title: Transcriptome-wide characterization of genetic perturbations

status: Public on May 05 2024

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

summary: Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of cellular perturbations at scale. However, the data produced by these screens are inherently noisy, limiting power to detect true effects with conventional differential expression analyses. Here, we introduce TRanscriptome-wide Analysis of Differential Expression (TRADE), a statistical framework which estimates the transcriptome-wide distribution of true differential expression effects from noisy gene-level measurements.

overall_design: This repository contains data from two large-scale pooled CRISPR screens with single-cell RNA sequencing readout (ie Perturb-seq) experiments in Jurkat and HepG2 cells. Jurkat and HepG2 screens were conducted in parallel. Cells were transduced with a lentiviral library bearing dual sgRNA expression vectors targeting a library consisting primarily of DepMap common essential genes at low infection rate. Cells were selected for sgRNA expression vector by FACS on day 3 post-transduction. On day 7 post-transduction, cells were harvested for single-cell RNA-sequencing on the 10x Genomics Chromium Single-Cell 3′ Gel Beads v3.

first: J

first: A

last: Nadig

first: L

last: O'Connor

middle: S

last: Weissman


title: Immune profiling-based targeting of pathogenic T cells with ustekinumab in ANCA-associated glomerulonephritis

status: Public on Jul 01 2024

city: Hamburg

first: Darius

last: Schaub

state: Hamburg

address: Billhorner Kanalstraße 22

department: Center for Biomedical AI

country: Germany

institute: University Medical Center Hamburg

type: Expression profiling by high throughput sequencing

summary: Antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis is a life-threatening autoimmune disease that often results in kidney failure caused by crescentic glomerulonephritis (ANCA-GN). To date, treatment of most patients with ANCA-GN relies on unspecific immunosuppressive agents that harbor serious adverse effects and limited efficiency. By performing spatial and single-cell transcriptome analysis, we characterized inflammatory niches in the kidneys of 34 patients with ANCA-GN and identified pro-inflammatory, cytokine producing CD4+ (TH1 and TH17 subsets) and CD8+ T cells (TC1 and TC17-like subsets) as a key pathogenic signature. Digital pharmacology identified ustekinumab, a monoclonal antibody targeting IL-12 and IL-23 in these T cells, as the most promising therapeutic drug to target. Based on these findings, four patients with relapsing ANCA-GN were treated with ustekinumab in combination with low-dose cyclophosphamide. Ustekinumab was given subcutaneously (90 mg) at weeks 0, 4, 12, and 24 and clinical and renal responses were evaluated at week 26. This treatment was well-tolerated and induced clinical response in all ANCA-GN patients, including an improved kidney function and Birmingham Vasculitis Activity Score. Our findings suggest that the pathogenesis-based treatment of ANCA-GN patients with ustekinumab is efficacious and warrants further investigation in clinical trials.

overall_design: ScRNA-seq of human samples from the kidney and peripheral blood, specifically from individuals with ANCA-associated glomerulonephritis, was performed from FACS-sorted CD3 positive T cells using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 50,000 reads per cell on an Illumina NovaSeq™ (P150).

middle: P

first: Jonas

last: Engeßer

first: Robin

last: Khatri

first: Stefan

last: Bonn

first: Christian

middle: F

last: Krebs

first: Ulf

last: Panzer


title: Designing Molecular RNA Switches with Restricted Boltzmann Machines

status: Public on May 06 2024

city: Paris

first: Pierre

last: HARDOUIN

state: France

address: 4 avenue de l'observatoire

department: CiTCoM

country: France

institute: Faculté de pharmacie UMR 8038

summary: Riboswitches are structured allosteric RNA molecules that change conformation in response to a metabolite binding event, eventually triggering a regulatory response. Computational modelling of the structure of these molecules is complicated by a complex network of tertiary contacts, stabilized by the presence of their cognate metabolite. In this work, we focus on the aptamer domain of SAM-I riboswitches and show that Restricted Boltzmann machines (RBM), an unsupervised machine learning architecture, can capture intricate sequence dependencies induced by secondary and tertiary structure, as well as a switching mechanism between open and closed conformations. The RBM model is then used for the design of artificial allosteric SAM-I aptamers. To experimentally validate the functionality of the designed sequences, we resort to chemical probing (SHAPE-MaP), and develop a tailored analysis pipeline adequate for high-throughput tests of diverse homologous sequences. We probed a total of 476 RBM designed sequences in two experiments, showing between 20% and 40% divergence from any natural sequence, obtaining ≈ 30% success rate of correctly structured aptamers that undergo a structural switch in response to SAM.

