1 mutations were more invasive and harbored distinct additional phenotypes, such as exophytic spread, cranial nerve invasion, and spinal dissemination. Collectively, these models reveal that different partner alterations produce distinct effects on pHGG cellular composition, latency, invasiveness, and treatment sensitivity.

overall_design: 7 mouse tumor models of K27M pHGG generated by in-utero electroporation of mutations, sequenced for single-nuclei. These 7 samples include 2 KPPMPIK replicates (H3.3K27M, PIK3CA E545K and PPM1D truncated), 3 KNF replicates (H3.3K27M, NF1 LOF and FGFR1-N457K) and 2 KPP replicates (H3.3K27M, P53 LOF and PDGFRA WT overexpression)

first: Michael

last: McNicholas

first: Antonella

last: De Cola

first: Steven

last: Hebert

first: Damien

last: Faury

first: Augusto

middle: F

last: Andrade

first: Nada

last: Jabado

first: Manav

last: Pathania


title: Single-Cell RNA Sequencing Maps Heterogeneity of Immune cells in mice with allogeneic cardiac transplantation

city: Harbin

first: zhong

middle: hua

last: tong

state: Heilongjiang Province

address: 194 Xuefu Road, Nangang District

institute: The Second Affiliated Hospital of Harbin Medical University

summary: The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb.

overall_design: one sample from lymph nodes of syngeneic cardiac transplanted mice and another sample from lymph nodes of allogeneic cardiac transplanted mice

first: Maomao

last: Zhang

first: Zhonghua

last: Tong

first: Ge

last: Mang


title: Systems analysis reveals differential expression of endocervical genes in African women randomised to DMPA-IM, LNG implant or Cu-IUD

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
Some evidence suggests that contraceptive use may influence the female genital tract (FGT) mucosal environment. However, comparative analysis of the effects of the most commonly used hormonal and non-hormonal contraceptives on the FGT host gene expression profile have not been evaluated in detail in a randomized clinical trial setting.
Among 188 women enrolled in the Evidence for Contraceptive Options and HIV Outcomes (ECHO) trial (Clinicaltrials.gov ID NCT02550067) between December 2015 and September 2017, we evaluated the effect of three contraceptive methods, injectable intramuscular depot medroxyprogesterone acetate (DMPA-IM), levonorgestrel (LNG) implant, and a non-hormonal T-380 copper intrauterine contraceptive device (Cu-IUD), on the endocervical host transcriptome at baseline and after one month of randomized contraceptive use, using RNA-Seq transcriptomic analysis.

overall_design:
After quality filtering, paired RNA-Seq data from 152 participants (DMPA-IM, n = 59; LNG-implant, n = 45; Cu-IUD, n = 48) were considered suitable for downstream differential expression analysis.
We found that participants randomized to Cu-IUD showed a larger perturbation to the endocervical transcriptome than those assigned to DMPA-IM and LNG implant and that these transcriptomic changes were associated with inflammatory and anti-viral host responses.
We found that DMPA-IM enriched for pathways associated with T cell responses while gene pathways associated with growth and metabolism were downregulated, and that these results were not strongly dependent on the microbiota composition at the time of contraceptive initiation.
LNG implant initiation had the mildest effect on endocervical gene expression but was associated with enrichment of growth factor signalling.
Our data highlight the varying biological impact of different contraceptives on the host environment, which is relevant for development of novel contraceptive methods and for improved counselling of women seeking contraception.

first: Prachi

middle: M

last: Gupta

first: Christina

last: Balle

first: Sydney

last: Nelson

first: Arghavan

last: Alisoltani

first: Bryan

last: Brown

first: Hosseana

last: Ayele

first: Jo-Ann

last: Passmore

first: Adam

middle: D

last: Burgener

first: Renee

last: Heffron

first: Heather

middle: B

last: Jaspan

middle: E

last: Bosinger


title: miRNA expression profile from Adipocyte-derived Small Extracellular Vesicles from the Serum and cerebrospinal fluid of Alzheimer Disease Patients and Controls

city: Washington

first: Rachael

last: Batabyal

address: 111 Michigan Ave NW

institute: Children's National Hospital

summary: Midlife obesity increases the risk of developing AD. Adipocyte-derived small extracellular vesicles (ad-sEVs) have been implicated as a mecha-nism in several obesity-related diseases. We hypothesized that ad-sEVs from patients with AD would contain miRNAs predicted to downregulate pathways involved in synaptic plasticity and memory formation. We isolated ad-sEVs from the serum and cerebrospinal fluid (CSF) of patients with AD and controls and compared miRNA expression profiles

overall_design: Ad-sEV miRNA was isolated from the serum (n=12 controls, n=17 AD) and cerebrospinal fluid (n=10 controls, n=14 AD). Total RNA was extracted using mirVana microRNA Isolation kits (Life Technologies). Total RNA was amplified with the Complete Seramir Exosome RNA Amplification Kit (System Biosciences, Mountainview, CA). RNA quality was assessed on a subset of these samples using the Agilent 2100 Bioanalyzer and nanodrop. RNA concentration was measured using a Qubit RNA Broad Range Assay Kit (Thermo Fisher Scientific, Waltham, MA). 1,000 ng of RNA was labeled with Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA) per the manufacturer’s instructions. Labeled RNA was hybridized to Affymetrix GeneChip microRNA 4.0 arrays. Chips were run using a Fluidics Station 450 Protocol (Affymetrix, Santa Clara, CA). The results were exported to Partek Genomics Suite for analysis.

middle: A

first: Ankush

last: Bansal

first: Laura

last: Reck Cechinel

first: Kayla

last: Authelet

first: Madeleine

last: Goldberg

first: Evan

last: Nadler

first: C

last: Keene

first: Suman

last: Jayadev

first: Kimiko

last: Domoto-Reilly

first: Gail

last: Li

first: Elaine

last: Peskind

first: Kazue

last: Hashimoto-Torii

first: Dedra

last: Buchwald

first: Robert

middle: J

last: Freishtat


title: Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections data

city: Tucson

first: Deepta

last: Bhattacharya

state: AZ

address: 1656 E Mabel St

department: Immunobiology

institute: University of Arizona

summary: Vaccine-induced immunity may impact subsequent de novo responses to drifted epitopes in SARS-CoV-2 variants, but this has been difficult to quantify due to the challenges in recruiting unvaccinated control groups whose first exposure to SARS-CoV-2 is a primary infection . Through local, statewide, and national SARS-CoV-2 testing programs, we were able to recruit cohorts of individuals who had recovered from either primary or post-vaccination infections by either the Delta or Omicron BA.1 variants. Regardless of variant, we observed greater Spike-specific and neutralizing antibody responses in post-vaccination infections than in those who were infected without prior vaccination. Through analysis of variant-specific memory B cells as markers of de novo responses, we observed that Delta and Omicron BA.1 infections led to a marked shift in immunodominance in which some drifted epitopes elicited minimal responses, even in primary infections. Prior immunity through vaccination had a small negative impact on these de novo responses, but this did not correlate with cross-reactive memory B cells, arguing against competitive inhibition of naïve B cells. We conclude that dampened de novo B cell responses against drifted epitopes are mostly a function of altered immunodominance hierarchies that are apparent even in primary infections, with a more modest contribution from pre-existing immunity, perhaps due to accelerated antigen clearance.

overall_design: SARS-CoV-2 antigen specific (PE+) memory B cells were sorted by fluoresence activated cell sorting (FACS) and analyzed using scRNA-seq

first: Grace

last: Quirk

first: Marta

last: Schoenle


title: Single cell profiling of CD4+ T cells from follicular lymphoma, diffuse large B cell lymphoma and tonsilar samples

city: Oslo

first: Ivana

last: Spasevska

address: Disenveien 9

country: Norway

institute: University of Oslo

summary: Tumor-infiltrating regulatory T cells contribute to an immunosuppressive tumor microenvironment. We applied single-cell RNA sequencing (scRNA-seq) , TCR sequencing combined with cellular indexing of transcriptomes and epitopes (CITE-seq) on CD4 T cells  to decipher the heterogeneity of intratumoral Tregs in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), compared with non-malignant tonsillar tissue.