sample_organism:
Bacteria
synthetic construct

platform_organism:
Bacteria
synthetic construct

overall_design: DNA oligonucleotides representing the 206 SAM-I aptamer natural sequences, and the two batches (100 and 450) of artificial sequences, preceded by the T7 promoter (5’CGGCGAATCTAATACGACTCACTATAGG3’) and followed by a tag sequence representing a 10 nucleotide bar code unique for each aptamer and a primer binding site, were purchased as an oligonucleotide pool (Twist bioscience®). The Tag sequence was designed to avoid interference with the aptamer secondary structure using RNAFold. The oligo pool was PCR amplified using the T7 promoter as forward primer and and five different reverse primers. RNAs were in vitro transcribed by using the T7 RNA polymerase and were checked for the absence of aberrant products on a 1% agarose gel. SHAPE chemical probing was performed as described previously [1]. Then, RNAs were then reverse transcribed with the Superscript III reverse transcriptase (Invitrogen®) and NGS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs®). Final products were sequenced by using the illumina technology (NextSeq 500/500 Mid 2x150 flowcell). Sequencing data were analyzed and reactivity maps were derived using ShapeMapper2.  [1] N. A. Siegfried, S. Busan, G. M. Rice, J. A. Nelson, and, K. M. Weeks. Rna motif discovery by shape and mutational profiling (shape-map). Nature methods, 11(9):959–965, 2014.

first: Jorge

last: Fernandez-de-Cossio-Diaz

last: Hardouin

first: Francois-Xavier

last: Lyonnet du Moutier

first: Andrea

last: DiGioacchino

first: Bertrand

last: Marchand

first: Yann

last: Ponty

first: Bruno

last: Sargueil

first: Remi

last: Monasson

first: Simona

last: Cocco


title: Auricular Malformations Driven by Copy Number Variations in a Hierarchical Enhancer Cluster and Dominant Enhancer Recapitulates Human Pathogenesis

status: Public on May 01 2024

city: Guangzhou

first: Xu

last: Xiaopeng

address: 96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District

country: China

institute: Guangzhou National Laboratory

summary: Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. While HMX1 downstream enhancer is associated to ear malformations, the mechanisms underlying bilateral constricted ear (BCE) remain unclear. Here, we identify a copy number variation (CNV) containing three enhancers—collectively termed the positional identity hierarchical enhancer cluster (PI-HEC)—that drives BCE by coordinately regulating HMX1 expression. Each enhancer exhibits distinct activity-location-structure features, and the dominant enhancer with high mobility group (HMG)-box and homeodomain TF motifs modulating its activity and specificity, respectively. Mouse models demonstrate that neural crest-derived fibroblasts with aberrant Hmx1 expression in the basal pinna, along with ectopic distal pinna expression, disrupt outer ear development, affecting cartilage, muscle, and epidermis. Our findings elucidate mammalian ear morphogenesis and underscore the complexity of synergistic regulation among enhancers and between enhancers and transcription factors.

overall_design: Using of scRNA-seq to trace Hmx1 expressed cells during mouse pinna development from E10.5 to E14.5

first: Xiaopeng

last: Xu

first: Qi

last: Chen

first: Qingpei

last: Huang

first: Timothy

last: C. Cox

first: Hao

last: Zhu

first: Jintian

last: Hu

first: Xi

last: Han

first: Ziqiu

last: Meng

first: Bingqing

last: Wang

first: Zhiying

last: Liao

first: Wenxin

first: Baichuan

last: Xiao

first: Ruirui

last: Lang

first: Jiqiang

last: Liu

first: Jian

first: Xiaokai

last: Tang

first: Jinmo

first: Qiang

last: Li

first: Ting

first: Qingguo

last: Zhang

first: Stylianos

last: E. Antonarakis

first: Jiao

first: Xiaoying

last: Fan

first: Huisheng

first: Yong-biao


title: Transcriptomic analysis of Pepck-Vpr mouse kidney

status: Public on Jun 12 2024

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

country: USA

institute: National Institutes of Health

summary: We analyzed the transcriptomic profiles Pepck-Vpr mouse kidney by single-nuclear RNA-seq.

overall_design: Transcriptomic profiles of Pepck-Vpr mouse kidney by single-nuclear RNA-seq

first: Khun

last: Zaw Latt

first: Shashi

last: Shrivastav

first: Jurgen

last: Heymann

first: Yongmei

last: Zhao

first: Cheryl

middle: A

last: Winkler

first: Jeffrey

middle: B

last: Kopp


title: Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [DNaseI-seq]

city: Seattle

first: Jeff

last: Vierstra

state: WA

address: 2211 Elliot Ave

institute: Altius Institute for Biomedical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes in the correct location and time. Here, we develop a straight-forward, one-shot approach to screen putative regulatory sequences identified in large-scale epigenomics profiling experiments for precise and programmable control of transgenes encoded within gene therapy viral vectors. We designed a library of 15,000 short sequences (~200bp) derived from a set of developmentally active DHS elements during human ex vivo erythropoiesis and cloned them into a GFP reporter lentiviral vector. In an erythroid progenitor cell line, these elements display a gradient of transcriptional enhancer activity, with some demonstrating equivalent activity to the canonical β-globin μLCR despite a 9-fold smaller size. We show that these elements are both highly cell type restricted and developmental stage specific both in vitro and in vivo. Finally, we replace the μLCR element with one of the novel short enhancers in a β-thalassemia lentiviral therapeutic vector and efficiently correct the thalassemic phenotype in patient-derived HSPCs. More broadly, our approach provides further insights into enhancer biology with wider implications into the development of highly cell type specific and efficacious viral vectors for human gene therapy.