overall_design: Single-cell suspensions from diagnostic samples from FL and DLBCL and healthy donor tonsilar samples were stained with Alexa750 viability dye, fluorochrome-coupled-, CITE-seq- and  TotalSeq-C hashtag antibodies. CD4 T cells from FL, DLBCL and tonsilar samples were isolated by fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq, TCR-seq and CITEseq.

first: June

middle: H

last: Myklebust

last: Sharma

first: Susanne

last: Lorenz


title: Biotransformed Bear Bile Powder Ameliorates Diet-induced Nonalcoholic Steatohepatitis in Mice

city: Beijing

first: Shan

last: Jiang

address: No. 16, Nanxiao Road/Street

institute: China Academy of Chinese Medical Sciences

summary: To evaluate the therapeutic effects and underlying mechanisms of BBBP against NASH

overall_design: There are three sets of samples, namely the Control group, Model group, and BBBPH group (JDH group), with 5 samples in each group.To establish a nonalcoholic steatohepatitis model, mice were fed on a high-fat high- sucrose diet (60% kcal fat, 20% kcal protein, 20% kcal carbohydrates and 0.2% cholesterol, D12492, Research Diets, USA) along with drinking water containing 42 g/L sugar (55% sucrose and 45% fructose by weight) for 20 weeks after which they were sacrificed. After 12 weeks, the high-fat high- sucrose diet-induced nonalcoholic steatohepatitis mice were divided into 2 groups (model and JDH (Biotransformed Bear Bile Powder) group). Then, mice in different groups were orally administered 150 mg/kg Biotransformed Bear Bile Powder (the JDH group, n=14) and saline (the model group) daily, concurrent with the high-fat high- sucrose diet.


title: Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers [RNA-seq]

city: Cambridge

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

summary: The BRG/Brahma-associated factors (BAF or mSWI/SNF) family of chromatin remodeling complexes are critical regulators of gene expression and are major determinants of cancer and other diseases. Two paralog ATPases, SMARCA4 and SMARCA2 (BRG1 and BRM, respectively), provide the enzymatic activity required for chromatin remodeling.   Here, we discover and characterize a novel series of compounds that potently and selectively inhibit SMARCA4/SMARCA2.  Mutational and biochemical studies demonstrate that these inhibitors act through a unique mode of inhibition, distinct from reported SMARCA4/SMARCA2 inhibitors.  Across a range of cancer cell lines, SMARCA4/SMARCA2 inhibition resulted in lineage-specific changes in chromatin accessibility at binding sites for key transcription factors (TFs).  In uveal melanoma (UM), BAF inhibition resulted in loss of enhancer occupancy of SOX10 and MITF, two essential TFs, leading to down-regulation of the melanocytic gene expression program.  In a mouse xenograft model of UM, SMARCA4/SMARCA2 inhibition was well tolerated and resulted in dose-dependent tumor regression correlating with pharmacodynamic modulation of BAF-target gene expression.  These data provide the foundation for first-in-human studies of BAF ATPase inhibition as a novel therapeutic to treat TF-dependent cancers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 92-1, MEL202 and MP41 cells treated with dual SMARCA4/SMARCA2 inhibitor FHT-1015 for 4h and 24h; 92-1 cells treated with PKC inhibitor IDE196 for 4h and 24h

first: Richard

last: Centore

first: Luis

last: Soares


title: Difference of LncRNAs expression between colorectal tumor tissues and paracancer normal intestinal mucosal tissues

city: Guangzhou

first: wang

middle: yi

last: qing

institute: South Medical University

summary: To identify the difference of LncRNAs expression between colorectal tumor tissues and paracancer normal intestinal mucosal tissues

overall_design: Either of the tissues,N1,N2,N3,C1,C2,C3,CM1,CM2 and CM3,is collected in Department of pathology , Nanfang Hospital(Guangzhou,China)

first: Wang

last: Shuang

last: Yiqing


title: Pkd2-dependent transcriptome profile in a newly estabilshed mouse Pkd2 knockout cell line

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary:
Purpose:  The goal of this study is to explore early changes of gene expression in the new mouse kidney Pkd2 knockout cell model. To identify compreshensive expressional changes of genes by Pkd2 knockout, transcriptomic changes by Pkd2 knockout induced by doxycycline treatment for 6 days at two different passages were profiled and analyzed.
Methods: Total RNAs were isolated from cells treated with or without doxycycline for 6 days. Four replicates of each group were generated. cDNA libraries were prepared and sequenced on Illumina HiSeq4000 platform and then sequence reads were qualified and quantified. Differential expression analysis were performed using edgeR.
Results: mRNA profiles of the new mouse kidney Pkd2 knockout cell model treated with doxycycline for 6 days were generated using an optimized RNA-Seq workflow. Transcript level quantification using the STAR quant mode was performed to calculate transcript abundance in each sample. Then differential expression analysis identified the differentially expressed genes at different passages of cell culture.
Conclusions: This study revealed early transcriptomic changes dependent on Pkd2 in a new in vitro Pkd2 knockout cell model of the mouse kidney.

overall_design: Early transcriptomic responses to Pkd2 knockout was studied using a doxycycline-inducible Pkd2 knockout cell line newly established from the Pkd2 knockout mouse.

first: Paul

last: Welling


title: Adaptive laboratory evolution of E. coli ndh gene deletion strain

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

summary: We have performed adaptive laboratory evolution of E. coli ndh gene deletion strain to examine the adaptive strategies of E. coli.

overall_design: Growth of E. coli on M9 minimal media supplemented with 4g/l Glucose at 37C was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.


title: Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers [WES]

overall_design: Whole exome sequencing (WES) analysis to identify resistance mutations in MP41 cells treated with dual SMARCA4/SMARCA2 inhibitor FHT-1015


title: Netrin-1 facilitates pancreatic cancer liver metastasis

city: Rochester

first: Chris

last: Harris

state: New York

address: 575 Elmwood Avenue

institute: University of Rochester Medical Center

summary: When pancreatic cancer cells metastasize to the liver, resident hepatic stellate cells release retinoic acid. Attached is an analysis of retinoic acid-induced genes in the highly metastatic murine pancreatic cancer cell line Ink4a

overall_design: The mouse pancreatic cell line Ink4a was treated for 16 hours with DMSO or with 5 nM all-trans-retinoic acid in vitro

first: Darren

last: Carpizo


title: Heterosis versus breakdown in cyprinid hybrids associated with SVCV infection revealed by transcriptome profile analysis of head kidney

city: Brno

first: Jiri

last: Vorel

address: Kotlarska 267/2

department: Department of Botany and Zoology

country: Czech Republic

institute: Masaryk University

summary: Whilst the hybrids of F1 generations usually experience heterosis for fitness-related traits (including the resistance to parasites), post-F1 generations, due to Dobzhansky–Muller genetic incompatibilities, express numerous disadvantageous traits (including susceptibility to parasites). Genetic disruption in hybrids may also result from the broken system of cyto-nuclear coadaptation. Maternal backcrosses (each parent having with the same mtDNA of parents) and paternal backcrosses (each parent having with different mtDNA of parents) have the same nuclear genetic compositions, but differ in cytoplasmic genetic elements, affecting their viability and survival. Spring viraemia of the carp virus (SVCV), a disease with a serious economic impact in aquacultures, affects almost exclusively cyprinids, primarily common carp, and causes high mortality, whilst gibel carp is a less susceptible species. Our study was focused on the transcriptome profile analysis of head kidney to reveal differential gene expression in highly susceptible common carp, weakly susceptible gibel carp, and hybrid lines, hypothetizing that the patterns of differential gene expression will reflect hybrid heterosis in F1 generations and hybrid breakdown in backcrosses and F2 generations. We expected the differences in differential gene expression between maternal and paternal backcrosses to be in line with the hypothesis of broken cyto-nuclear coadaptation.