overall_design: DNase I seq of WT and TALEN genome edited, homozygous for the deletion of either PVT1 or PPARA enhancer elements.

first: Nikoletta

last: Psatha

first: Pavel

last: Sova

first: Grigorios

last: Georgolopoulos

first: Kiriaki

last: Paschoudi

first: Mineo

last: Iwata

first: Jordan

last: Bloom

first: Tatyana

last: Ulyanova

first: Hao

last: Wang

first: Alexandra

last: Kirtsou

first: Ninos-Ioannis

last: Vasiloudis

first: Matthew

last: Wilken

first: John

last: Stamatoyannopoulos

first: Evangelia

last: Yannaki

first: Thalia

last: Papayanopoulou

first: George


title: Embryonic myeloid cells orchestrate niche cell homeostasis critical for the establishment of the definitive HSC pool [II]

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: The lifelong replenishment of blood cells relies on the function of definitive HSCs that migrate to the bone marrow during development. This process is tightly controlled by the bone marrow microenvironment. Embryonic macrophages emerge before the onset of definitive hematopoiesis, seed into discrete tissues and contribute to specialized resident macrophages throughout life. However, the functional impact of embryonic macrophages on HSCs or the niche remains unknown. Here, by taking advantage of a lineage tracer mouse tool we show that bone marrow macrophages consist of two ontogenetically distinct cell populations from embryonic and adult hematopoiesis. Mice lacking embryonic myeloid cells have decreased HSC numbers in the bone marrow accompanied by an increase of stem cells in the liver of neonate mice. The emergence of HSCs from embryonic sources is unperturbed because pre-HSC and HSC numbers are normal, suggesting a key role for embryo-derived myeloid cells in orchestrating HSC trafficking around birth. We show here that the establishment of a normal cellular niche space in the bone marrow critically depends on embryonic myeloid cells that are important for the development of mesenchymal stromal cells, but not other non-hematopoietic niche cells, providing evidence for a specific role for embryo-derived myeloid cells in the establishment of a normal niche environment pivotal for HSC homing.

overall_design: PolyA selected mRNA sequenced for 5 bone marrow samples from 3 weeks old mice in two groups: wild-type HSCs (CD48- CD150+ KSL), Rank knockin HSCs (RankCre-ki/wt;Csf1rfl/-)

first: Gülce

last: Perçin

first: Stephan

last: Culemann

first: Mathias

last: Lesche

first: Susanne

last: Reinhardt

first: Steve

last: Hoffmann

first: Claudia

last: Waskow


title: Effect of VGLL2-NCOA2, YAP5SA and GFP overexpression on chromatin accessibility profiling in HEK293T cells (ATAC-Seq)

status: Public on May 22 2024

city: WORCESTER

first: Susu

last: Guo

state: MA

address: 7 Pocono Road

institute: UMASS Chan Medical School

summary: The vestigial like family proteins (VGLL) are thought to regulate transcription by interacting with the TEA domain transcription factors (TEAD), the primary mediators of the Hippo pathway. However, the functional regulation of VGLL proteins remains poorly characterized. Here, we explored the molecular mechanism of two VGLL2 and TEAD1 fusion proteins generated by recurrent translocations in spindle cell rhabdomyosarcoma. We demonstrated that, compared to VGLL2 and TEAD1 alone, VGLL2-NCOA2 and TEAD1-NCOA2 act as strong transcriptional activators of TEAD-mediated transcription. Although VGLL2-NCOA2 and Yes1 associated transcriptional regulator (YAP) control overlapping transcriptional programs and chromatin landscapes, the downstream transcription induced by the fusion proteins does not require YAP and WW domain containing transcription regulator 1 (TAZ). Furthermore, VGLL2-NCOA2 and TEAD1-NCOA2 fusions engage distinct epigenetic regulation by recruiting E1A binding protein p300 (p300) to drive TEAD-dependent transcription. We showed that small molecule p300 inhibition can suppress VGLL2-NCOA2 and TEAD1-NCOA2-induced oncogenic transformation both in vitro and in vivo. Overall, our data reveal a tumorigenic mechanism of VGLL and TEAD fusion proteins that is related to the Hippo pathway but independent of YAP/TAZ, suggesting potential therapeutic strategies for tumors carrying VGLL, TEAD, or nuclear receptor coactivator (NCOA) gene rearrangements.