sample_organism: Carassius gibelio x Cyprinus carpio 'xingguonensis'

overall_design: The pattern of differential gene expression revealed from the transcriptomic analysis of head kidney was linked to the resistance or susceptibility to SVCV infections in two pure species, C. gibelio and C. carpio, and their various generations of inter-specific hybrids. We evidenced hybrid heterosis for F1 generations of hybrids, mostly reflected by similarity in the down-regulation of DE genes classified within the viral infection disease category. High hybrid breakdown was documented throughout the transcriptomic analysis for paternal backcross generations and F2 generation of hybrids, confirming the broken system of cyto-nuclear coadaptation in those post-F1 generations. This evidence may support the role of intrinsic selection acting against inter-specific hybridization in freshwater fish. Total RNA was isolated from the head kidney of each fish specimen. For extraction, PureLink RNA Mini Kit (Ambion) with Trizol reagent (Thermo Fisher Scientific) and on-column PureLink DNase treatment were used. In total, 70 samples from 3 dpi (by SVCV) sampling and from non-infected fish with an acceptable RIN (RNA integrity number – RIN > 7) were used for DNA library preparation.

first: Andrea

last: Šimková

first: Kristína

last: Křížová

first: Kristýna

last: Koukalová

first: Lukáš

last: Vetešník

first: Václav

last: Hejret

first: Lenka

last: Gettová

first: Jiří

first: Nikol

last: Reslová

first: Vojtěch

last: Bystrý


title: Analysis of differential gene expression in the degradation of doxycycline by Chryseobacterium sp. WX1

first: Xiuli

last: Chen

state: Beijing

address: 9/5000  School of Environmental Science

institute: Peking University

summary: We isolated an efficient doxycycline degrading strain Chryseobacterium sp. WX1. To investigate gene expression patterns during doxycyclinedegradation by strain WX1, we conducted a comparative transcriptomic analysis using cultures of strain WX1 with and without doxycycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Chryseobacterium sp. WX1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.

overall_design: Control groups (WX1_CK): cultures of strain WX1 without doxycycline addition. Experimental groups (WX1_DOX):cultures of strain WX1 with 50 mg/L doxycycline.

first: Shuguang

last: Xie


title: Repeated peripheral infusions of anti-EGFRvIII CAR T cells in combination with pembrolizumab remodel the tumor microenvironment in de novo glioblastoma

city: Geneva

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: Treatment efficacy with chimeric antigen receptor (CAR) T cell therapy in glioblastoma (GBM) is undermined by an immunosuppressive tumor microenvironment (TME). We previously showed that CAR T cell therapy targeting epidermal growth factor receptor variant III (EGFRvIII) produces anti-tumor activity against recurrent GBM and causes upregulation of programmed death-ligand 1 (PD-L1) in the TME. Here, we conducted a phase I trial to study the safety and tolerability of CART-EGFRvIII cells administered concomitantly with the PD-1 inhibitor pembrolizumab in patients with newly diagnosed, EGFRvIII+ GBM (n=7). Treatment was well tolerated in this small cohort without incidence of dose-limiting toxicity. However, no signal of efficacy was detected with a median progression-free survival of 5.2 months (90% CI, 2.9 – 6.0 months) and overall survival of 11.8 months (90 % CI, 9.2 – 14.2 months). We aimed to elucidate reasons for limited efficacy through correlative analyses. Using BBZ qPCR, we found circulating CAR T cells in 5 out of 7 patients at the time of repeat resection, but only in 1 patient in the tumor. However, shared T-cell receptors (TCRs) were found between the infusion product and the relapsed tumors, which could indicate an infiltration but lack of persistence of the CAR T cells. We further compared the tumor microenvironment of the tumors harvested before and after CAR+aPD1 administration using single cell RNA sequencing and observed comparable proportions of the major immune cell subsets. However, the myeloid and T cells infiltrating the tumors significantly evolved, with more exhausted, regulatory, and IFN-stimulated T cells at the relapse. At that time, the amount of IFN-stimulated T cells positively correlated with time from relapse to death. Together, these findings suggest that the combination of CAR T cells and PD-1 inhibition in GBM is safe and biologically active but, given the lack of efficacy, also indicate a need to consider alternative immunotherapeutic strategies. ClinicalTrials.gov registration: NCT03726515.

overall_design: Biopsies and blood from patients with newly diagnosed, EGFRvIII+ GBM (n=7) were collected. N=3 patients had pre and post-treatment biopsies.

first: Cecile

last: Alanio

first: Denis

last: Migliorini

first: Donald

last: O’Rourke

first: Lamia

last: Lamrani

first: Stephen

last: Bagley

first: Zev

last: Binder


title: Selective Reduction of Visceral Adipose Tissue with Injectable Ice Slurry

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Reduction in visceral adipose tissue (VAT) mass reduces body weight and metabolic disease risk in obese patients. However surgical removal of VAT is highly invasive and thus not clinically feasible. We developed an injectable ice slurry for selective reduction of adipose tissue through cryolipolysis. The aim of this study was to investigate safety, feasibility and mechanism of ice slurry-induced cryolipolysis of VAT. Perigonadal VAT in diet-induced obese mice and rats was subjected to slurry or sham treatment. Body weight and blood chemistry were monitored for 56 days post-treatment. Histological analysis and molecular studies were performed to elucidate mechanisms of fat reduction. Treatment of VAT was well tolerated in all animals. Slurry induced adipocyte cell death via selective cryolipolysis; significant weight loss was noted at day 21 post-treatment. RNA sequencing from treated VAT samples showed increased expression of genes involved in inflammation, immune response, collagen biosynthesis and wound healing, and decreased expression of adipokines. This study demonstrates that slurry treatment is safe and effective in inducing cryolipolysis of VAT and subsequent weight loss in rodents. Ice slurry is promising as a minimally-invasive treatment to reduce visceral adipose tissue.

overall_design: Adult male Sprague-Dawley rats (200g and 8 weeks old) were fed with high fat diet (rodent diet with 60 kcal% fat) for 9 weeks prior to the treatment and then for the duration of study. Twenty rats were used in this study. Perigonadal adipose tissue on one side was exposed through an abdominal incision, and injected with 10 ml of slurry prior to closing the incision with sutures.  Animals were sacrificed at 24 hours, 1 days, 3 days and 14 days.

first: Sara

last: Moradi Tuchayi

middle: S

first: Lilit

last: Garibyan

first: Marc

last: Wein


title: A Meta-Atlas of the Developing Human Cortex Identifies Modules Driving Cell Subtype Specification

city: Los Angeles

first: Patricia

last: Nano

state: CA

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

summary: During development, the human brain orchestrates the generation of hundreds of diverse cell types, and recent transcriptomic atlases of the developing human cortex provide new opportunities to identify novel regulators of cell fate specification. We have conducted an integrated meta-analysis of seven recently published single-cell transcriptomic profiles of the developing human cortex, generating a meta-atlas of 225 meta-modules. By tracking the activity of these meta-modules throughout development and comparing this to datasets from the adult human as well as the developing and adult mouse, we identified modules with potential roles in the transition from neurogenesis to gliogenesis and neuronal subtype maturation. The cell type and developmental state at which these modules exist was validated in primary samples from the developing human brain. Of particular interest, we identified and validated a module associated with both developing human deep layer neurons and human adult deep layer neuronal subtypes expressing the terminal differentiation marker FEZF2. Though FEZF2 is neither a member of nor co-expressed with our deep layer-associated gene module, almost half of module genes are putative FEZF2 targets, including TSHZ3, a transcription factor associated with neurodevelopmental disorders such as autism. Knockdown experiments in human cortical organoid models confirm that both FEZF2 and TSHZ3 are necessary for deep layer neuron specification. Importantly, we observe that subtle manipulations of these transcription factors result in slight changes in module activity, but together yield strong differences in cell fate. Our analyses therefore reveal a gene network that required to generate deep layer neuronal subtypes, demonstrating the ability of our meta-atlas to engender further mechanistic analyses of cortical fate specification. We anticipate this resource being useful for the study of co-expression programs across diverse biological questions related to the developing neocortex.

overall_design: Human cortical organoid models were used to functionally interrogate the role of module 20 in the specification of human deep layer neurons. Stem cells were passaged in the presence of lentivirus expressing an shRNA construct and an mCherry coding sequence. One of four shRNA sequences were used: a scrambled (scram) sequence, two FEZF2-targeting sequences, and a TSHZ3-targeting sequence. After a minimum of 12 days in culture, stem cells were used to generate cortical organoids, in which a subset of cells express shRNA as indicated by mCherry fluorescence. The resulting FEZF2 or TSHZ3 knock-down organoids were maintained for a minimum of 7 weeks prior to characterization with single-cell RNA sequencing.

middle: R

first: Aparna

last: Bhaduri


title: Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers [ChIP-seq]

first: Salih

last: Topal

overall_design: Comparative genomic binding profiling analysis of ChIP-seq data for BRG1, SOX10, MITF, TFAP2A and H3K27ac in 92-1 treated with dual SMARCA4/SMARCA2 inhibitor FHT-1015 for 4h

first: Richard

last: Centore

first: Luis

last: Soares


title: The miRNA-mediated gene regulatory network in hippocampus and hypothalamus of the aging mouse

city: Bongmyeongdong

first: Mihye

last: Lee

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

type: Non-coding RNA profiling by high throughput sequencing

summary:
Aging leads to time-dependent functional decline of all major organs. In particular, the aging brain is susceptible to cognitive decline and several neurodegenerative diseases. To characterize the aging process and understand the underlying molecular mechanisms, numerous studies have examined changes in gene expression in the aging mouse brain using high-throughput sequencing. However, microRNA-mediated post-transcriptional regulation of gene expression has not yet been comprehensively  elucidated.
In this study, we performed global analysis of mRNA and microRNA expression simultaneously in the hypothalamus and hippocampus of young and aged mice. We identified aging-dependent differentially expressed genes, most of which were specific to the hypothalamus or hippocampus.

overall_design:
For mRNA sequencing, a total of 6 samples were prepared from each hippocampus and hypothalamus tissue, 3 biological replicates in young (2 months old) and aged mice (15 months old).
For small-RNA sequencing, a total of 6 samples were prepared from each hippocampus and hypothalamus tissue, 3 biological replicates in young (2 months old) and aged mice (15 months old).

first: Jong-seok

last: Moon

first: Choijamts

last: Munkzhul

first: Sun

last: Yi


title: Expression profiles of Col-0, adf4 and ADF1-4Ri (in which expressions of all of subclass I ADFs were downregulated) uninfected and Golovinomyces orontii-infected leaves

city: Sakai

first: Noriko

last: Inada

email: norikoinada@omu.ac.jp, norikoq@me.com

state: Osaka

address: Gakuen-cho 1-1, Naka-ku

department: Agriculture

institute: Osaka Metropolitan University

summary:
ACTIN DEPOLYMERIZING FACTORs are involved in regulation of various aspects of plant physiologies, including plant immunity. However, it was not known how ADF regulates those plant physiologies.
We hypothesized that ADFs regulate gene expression through regulation of nuclear organization. To test this hypothesis, we performed microarray analysis for A. thaliana adf mutants that were both uninfected and infected with powdery mildew.

overall_design: Plants were grown at 12h L/12h D at 22 oC, and mature leaves of 4 week old plants were used for RNA extraction. For G. orontii infection, 4 week old plants were infected with G. orontii conidiospores, and mature leaves at 3 or 5 days post inoculation were sampled.


title: Efficient targeted integration in proliferating patient hepatocytes for inherited liver diseases

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: Hepatocyte transplantation has shown great potential for treating inherited liver diseases. However, its prolonged clinical therapeutic efficacy is still hindered by serious immune rejection from the host immunological responses to the allogeneic hepatocytes and there is still no an effective approach to generate clinically available autologous hepatocytes for transplantation therapy. Here, we report advanced medium conditions that allow 10,000-fold expansion of primary human hepatocytes from patients suffering inherited liver diseases, providing a new autologous hepatocytes source to this problem. Moreover, we developed a CRISPR–Cas9 genome-targeting system that combines Cas9 ribonucleoproteins and adeno-associated viral vector delivery of a homology-independent large donor (greater than three kilobase) to achieve efficient targeted integration at the AAVS1 safe harbor locus in patient-derived proliferating human hepatocytes (ProliHHs). We further applied this strategy to correct a pathogenic OTC and FAH mutation in ProliHHs and demonstrated improved gene expression, while preserving cell viability for the expansion and purification of edited ProliHHs. Importantly, these edited ProliHHs repopulate into injured mouse liver at a level near to primary human hepatocytes, and they undergo maturation to successfully treat the tyrosinemia mouse model following transplantation in vivo. Thus, this study provides a new autologous hepatocyte therapy techniques that enable large-scale expansion and ex vivo gene correction in patient-derived transplantable ProliHHs, which holds the potential for modeling and treating human liver disease.

overall_design: During the culture process, transcriptional profiling in PHHs and ProliHHs from pateints with inherited liver diseases were generated by RNA-seq analysis.Comparative gene expression profiling analysis of RNA-seq data for healthy-donor and patient derived PHH/ProliHH.

first: Kun

last: Zhang

first: Xiaolong

last: Ma


title: Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers [PRO-seq]

overall_design: Comparative nascent mRNA expression profiling analysis of PRO-seq data for MP46 cells treated with dual SMARCA4/SMARCA2 inhibitor FHT-1015 for 15 min and 1h.


title: Deletion of Sufu in macrophages promotes inflammatory responses

first: jiayin

last: Peng

address: Yueyang Road

institute: Center for Excellence in Molecular Cell Science

summary: Sepsis is a potentially life-threatening condition caused by the body's response to a severe infection. However, the pathogenesis of sepsis remains unclear. Here, we found that Suppressor of Fused (Sufu), a classical negative regulator of Hedgehog signaling, is downregulated in patients with sepsis and in murine peritoneal macrophages treated with lipopolysaccharide (LPS). Deletion of Sufu aggravated LPS-induced lung injury and lethality in mice, and augmented LPS induced proinflammatory gene expression in cultured macrophages. By RNA-seq transcriptome profiling, we identified Sufu as a negative regulator of the TLR-triggered inflammatory response.

overall_design: To study the regulatory mechanism of Sufu in LPS-induced inflammatory signaling, we also performed RNA-seq in PEMs from WT and Sufu-cKO mice 3 hours after LPS challenge.

first: Yehua

last: Li

first: Jiayin

first: Yun

last: Zhao


title: RNA-seq Analysis of Prostate Cancer Cell Under Erastin Exposure

city: nan ning

first: 周

last: 青鸟

address: shaungyonglu street num 22

institute: Guangxi Medical University

summary: In order to investigate which genes with different expression in prostate cancer(PCa) cells(LNCaP and PC3) after erastin exposure, and identify the essential ferroptosis related genes (FRGs) associated with ferroptosis in PCa cell. 5.0µM erastin was added in cell medium, and we performed gene expression profiling analysis using data obtained from RNA-seq of 12 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP and PC3 cells and its erastin-treatment groups.