overall_design: To investigate the effect of VGLL2-NCOA2 fusion protein and YAP5SA protein on chromatin accessibility profiling, VGLL2-NCOA2, YAP5SA and GFP plasmids were transfected into HEK293T cells and ATAC-seq was used to detect chromatin accessibility profiling.

first: Junhao

last: Mao

first: Xiaodi

last: Hu

first: Lifang

last: Ma


title: VGLL2-NCOA2 and TEAD1-NCOA2 fusions recruited p300 to drive TEAD-dependent transcription (CUT&RUN)

overall_design: To investigate the effect of VGLL2-NCOA2, TEAD1-NCOA2, YAP5SA and p300 on transcription, plasmids were transfected into HEK293T cells and CUT&RUN was used to detect chromatin accessibility profiling.


title: Transcriptomic analysis of transgenic mouse kidney glomeruli with HIV-associated nephropathy (Tg26) and human APOL1 variants expression [bulk RNA-seq]

first: Teruhiko

last: Yoshida

summary: We analyzed the transcriptomic profiles of glomeruli from BAC/APOL1xTg26 mouse kidney by bulk mRNA-seq.

overall_design: Transcriptomic profiles of glomeruli from BAC/APOL1xTg26 mouse kidney by bulk mRNA-seq

first: Khun

last: Zaw Latt

first: Yongmei

last: Zhao

first: Shashi

last: Shrivastav

first: Cheryl

last: Winkler

first: Jeffrey

last: Kopp


title: Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [DNAseq]

first: Jeff

last: Vierstra

overall_design:
DNAseq of  HUDEP-2 cells transduced with a library of 15,000 short DNA sequences cloned in a GFP-reporter lentiviral vector for assaying transcriptional enhancers. Additionally,
We then performed DNase I seq as well as CUT&RUN experiments targeting GATA1, TAL1, H3K27ac and H3K9me3 to identify chromatin features associated with transcriptional enhancer acrivity
Finally we performed genetic deletion experiments of two identified enhancer elements and performed DNaseI and RNA-seq to validate deletion of the hypersensitive sites and identify gene expression changes in cis as a result of the element deletion.

first: Nikoletta

last: Psatha

first: Pavel

last: Sova

first: Grigorios

last: Georgolopoulos

first: Kiriaki

last: Paschoudi

first: Mineo

last: Iwata

first: Jordan

last: Bloom

first: Tatyana

last: Ulyanova

first: Hao

last: Wang

first: Alexandra

last: Kirtsou

first: Ninos-Ioannis

last: Vasiloudis

first: Matthew

last: Wilken

first: John

last: Stamatoyannopoulos

first: Evangelia

last: Yannaki

first: Thalia

last: Papayanopoulou

first: George


title: Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [CUT&RUN]


title: Multiomics approach reveal novel insights in FUS driven Juvenile Amyotrophic Lateral Sclerosis: a family quartet analysis

status: Public on May 25 2024

city: New Delhi

first: Vibha

last: Taneja

state: Delhi

address: Rajinder Nagar

department: Research

country: India

institute: Sir Ganga Ram Hospital

summary: We have identified a novel de novo variation in FUS gene in a sporadic juvenile ALS patient. FUS is an RNA-binding protein actively involved in various aspect of nucleic acid metabolism. We performed RNA-seq to identify altered transcriptome in juvenile ALS.

overall_design: Identify differentially expressed genes from RNA-seq data in proband compared to family quartet (Father, mother, sister) and control (an unrelated age and gender matched healthy control)

first: Sagar

last: Verma

first: Shiffali

last: Khurana

first: Mandaville

last: Gourie-Devi

first: Ish

last: Anand

first: Yuvraj

last: Vats

first: Arpita

last: Singh

first: Manivannan

last: Jothiramajayam

first: Pallavi

last: Kshetrapal

first: Ankkita

last: Sharma

first: Saima

last: Wajid

first: Nirmal

middle: K

last: Ganguly

first: Pradip

last: Chakraborti


title: Rhamnogalacturonan Lyase 1 (RGL1), as a suppressor of E3 ubiquitin ligase Arabidopsis thaliana Ring Zinc Finger 1 (AtRZF1), is involved in dehydration response to mediate proline synthesis and pectin rhamnogalacturonan-Ⅰ composition