first: Qingniao

last: Zhou

first: Fan

last: Wu


title: Investigating the expression signatures of circRNA in pulmonary arteial hypertension

first: Tiantai

address: No. 1, Xiannongtan Street

department: Institute of Materia Medica

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To investigate the underlying mechanism of pulmonary hypertension, the model of hypoxia-treated pulmonary arterial hypertension (PAH) rats were constructed to detect the differentially expressed profile of circRNAs in lung tissue of PAH rat. The whole genome microarray expression profiling analysis as a discovery platform have been employed to identify genes difference.

overall_design: The male rats were exposed to hypoxia (10% oxygen) in a ventilated chamber to induce pulmonary arterial hypertension model, and control rats were exposed to normoxic condition. After 3 weeks late, the lung tissue was collected to detect the circRNA expression profile.

first: Lan

last: Sun


title: Single-cell and spatial transcriptomics profile of porcine jejunum and ileum containing Peyer's patches

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: To establish better understanding of cells found in jejunal and ileal Peyer's patches of pigs, we utilized single-cell RNA sequencing scRNA-seq and spatial transcriptomics to recover and analyze cells and spatial regions from sections of jejunum and ileum containing Peyer's patches. Cells identified via single-cell RNA sequencing included B, T/innate lymphoid cell, myeloid, epithelial, and stromal lineage cells. Spatial dots recovered via spatial transcriptomics belonged to regions including villi, crypts, interfollicular/parafollicular zones, follicles, and muscularis. Overall, results provide new information on regional localization and transcriptional profiles of cells in the pig small intestine.

overall_design: Tissues were collected from 7.5 week old pigs from distal ileum containing Peyer's patches and jejunum where the distal-most discrete Peyer's patch was located. Tissues for spatial transcriptomics were frozen and cryosectioned onto 10X Visium spatial transcriptomics slides. Cells were isolated with a collagenase incubation and mechanical dissociation and processed for single-cell RNA sequencing with the 10X Chromium protocol. Libraries were prepared using Illumina library prep and sequenced using Illumina HiSeq 3000 and NovaSeq 6000 for single-cell RNA sequencing data and a NovaSeq 6000 for spatial transcriptomics data.

first: Jayne

last: Wiarda

first: Adrienne

middle: L

last: Shircliff

first: Judith

last: Stasko

first: Mark

last: Ackermann

first: Crystal

last: Loving


title: Investigating TIAM1 in NSCLC (RNA-Seq)

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

summary: The T lymphoma invasion and metastasis inducing protein 1 (TIAM1) is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RAC1. We have shown that nuclear TIAM1promotes the migration of NSCLC cells. To investigate the requirement for TIAM1 in regulating gene expression of NSCLC cells, we performed RNA-seq on H441 cells transfected with either siRNA for TIAM1 (siTIAM1) or a control siRNA (siControl) to identify differentially expressed genes.

overall_design: mRNA profiles of control or TIAM1 knockdown H441 cells, generated from 3 independent experiments using RNA-seq

first: Lucy

last: Ginn

first: Joe

last: Maltas

first: Martin

last: Baker

first: Anshuman

last: Chaturvedi

first: Leah

last: Wilson

first: Ryan

last: Guilbert

first: Fabio

last: Amaral

first: Lynsey

last: Priest

first: Holly

last: Mole

first: Fiona

last: Blackhall

first: Zoi

last: Diamantopoulou

first: Adam

last: Hurlstone

first: Angeliki

last: Malliri


title: Investigating TIAM1 in NSCLC (ChIP-Seq)

summary: The T lymphoma invasion and metastasis inducing protein 1 (TIAM1) is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RAC1. We have shown that nuclear TIAM1 promotes the migration of NSCLC cells and regulates the expression of adhesion genes as part of a repressive complex. To further investigate this, we performed ChIP-Seq analysis to determine the enrichment of TIAM1, TRIM28 and H3K9me3 to chromatin in H441 cells.

overall_design: ChIP-seq analysis of TIAM1, TRIM28 and H3K9me3 on H441 cells.


title: Effect of Apold1 KO in mouse endothelial cells gene expression

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

institute: ETH Zürich

summary: Endothelial cells (ECs) can detect oxygen and nutrient shortages in tissues and are able to adapt by inducing proliferation and migration into ischemic areas. Here, we present results that elucidate the striking role of a novel, EC/mural cell-specific gene, Apold1, in regulating pathological angiogenesis in ischemia. Screening of the transcriptomic profile by bulk RNAseq of wild type (WT) and Apold1-/- isolated muscle endothelial cells (ECs) revealed minor transcriptional differences upon Apold1 knockout. In contrast RNA sequencing on primary ECs derived from Apold1-/- or WT ECs, which were briefly (16 hrs) cultured in angiogenic medium, showed striking differences.

overall_design: Comparative mRNA gene expression analysis of ECs that were isolated by FACS sorting from mouse hind leg muscles. Two experiments were performed, one (5vs5) comparing Apold1KO vs WT in sorted cells directy after sorting, and one experiment (3vs3) comparing Apold1KO vs WT in sorted cells after briefly (16 hrs) cultureing in angiogenic medium

first: Zheng

last: Fan

first: Raphaela

last: Ardicoglu

first: Johannes

last: Bohacek

first: Katrien

last: De Bock


title: The catalytic activity of TET1 is required for human germ cell fate choice [bACE-Seq]

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: Primordial germ cell (PGC) is the foundation of the germline which become gametes and transmit genetic and epigenetic information to the next generation.  The segregation of germline and soma is critical yet well-characterized in human during embryonic development due to ethical consideration.  Here we discover that human TET1 (Ten-eleven translocation 1) acts as a safety check of germline cell fate.  Using CRISPR/Cas9 to knock-out TET1 catalytic domain, we demonstrate extremely low hPGCLC (hPGC-like cell) competency of undifferentiated pluripotent stem cell lines.  We plot whole-genome 5’hydroxymethylation (5hmC) profiles to elucidate global as well as locus-specific 5hmC enrichment in hPGCLCs, indicating the DNA oxygenase activity of TET1 is active during hPGCLC differentiation.

overall_design: We applied bisulfite apobec-coupled epigenetic sequencing (bACEseq) in hESC and hPGCLC in 2 cell lines (UCLA1 and UCLA2) and TET1 CDKO hESC (UCLA1) with replicates to measure genome-wide 5-hydroxymethyation (5hmC) level.

last: Clark


title: Transcriptomic Analysis Reveals the Inability of Recombinant AAV8 to Activate Human Monocyte-Derived Dendritic Cells

city: Nantes

first: Mickael

last: Guilbaud

address: 22 Boulevard Bénoni Goullin

summary: Recombinant Adeno-Associated Virus (rAAV) is considered as one of the most successful and widely used viral vector for in vivo gene therapy. However, host immune responses to the vector and/or the transgene product remain a major hurdle to successful AAV gene transfer. In contrast to anti-vector adaptive immunity, the initiation of the innate immunity towards rAAV is still poorly understood but is directly dependent on the interaction between the viral vector and innate immune cells. Here, we used a quantitative transcriptomic-based approach to determine the activation of inflammatory and anti-viral pathways after rAAV8-based infection of monocyte-derived Dendritic Cells (moDC) obtained from 12 healthy human donors. We have shown that rAAV8 particles are efficiently internalized, but that this uptake does not induce any detectable transcriptomic change in moDC cells in contrast to an adenoviral infection which upregulates anti-viral pathways. These findings suggest an immunological favorable profile for rAAV8 serotype with regards to in vitro activation of moDC cell model. Transcriptomic analysis of rAAV-infected innate immune cells is a powerful method to determine the ability of the viral vector to be seen by these sensor cells, which remains of great importance to better understand the immunogenicity of rAAV vectors and to design immune-stealth products.

overall_design: Transcriptomic analysis of human monocyte-derived dendritic cells at 48h under non-activated, LPS-R848 treatment and 2 distinct activation states: rAAV8 infection or Adenovirus infection

first: Samer

last: Masri

first: Laure

last: Carre

first: Nicolas

last: Jaulin

first: Céline

last: Vandamme

first: Célia

last: Couzinié

first: Aurélien

last: Guy-Duché

first: Jean-Baptiste

last: Dupont

first: Allwyn

last: Pereira

first: Eric

last: Charpentier

first: Laurent

last: David

first: Gwladys

last: Gernoux

first: Mickaël

first: Oumeya

last: Adjali


title: The expression signatures of circRNA in MCT-induced pulmonary arterial hypertension rat

city: Beijing

first: Tiantai

last: Zhang

summary: To investigate the underlying mechanism of pulmonary hypertension, the model of monocrotaline (MCT)-treated pulmonary arterial hypertension (PAH) rats were constructed to detect the differentially expressed profile of circRNAs in lung tissue of PAH rat. The whole genome microarray expression profiling analysis as a discovery platform have been employed to identify genes difference.

overall_design: The male rats were treated with monocrotaline (MCT) to induce pulmonary arterial hypertension model.  One dose of MCT (60 mg/kg) was injected Intraperitoneally into animals. Control rats were injected with the equivalent volume of dissolvent solution according to their weights. After 4 weeks late, the lung tissue was collected to detect the circRNA expression profile.

first: Lan

last: Sun


title: The catalytic activity of TET1 is required for human germ cell fate choice [Bisulfite-Seq]

first: Fei-Man

last: Hsu

overall_design: We applied WGBS in hESC and hPGCLC in 2 cell lines (UCLA1 and UCLA2) and TET1 CDKO hESC (UCLA1) with replicates.


title: Cardiac fibroblasts of dilated cardiomyopathy patients

city: Sutia

first: Hidehiro

last: Suginobe

address: 2-2, Yamadaoka

department: Pediatrics

institute: Osaka University

summary: To investigate the physiological characteristics of cardiac fibroblasts (CF) from pediatric dilated cardiomyopathy (DCM) patients, CFs were harvested from left ventricular free wall at the heart transplantation. We then performed RNA-seq for 7 different lines of CFs.

overall_design: Comparative gene expression profiling analysis of RNA-seq for four independent CF cell lines of pediatric DCM and three independent CF cell lines of healthy donors

first: Tsuru

last: Hirofumi

first: Suginobe

last: Hidehiro

first: Ishida

last: Hidekazu


title: A TIAM1-TRIM28 complex mediates epigenetic silencing of protocadherins to promote migration of lung cancer cells

first: Tim

last: Somervaille

summary: Lung cancer is the leading cause of cancer deaths. Its high mortality is associated with high metastatic potential. Here, we show that the RAC1-selective guanine nucleotide exchange factor T cell invasion and metastasis-inducing protein 1 (TIAM1) promotes cell migration and invasion in the most common subtype of lung cancer, non-small-cell lung cancer (NSCLC), through an unexpected nuclear function. We show that TIAM1 interacts with TRIM28, a master regulator of gene expression, in the nucleus of NSCLC cells. We reveal that a TIAM1-TRIM28 complex promotes epithelial-to-mesenchymal transition, a phenotypic switch implicated in cell migration and invasion. This occurs through H3K9me3-induced silencing of protocadherins and by decreasing E-cadherin expression, thereby antagonizing cell–cell adhesion. Consistently, TIAM1 or TRIM28 depletion suppresses the migration of NSCLC cells, while migration is restored by the simultaneous depletion of protocadherins. Importantly, high nuclear TIAM1 in clinical specimens is associated with advanced-stage lung adenocarcinoma, decreased patient survival, and inversely correlates with E-cadherin expression.

overall_design: Refer to individual Series

first: Lucy

last: Ginn

first: Joe

last: Maltas

first: Martin

last: Baker

first: Anshuman

last: Chaturvedi

first: Leah

last: Wilson

first: Ryan

last: Guilbert

first: Fabio

last: Amaral

first: Lynsey

last: Priest

first: Holly

last: Mole

first: Fiona

last: Blackhall

first: Zoi

last: Diamantopoulou

first: Adam

last: Hurlstone

first: Angeliki

last: Malliri


title: The catalytic activity of TET1 is required for human germ cell fate choice [scRNA-seq]

first: Fei-Man

last: Hsu

overall_design: We applied scRNAseq in hESCs, iMeLCs and D4 aggregate cells during hPGCLC differentiation in Control (CTRL, 3 replicates) and TET1 catalytic domain knockout (CDKO, 3 replicates) lines.

last: Clark


title: Purification-sequencing of RNA super-assemblies.

city: Nice

first: Arnaud

last: Hubstenberger

address: 28 avenue Valrose

department: IBV

institute: Université Côte D'Azur

summary:
C. elegans oogenesis arrest offers a unique and biologically relevant opportunity to investigate how condensation reorganizes the transcriptome in the context of cellular adaptation to quiescence. To investigate how RNA self-organization into condensates controls mRNA cytosolic stoichiometries depending on sequence identity and translational activity, we adapted a new Fluorescent Activated Particle Sorting (FAPS) method to selectively sort germline P-bodies from C. elegans oocytes. Fluorescently labelled in oocytes, GFP:CAR-1 P-bodies were formaldehyde fixed and FAPS sorted from whole animal extracts by their size and fluorescence.
We then performed gene expression profiling analysis using data obtained from RNA-seq of oocyte P-bodies, dissected oocytes and whole animal extracts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for oocyte P-bodies, dissected oocytes and whole animal extracts.

first: Szilvia

last: Ecsedi

first: Andres

last: Cardona-Echeverry


title: Gene expression signatures in Arabidopsis thaliana roots under sufficient nitrogen or mild nitrogen deficiency

city: Seeland

first: Anja

last: Hartmann

state: Saxony-Anhalt

address: Corrensstraße 3

department: PZB

country: Germany

institute: IPK Gatersleben

summary: To optimize access to nitrogen under limiting conditions, root systems must continuously sense and respond to local or temporal fluctuations in nitrogen availability. In Arabidopsis thaliana and several other species, external N levels that induce only mild deficiency stimulate the emergence of lateral roots and especially the elongation of primary and lateral roots. However, the identity of the genes involved in this coordination remains still largely elusive. In order to identify novel genes and mechanisms underlying nitrogen-dependent root morphological changes, we investigated time-dependent changes in the root transcriptome of Arabidopsis thaliana plants grown under sufficient nitrogen or under conditions that induced mild nitrogen deficiency.

overall_design: Gene expression in whole roots of Arabidopsis thaliana was measured after transferring seven-day-old seedlings for 0, 1, 2 and 4 days to 11.4 mM nitrogen (N-sufficient; control) or 0.55 mM nitrogen (mild N deficiency). Three biological replicates were used.

first: Nicolaus

last: von Wirén

first: Ricardo

last: Giehl


title: The catalytic activity of TET1 is required for human germ cell fate choice

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


title: The catalytic activity of TET1 is required for human germ cell fate choice [bulk RNA-seq]

overall_design: We applied bulk RNAseq in hESCs and iMeLCs during hPGCLC differentiation in Control (CTRL, 3 replicates) and TET1 catalytic domain knockout (CDKO, 3 replicates) lines.


title: Grainyhead-like 2 influences renal cyst growth in a mouse model

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: To characterize GRHL2 as a potential progression modifier and therapeutic target in autosomal-dominant polycystic kidney disease.

overall_design: Kidneys of wildtype, Grhl2 knockout, and Myc overexpression mice were characterized using histology, immunnofluorescence, Western blotting, RT-qPCR, and RNA-sequencing.