status: Public on Apr 29 2024

city: GWANGJU

first: Cheol Soo

last: Kim

address: 77 YONGBONG-RO, BUK-GU

country: South Korea

institute: Chonnam National University

summary: Proline metabolism plays a crucial role in both environmental stress responses and plant growth. However, the specific mechanism by which proline contributes to abiotic stress processes remains to be elucidated. In this study, we utilized atrzf1 (Arabidopsis thaliana ring zinc finger 1) as a parental line for T-DNA tagging mutagenesis and identified a suppressor mutant of atrzf1, designated proline content alterative 31 (pca31). The pca31 mutant suppressed the insensitivity of atrzf1 to dehydration stress during early seedling growth. Using Thermal Asymmetric Interlaced-PCR, we found that the T-DNA of pca31 was inserted into the promoter region of the At2g22620 gene, which encodes the cell wall enzyme Rhamnogalacturonan Lyase 1 (RGL1). Enzymatic assays indicated that RGL1 exhibited rhamnogalacturonan lyase activity, influencing cell wall pectin composition. The decrease in RGL1 gene expression suppressed the transcriptomic perturbation of the atrzf1 mutant. Silencing of the RGL1 gene in atrzf1 resulted in a sensitive phenotype similar to pca31 under osmotic stress conditions. Treatment with mannitol, salt, hydrogen peroxide and abscisic acid induced RGL1 expression. Furthermore, we uncovered that RGL1 plays a role in modulating root growth and vascular tissue development. Molecular, physiological, and genetic experiments revealed that the positive modulation of RGL1 during abiotic stress was linked to the AtRZF1 pathway. Taken together, these findings establish that pca31 acts as a suppressor of atrzf1 in abiotic stress responses through proline and cell wall metabolisms.

overall_design: As pca31 is a suppressor of atrzf1 in the osmotic stress response and pectin RG-I composition level, we hypothesized that AtRZF1 and RGL1 oppositely modulate a number of target genes. To test this hypothesis, we analyzed transcriptomic changes in WT, atrzf1, and pca31 through RNA sequencing (RNA-seq) experiments.

first: Ji-Hee

last: Min

first: Cho-Rong

last: Park

first: Ying

last: Gong

first: Moon-Soo

last: Chung

first: Seung-Hee

last: Nam

first: Hye Sup

last: Yun


title: Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors

first: Jeff

last: Vierstra

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

overall_design: Refer to individual Series


title: Embryonic myeloid cells orchestrate niche cell homeostasis critical for the establishment of the definitive HSC pool

status: Public on Apr 30 2024

first: Konstantin

last: Riege

overall_design: PolyA selected mRNA sequenced for 12 bone marrow samples from 8 weeks old mice in four groups: HSC derived macrophages (adult), embryonic progenitor derived macrophages (Rank positive linage traced, eYFP positive), Ly6Clo monocytes, Ly6Chi monocytes

first: Gülce

last: Perçin

first: Stephan

last: Culemann

first: Mathias

last: Lesche

first: Susanne

last: Reinhardt

first: Steve

last: Hoffmann

first: Claudia

last: Waskow


title: KLF5 promotes stemness and PARPi resistance through regulation of Vimintin in ovarian cancer

city: Jinan

first: shourong

last: wang

address: No. 107, Wenhua West Road, Lixia District, Jinan City, Shandong Province

institute: Qilu Hospital，Shandong University

summary: To investigate the function of KLF5 in  ovarian cancer, we established SKOV3 cell lines in which KLF5 has been knocked down by shRNA.Cells were collected and performed RNA sequencing.

overall_design: SKOV3-sh-NC cells and SKOV3-sh-KLF5 were collected.Each group contains three replicates.

first: Huimin

last: Xiao

first: Shourong

last: Wang


title: Adenoviral vector transduced in vitro differentiated C57bl6 BMDM cells

status: Public on Apr 21 2024

city: Duarte

first: Siqi

last: Chen

state: CA

address: E 1500 Duarte Rd.

department: Department of Immuno-Oncology

institute: City of Hope Beckman Research Institute

summary: Total mRNA was extracted at 48 hour post transduction using Qiagen RNeasy Kits following the manufacture’s protocol.1 ug ofRNAwas used for cDNA library construction and bulk RNA sequencing were performed by Novogene (Sacramento CA). RNA-seq raw data were analysised using Partek Flow. Briefly, sequencing reads were aligned to the mouse or human genome using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a). Aligned reads were then quantified to transcriptome (mm10; Ensembl Transcripts release 100), and normalized (Median Ratio normalization). Differentiated gene expression analysis (DESeq2) were performed to generate raw counts

overall_design: in vitro differentiated murine bone marrow derived macrophages on differentiation day 5 were replated, and transduced with mock (untreated), adenovirus carring GFP (empty vector) or HER2 targeting therapeutic payload (HER2.eSPR) on day 6. cells were collected on day 10 for RNA extraction.

first: Mingye

last: Feng


title: Auricular Malformations Driven by Copy Number Variations in a Hierarchical Enhancer Cluster and Dominant Enhancer Recapitulates Human Pathogenesis [RNA-seq]

first: Xu

last: Xiaopeng

overall_design: Expression profiles of mouse embryo E14.5 pinna structure between wild-type and transgenic mEC1 knock-in (KI) mouse model

first: Xiaopeng

last: Xu

first: Qi

first: Qingpei

last: Huang

first: Timothy

last: C. Cox

first: Hao

last: Zhu

first: Jintian

last: Hu

first: Xi

last: Han

first: Ziqiu

last: Meng

first: Bingqing

first: Zhiying

last: Liao

first: Wenxin

first: Baichuan

first: Ruirui

last: Lang

first: Jiqiang

last: Liu

first: Jian

first: Xiaokai

last: Tang

first: Jinmo

first: Qiang

last: Li

first: Ting

first: Qingguo

last: Zhang

first: Stylianos

last: E. Antonarakis

first: Jiao

first: Xiaoying

last: Fan

first: Huisheng

first: Yong-biao


title: Effect of splenectomy on liver regeneration after 70% resection in a mouse model.

status: Public on Apr 16 2024

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

summary: In this work, the effect of splenectomy on liver regeneration was studied. For this purpose in 1 series of experiments the animals were reproduced splenectomy, and after 7 days 70% liver resection was performed. It was found that spleen removal leads to a decrease in the migration of Ly6C+ monocytes into the regenerating liver. Using transcriptional analysis it was shown that spleen and peripheral blood monocytes differ in the expression of genes associated with the synthesis of surface receptors necessary for cell migration. The obtained data explain the reason for the preferential migration of spleen monocytes rather than peripheral blood monocytes into the regenerating liver.

overall_design: A model of resection of 70% of the liver mass was reproduced in mice. 24 hours after resection, blood (n=3) and spleen (n=3) were collected from animals, from which CD115+ monocytes were obtained by magnetic sorting and used in the study. Monocytes from peripheral blood (n=3) and spleen (n=3) of intact animals, obtained by magnetic sorting by CD115 marker, served as control.

first: Andrey

last: Elchaninov


title: Auricular Malformations Driven by Copy Number Variations in a Hierarchical Enhancer Cluster and Dominant Enhancer Recapitulates Human Pathogenesis [PC-HiC]

first: Xu

last: Xiaopeng

summary:
Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. While HMX1 downstream enhancer is associated to ear malformations, the mechanisms underlying bilateral constricted ear (BCE) remain unclear. Here, we identify a copy number variation (CNV) containing three enhancers—collectively termed the positional identity hierarchical enhancer cluster (PI-HEC)—that drives BCE by coordinately regulating HMX1 expression. Each enhancer exhibits distinct activity-location-structure features, and the dominant enhancer with high mobility group (HMG)-box and homeodomain TF motifs modulating its activity and specificity, respectively. Mouse models demonstrate that neural crest-derived fibroblasts with aberrant Hmx1 expression in the basal pinna, along with ectopic distal pinna expression, disrupt outer ear development, affecting cartilage, muscle, and epiderm
 is. Our findings elucidate mammalian ear morphogenesis and underscore the complexity of synergistic regulation among enhancers and between enhancers and transcription factors.

overall_design: Promoter capture HiC (PC-HiC) data of H9 derived cranial neural crest cell

first: Xiaopeng

last: Xu

first: Qi

last: Chen

first: Qingpei

first: Timothy

first: Hao

first: Jintian

first: Xi

first: Ziqiu

first: Bingqing

last: Wang

first: Zhiying

first: Wenxin

last: Xiao

first: Yong-Biao


title: Programmed RNA Editing with an Evolved Bacterial Adenosine Deaminase

city: Chicago

last: Yan

state: Illinois

address: 929 E 57th St, GCIS E535

institute: University of Chicago


title: Auricular Malformations Driven by Copy Number Variations in a Hierarchical Enhancer Cluster and Dominant Enhancer Recapitulates Human Pathogenesis [CUT&RUN]

overall_design: Analysis of CUT&RUN samples to validate transcription factor (TF) binding profile in H9-derived cranial neural crest cells (hCNCCs) using different antibodies

last: Huang

last: C. Cox

last: Zhu

last: Hu

last: Han

first: Baichuan

first: Ruirui

first: Jiqiang

first: Jian

first: Xiaokai

first: Jinmo

first: Qiang

first: Ting

first: Qingguo

first: Stylianos

first: Jiao

first: Xiaoying

first: Huisheng


title: Programmed RNA Editing with an Evolved Bacterial Adenosine Deaminase I

first: Hao

summary: To investigate the transcriptome-wide off-target editing profile of a programmed RNA editing system-DECOR.

overall_design: Comparative RNA editing analysis of RNA-seq data for HEK293T cells treated with RNA base editors

first: Yan

last: Hao

first: Tang

last: Weixin


title: Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

status: Public on Apr 07 2024

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

institute: Institute Pasteur

overall_design: MNase digestion of yeast nuclei followed by paired-end sequencing on the following strains: WT, isw2Δ, itc1Δ, itc1ΔN, isw2Δ itc1ΔN, isw1Δ chd1Δ, isw1Δ chd1Δ isw2Δ, isw1Δ chd1Δ itc1ΔN

first: Felix

last: Mueller-Planitz


title: The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics

status: Public on Apr 09 2024

city: Thousand Oaks

first: David

middle: Joseph

last: Sherman

state: California

address: 1 Amgen Center Drive, B29 DZ 2H

department: Discovery Research

institute: Amgen Inc.