first: Zeliha

middle: Y

last: Yurtdas

first: Ergin

last: Kilic

first: Peter

last: Boot

first: Markus

last: Landthaler

first: Klaus

last: Jung

first: Kai

last: Schmidt-Ott


title: A grainyhead transcription factor Tfcp2l1 controls the timing for lung alveolar regeneration

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania


title: RNautophagic regulation of DNMT3a-dependent DNA methylation

city: Hangzhou

first: Liyuan

last: Zhu

state: Zhejiang

address: NO.3, East Qingchun Road, Shangcheng Distinct

department: Sir Run Run Shaw Hospital, School of Medicine

institute: Zhejiang University

summary: Calorie restriction has long been known to extend lifespans and inhibit carcinogenesis in multiple species by slowing age-related epigenetic changes while the underlying mechanisms remain largely unknown. Herein, we found that starvation activated autophagy to remodel DNA methylation profile by inhibiting DNMT3a expression. Autophagy is impaired in chemoresistance which was associated with differential DNA methylation and could be reversed by DNMT3a inhibition. Autophagy activation decreases the expression of DNMT3a mRNA, accompanied with the downregulation of chemoresistance-related Linc00942. Knockdown of Linc00942 reduces DNMT3a expression and genome-wide DNA methylation while Linc00942 overexpression increased DNMT3a expression and correlated hypermethylation in cancer cells and primary tumor tissues. As a result, inhibition of autophagy increases Linc00942 expression to promote chemoresistance and autophagy activation or hypomethylating agent decitabine restores chemosensitivity by reducing global DNA methylation. Taken together, our study identifies a novel methylation cascade linking impaired RNautophagy to global hypermethylation in chemoresistance, and provides a rationale for repurposing decitabine to overcome chemoresistance in cancer treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SGC7901 chemoresistant cells to DDP and its KD derivatives (siLinc00942).

first: Hongchuan

last: Jin

first: Lifeng

last: Feng

first: Yiran


title: A grainyhead transcription factor Tfcp2l1 controls the timing for lung alveolar regeneration (scRNA-Seq)

summary: Alveolar epithelial type 2 (AT2) cells are facultative progenitor cells that drive adult alveolar regeneration after acute lung injury. Using transcriptomic analyses from in vivo mouse injury models, we define the role of Tfcp2l1 in regulating AT2 cell behavior during lung regeneration.

overall_design: To determine the role of Tfcp2l1 in AT2 cells, we generated SftpcCreERT2; R26REYFP or SftpcCreERT2; Tfcp2l1fl/fl; R26REYFP mice, allowing us to inactivate Tfcp2l1 in AT2 cells and trace their fate. To assess whether Tfcp2l1 regulates AT2 cell-mediated lung regeneration,    each mouse line received three doses of 200mg/kg tamoxifen and 14 days after induction; these mice were infected intranasally with 50μL of a 1LD50 dose of mouse-adapted H1N1 PR8 influenza virus. 14 days post-viral infection, mouse lungs were isolated, and lineage traced cells (YFP+) were cell sorted to generate respective libraries for genome profiling

first: Fabian

last: Cardenas-Diaz

middle: P

first: Edward

last: Morrisey


title: A grainyhead transcription factor Tfcp2l1 controls the timing for lung alveolar regeneration (RNA-Seq)


title: Single-cell sequencing of mCherry/NGFR transduced cells from mouse hippocampus

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary: Control mCherry virus (Lv13) and mouse mCherry NGFR virus (Lv16) were injected in the Wild Type mouse brain and at 3 dpi, the hippocampi of the mouse were dissected, dissociated, and mCherry positve cells were sorted by FACS for single-cell sequencing.

overall_design: Virus transduced cells expressing mCherry reporter were enriched by FACS sorting and single-cell seqencing was performed by using 10X Genomics.

first: Tohid

last: Siddiqui

first: Mehmet

middle: I

last: Cosacak


title: Transcriptome profiling of normal breast tissue

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

summary: The Susan G. Komen Tissue Bank at Indiana University Simon Comprehensive Cancer Center (KTB) is the only repository of normal breast tissues donated by healthy women. Here, we examined the transcriptome profiling of  normal breasts from 190 healthy women, including  62 African Americans, 11 Asians, and 109 Caucasians. Correlation analysis between geen expression and risk factors for breast cancer (such as smoking, BMI, age, racial background) was performed.

overall_design: Fresh frozen normal breast tissues were obtained from the Komen tissue Bank at IUSCCC and processed for RNA extraction using the AllPrep DNA/RNA/miRNA Kit (Qiagen). The RNA was then submitted to the Center for Genomics and Bioinformatics at IU Bloomington for whole transcriptome analysis.

first: Rana

last: German

first: Ram

last: Podichetti

first: Douglas

last: Rusch

first: Hongyu

last: Gao

first: Anna

middle: M

last: Storniolo


title: Genome stability in different mouse embryonic stem cells [exome-seq]

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

summary: Naïve mouse ESCs exhibit full term developmental competence thus hold great potential in regenerative medicine. Maintaining genome stability is essential for potential application of ESCs in stem cell therapy. While ESC potency fluctuate with retrovirus activity, it is unclear whether long-term cultures affect retrotransposition and genomic stability. We compared retrotransposons in naïve ESCs using various approaches. We show that feeder-serum based culture conditions and small molecule LCDM maintain appropriate expression of retrovirus activity following long-term cultures, whereas cultures under 2iLif and a2i result in aberrant upregulation of retrotransposons. This leads to high frequent retrotransposition. Moreover, naïve ESCs on feeder-serum based culture conditions and small molecule LCDM still generate complete ESC pups by TEC assay, functional test of pluripotency, following long-term cultures, despite that all culture conditions maintain high expression levels of pluripotent genes such as Oct4, Nanog, Klf4 and Sox2. Meanwhile, long telomeres are maintained in ESCs under cultures in Feeder-serum and LCDM conditions but telomeres shortened in other conditions with increasing passages. These data provide insights into retrotransposition, genomic stability and pluripotency of naïve ESCs.

overall_design: We used 5 different ESC culture conditions to do Exome-seq for analyzing the mutations in different ESCs; and we also do ATAC-seq for analyzing mutations in turmors derived from ESC-derived mice (by tetraploid complementary assay)


title: Genome stability in different mouse embryonic stem cells super


title: Genome stability in different mouse embryonic stem cells

overall_design: We used 5 different ESC culture conditions to do RNA-seq for analysis the gene expression of pluripotent genes, Endogenous retroviruses and epigenetic regulators.


title: Genome stability in different mouse embryonic stem cells [ATAC-seq]

overall_design: We used 5 different ESC culture conditions to do ATAC-seq for analysis the chromatin accessibility of global genome, pluripotent genes, endogenous retroviruses and epigenetic regulators.


title: Gene Profiles of Mesenchymal Stromal  Cells from Different Tissue

city: Bethesda

first: Junji

last: Xu

address: 9000 Rockville Pike

institute: NIH, NIDCR

summary: Mesenchymal stromal stem cells from human bone marrow (BMSCs), adipose tissuse (ADSCs) were purchased from ATCC. Human exfoliated deciduous dental pulps were cultured in vitro and purified to get stem cells from human exfoliated deciduous teeth (SHED). Markers of MSCs were checked before scRNA seq.

overall_design: Single cell RNA sequecing on BMSCs, ADSCs and SHED

first: Ousheng

last: Liu

first: Daniel

last: Martin

first: Zheng

last: Wei

first: Robert

last: Morell

first: Wanjun

last: Chen


title: Transcriptome profile of IFT20 Floxed mouse RPE cells all positve for DCT Cre

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary: To analyse gene expression differences between Control and IFT20/DCT-Cret mouse RPE cells at three different time points.

overall_design: Total RNA was extracted from Retinal Pigment Epithelial Cells  at 3 different time points

first: R

first: S

last: Schneider

first: H

last: May-Simera


title: LPS binding protein and activation signatures are upregulated during asthma exacerbations in children