summary: Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD. Despite its discovery twenty years ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and  characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-drivencellular change.

overall_design: To investigate the transcriptional changes induced by PNPLA3-I148M, we established Hep3B cell lines expressing endogenous PNPLA3 (WT) or mutant PNPLA3-I148M (I148M). We then performed gene expression profiling obtained from RNA-Seq of the two cell lines with no treatment and treated with oleic acid for 0.5, 1, 2, 4, and 24 h. We compared the gene expression profiles between the cell lines under each treatment condition.

middle: J


title: Effect of knockout of DNAJC12 on gene expression in SH-SY5Y cells [ChIP-seq]

status: Public on Mar 31 2024

city: Shanghai

first: Xi

last: Mo

address: Dongfang Road

department: Pediatric Translational Medicine Institute

institute: Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine

summary: We here reported DNAJC12 levels are negatively correlated with the prognosis of children with neuroblastoma and the knockout of DNAJC12 improves cell proliferation and invasion in neuroblastoma cells.DNAJC12 knockout results in  increase of intracellular lactic acid and H4K5la modification level. DNAJC12 affects COL1A1 gene transcription by regulating H4K5la modification level and plays an important role in neuroblastoma metastasis.

overall_design: Chromatin immunoprecipitation DNA-sequencing for histone modification H4K5la in SH-SY5Y wildtype cells and DNAJC12 knockout cells

last: Shen

first: Yaqi

last: Yang

first: Jiejun

last: Wen


title: Transcriptome changes associated with targeting mTORC1 in endothelial cells

status: Public on Apr 01 2024

city: Nashville

first: Jin

last: Chen

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

summary: Tumor metastasis, the main cause of death in cancer patients, requires outgrowth of tumor cells after their dissemination and residence in microscopic niches. Nutrient sufficiency is a determinant of such outgrowth. Fatty acids (FA) can be metabolized by cancer cells for their energetic and anabolic needs, thereby supporting metastatic progression. The vascular endothelium serves as a barrier to access of molecules into tissues, but it is unclear how fatty acid delivery to early metastatic tumors is regulated. Using a mouse model of metastatic outgrowth in the lung, we show that tumor endothelium actively promotes tumor growth by transferring FA into developing metastatic tumors. Tumor burden was significantly reduced upon endothelial-specific targeted deletion of Raptor, a unique component of the mTORC1 complex (RptorECKO). The goal of this study was to investigate how targeting Raptor/mTORC1 impacts endothelial cells.

overall_design: Control (WT) or Raptor knockout (KO) mouse primary microvascular endothelial cells were analyzed for gene expression changes.  Four biological replicates were included in the analysis, which were generated from independent experiments.

first: Deanna

middle: N

last: Edwards


title: Effect of knockout of DNAJC12 on gene expression in SH-SY5Y cells [RNA-seq]

overall_design: To investigate the function of DNAJC12 in regulating SH-SY5Y cell invasion, we established SH-SY5Y cell lines in which DNAJC12 gene has been knockout via Crispr/cas9


title: G-quadruplex stabilizer CX-5461 effectively combines with ionizing radiation to selectively target ATRX-deficient malignant glioma [RNA-seq]

status: Public on Mar 18 2024

city: Houston

first: Sharvari

last: Dharmaiah

state: TX

address: 2130 W. Holcombe Blvd.

institute: MD Anderson Cancer Center

summary: Mutational inactivation of α-thalassaemia/mental retardation X-linked (ATRX) represents a defining molecular feature in large subsets of adult and pediatric malignant glioma. ATRX deficiency gives rise to abnormal G-quadruplex (G4) DNA secondary structures at GC-rich regions of the genome, altering chromatin accessibility and enhancing DNA damage. Building on earlier work, we sought to assess the extent to which pharmacological G4 stabilization selectively enhances DNA damage and cell death in preclinical models of ATRX-deficient glioma. Deploying the G4 stabilizer CX-5461 in patient-derived glioma stem cells (GSCs) in vitro and in GSC murine flank and intracranial xenografts in vivo, we evaluated efficacy as both a single agent and in combination with ionizing radiation (IR), a central element of current treatment standards. CX-5461 promoted dose-sensitive lethality in ATRX-deficient GSCs relative to ATRX-intact controls. Mechanistic studies revealed that CX-5461 disrupted histone variant H3.3 deposition, enhanced replication stress and DNA damage pathways, activated p53-independent apoptosis, and induced G2/M arrest selectively in ATRX-deficient GSCs. These data were corroborated in vivo, where we notably demonstrated that combinational treatment leads to profound tumor growth delay and prolonged survival exclusively in ATRX-deficient flank tumors. In its totality, our work substantively demonstrates efficacy and defines mechanisms of action for a novel therapeutic strategy targeting ATRX-deficient malignant glioma, laying the groundwork for clinical translation.