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

summary: Asthma exacerbations in children are associated with respiratory viral infection and atopy, resulting in systemic immune activation and infiltration of immune cells into the airways. The gene networks driving the immune activation and subsequent migration of immune cells into the airways remains incompletely understood. Cellular and molecular profiling of PBMC was employed on paired samples obtained from atopic asthmatic children (n = 19) during acute virus-associated exacerbations and later during convalescence. Systems level analyses were employed to identify coexpression networks and infer the drivers of these networks, and validation was subsequently obtained via independent samples from asthmatic children. During exacerbations, PBMC exhibited significant changes in immune cell abundance and upregulation of complex interlinked networks of coexpressed genes. These were associated with priming of innate immunity, inflammatory and remodelling functions. We identified activation signatures downstream of bacterial LPS, glucocorticoids and TGFB1. We also confirmed that LPS binding protein was upregulated at the protein-level in plasma. Multiple gene networks known to be involved positively or negatively in asthma pathogenesis, are upregulated in circulating PBMC during acute exacerbations, supporting the hypothesis that systemic pre-programming of potentially pathogenic as well as protective functions of circulating immune cells preceeds migration into the airways. Enhanced sensitivity to LPS is likely to modulate the severity of acute asthma exacerbations through exposure to environmental LPS.

overall_design: The study design consisted of 19 paired samples from acute exacerbation of asthma (acute visit =AV) and following recovering at convalescence (CV). RNA-Seq profiles were generated by sequencing llumina HiSeq2500, 50bp single-end reads, v4 chemistry. Each sample was sequenced across two lanes.

middle: C

first: Jonatan

last: Leffler

first: Ingrid

last: Laing

first: Joelene

last: Bizzintino

first: Siew-Kim

last: Khoo

first: Peter

middle: N

last: LeSoeuf

middle: D

last: Sly

first: Deborah

last: Strickland

first: Patrick

middle: G

last: Holt

first: Anthony

last: Bosco


title: Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers [ATAC-seq]

status: Public on Sep 11 2023

city: Cambridge

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

summary: The BRG/Brahma-associated factors (BAF or mSWI/SNF) family of chromatin remodeling complexes are critical regulators of gene expression and are major determinants of cancer and other diseases. Two paralog ATPases, SMARCA4 and SMARCA2 (BRG1 and BRM, respectively), provide the enzymatic activity required for chromatin remodeling.   Here, we discover and characterize a novel series of compounds that potently and selectively inhibit SMARCA4/SMARCA2.  Mutational and biochemical studies demonstrate that these inhibitors act through a unique mode of inhibition, distinct from reported SMARCA4/SMARCA2 inhibitors.  Across a range of cancer cell lines, SMARCA4/SMARCA2 inhibition resulted in lineage-specific changes in chromatin accessibility at binding sites for key transcription factors (TFs).  In uveal melanoma (UM), BAF inhibition resulted in loss of enhancer occupancy of SOX10 and MITF, two essential TFs, leading to down-regulation of the melanocytic gene expression program.  In a mouse xenograft model of UM, SMARCA4/SMARCA2 inhibition was well tolerated and resulted in dose-dependent tumor regression correlating with pharmacodynamic modulation of BAF-target gene expression.  These data provide the foundation for first-in-human studies of BAF ATPase inhibition as a novel therapeutic to treat TF-dependent cancers.

overall_design: Comparative chromatin accessibility profiling analysis of ATAC-seq data for 92-1,22RV1,RD,A375,DU4475,HCT116 cells treated with dual SMARCA4/SMARCA2 inhibitor FHT-1015 for 4h

first: Richard

last: Centore

first: Luis

last: Soares


title: Melanoma cells repress Desmoglein 1 in keratinocytes to promote tumor cell migration

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: Melanoma is an aggressive cancer typically arising from transformation of melanocytes residing in the basal layer of the epidermis, where they are in direct contact with surrounding keratinocytes. The role of keratinocytes in shaping the melanoma tumor microenvironment remains understudied. We previously showed that temporary loss of the keratinocyte-specific cadherin, Desmoglein 1 (Dsg1) controls paracrine signaling between normal melanocytes and keratinocytes to stimulate the protective tanning response. Here, we provide evidence that melanoma cells hijack this intercellular communication by secreting factors that keep Dsg1 expression low in surrounding keratinocytes, which in turn generate their own paracrine signals that enhance melanoma spread through CXCL1/CXCR2 signaling. Evidence suggests a model whereby paracrine signaling from melanoma cells increases levels of the transcriptional repressor Slug, and consequently decreases expression of the Dsg1 transcriptional activator Grhl1. Together, these data support the idea that paracrine crosstalk between melanoma cells and keratinocytes resulting in chronic keratinocyte Dsg1 reduction contributes to melanoma cell movement associated with tumor progression.

overall_design:
Melanoma cell lines treated with conditioned media from keratinocytes expressing shNT or shDsg1. Keratinocytes and melanocytes were isolated from discarded neonatal foreskin provided by the Northwestern University Skin Biology and Diseases Research-Based Center (NUSBDRC) as previously described (Roth-Carter et al., 2022). Keratinocytes were grown in M154 medium (Life Technologies) supplemented with human keratinocyte growth supplement (Life Technologies), 1,000 x gentamycin/amphotericin B solution (Life Technologies), and 0.07mM CaCl2.
Keratinocytes were treated with conditioned media from melanoma cells for 48 hours and melanoma cells were cultured with conditioned media from keratinocytes expressing shNT or shDsg1 for 24 hours. Total RNA was extracted from cells using the Quick-RNA miniprep kit (Zymo Research) following the manufacturer’s protocol. Novogene Co., LTD conducted preparation of the mRNA library and transcriptome sequencing.
Differential expression analysis was performed using DESeq2, with a batch correction to account for keratinocyte clonal variation. Genes with p-value < 0.05 and |log2(FoldChange)| > 1 were considered to be differentially expressed.

first: Hope

middle: E

last: Burks

first: Jenny

last: Pokorny

first: Jennifer

last: Koetsier

first: Quinn

last: Roth-Carter

first: Christopher

last: Arnette

first: Pedram

last: Gerami

first: John

middle: T

last: Seykora

first: Jodi

last: Johnson

first: Kathleen

middle: J

last: Green


title: A Single-Cell Transcriptomic Atlas Characterizes Age-Related Changes of Murine Cranial Stem Cell Niches

city: Chengdu

first: Bo

last: Li

state: Sichuan

address: No. 14, 3rd Section, Renminnan Road

department: Department of Orthodontics

institute: West China School of Stomatology

summary: The bone tissue undergoes constant turnover, which relies on skeletal stem cells (SSCs) and/or mesenchymal stem cells (MSCs) and their niches. SSCs/MSCs and their perivascular niche within the bone marrow are well characterized in long bones. As for cranial bones, besides bone marrow, the suture mesenchyme has been identified as a unique niche for SSCs/MSCs of craniofacial bones. However, a comprehensive study of the two different cranial stem cell niches at single-cell resolution is still lacking. In addition, during the progression of aging, age-associated changes in cranial stem cell niches and resident cells remain uncovered. In this study, we investigated age-related changes in cranial stem cell niches via single-cell RNA sequencing (scRNA-seq).

overall_design: Mouse cranial bone marrow tissue was harvested from wild-type C57BL/6 mice of three different age groups, i.e., two months old (02m), twelve months old (12m), and eighteen months old (18m), with six to eight male mice (6M-8M) in each group. In total, six libraries were created, including three libraries of cranial bone marrow adjacent to the suture (CBMA_02m; CBMA_12m; CBMA_18m) and three libraries of cranial bone marrow distant from the suture (CBMD_02m; CBMD_12m; CBMD_18m).