overall_design: Comparative gene expression profiling analyses of RNA-seq data for patient-derived glioma stem cells (GSCs) treated for 48 hours with either Vehicle (DMSO) or G4 stabilizer CX-5461 (1 µM). GSC lines were treated in triplicates for each condition (VEH or CX) and are as follows: TS 543-sh590 (ATRX-/-), TS 543 (ATRX wt), TS 603 (ATRX wt), GS 5-22 (ATRX -/-), and GS 8-18 (ATRX -/-).

first: Prit

last: Malgulwar

first: Jason

middle: T

last: Huse


title: The BMAL1/HIF2A heterodimer modulates circadian variations of myocardial injury

status: Public on Mar 20 2024

first: Holger

middle: K.

last: Eltzschig

department: Department of Anesthesiology

institute: The University of Texas Health Science Center at Houston

summary: Cardiac injury following myocardial infarction exhibits a circadian pattern, yet the underlying mechanism remains unclear. To elucidate genes governing circadian variation of myocardial injury, we conducted transcriptomic profiling of left-ventricular tissues from mice or humans experiencing myocardial injury at different daytimes. Through comprehensive analyses, including transgenic mouse models and functional studies, we identified BMAL1 as a pivotal transcription factor modulating diurnal variation of myocardial injury. Remarkably, we discovered that BMAL1 regulates circadian-dependent cardiac injury by forming a transcriptionally active heterodimer with HIF2A. Substantiating this finding, we determined the cryo-EM structure of the BMAL1/HIF2F/DNA complex, revealing a previously unknown capacity for structural rearrangement within BMAL1. Furthermore, we confirmed amphiregulin (AREG) as a transcriptional target of the BMAL1/HIF2A heterodimer, critical for modulating circadian variation of myocardial injury. Finally, targeting the BMAL1/HIF2A-AREG pathway via timed AREG administration or enhancing circadian rhythm pharmacologically offered significant cardioprotection, implicating this pathway in treating ischemic heart disease.

overall_design:
C57BL/6J mice were subjected to myocardial ischemia and reperfusion injury via left coronary artery ligation for 45 minutes, followed by 2 hours of reperfusion at different times ( ZT8 and ZT20) under standard 12 h light/12 h dark entrainment conditions
We conducted RNA-Seq analysis on the AAR from C57BL/6J mice subjected to myocardial ischemia and reperfusion injury at two distinct time points: ZT8 and ZT20. (n=3)

first: Wei

last: Ruan

first: Tao

last: Li

first: Jaewoong

last: Lee

first: In

middle: H

last: Bang

first: Wankun

last: Deng

first: Xinxin

last: Ma

first: Seung-Hee

last: Yoo

first: Boyun

last: Kim

first: Jiwen

first: Xiaoyi

last: Yuan

first: Yu

last: An

first: Yin-Ying

last: Wang

first: Yafen

last: Liang

first: Matthew

last: Deberge

first: Dongze

last: Zhang

first: Zhen

last: Zhou

first: Yanyu

first: Josh

last: Gorham

first: Jonathan

last: Seidman

first: Christine

first: Sary

last: Aranki

first: Ragini

last: Nair

first: Lei

first: Jagat

last: Narula

first: Zhongming

last: Zhao

first: Jochen

middle: D

last: Muehlschlegel

first: Kuang-Lei

last: Tsai


title: Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level [RNA]

status: Public on Apr 25 2024

city: Baoding

first: Qing

last: LIU

state: Hebei

address: Lingyusi Street

department: College of Horticulture, College of Life Sciences

country: Afghanistan

institute: Hebei Agricultural University

summary: Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. In this study, we aimed to elucidate the TRNs of Arabidopsis under osmotic stress at the single-cell level by employing single-cell multi-omics technology to simultaneously examine gene expression and chromatin accessibility of 16,670 Arabidopsis root tip nuclei. We performed 12,968 peak-to-gene linkage at bona fide single-cell level, instead of previous computational integration at cell type level, which enabled us to obtain an unprecedented resolution to reconstruct transcriptional regulation. Pseudotime developmental trajectories revealed that osmotic stress led to shift the developmental status of Suberin synthetic endodermis (Suberin-endo) and trichoblast cells. We identified candidate stress-related cell-specific enhancers and cis-regulatory elements as well as potential target genes, and uncovered large cellular heterogeneity. We also found that cis-regulatory elements became accessible prior to gene expression and these cis-regulatory elements could form a positive feedback loop with epigenetic modification H3K4me3 in response to osmotic stress in columella cells.

overall_design: In this study, we used the 10x Chromium Single Cell Multiome ATAC + Gene Expression platform to simultaneously perform transcriptome and chromatin accessibility sequencing within the same cell in Arabidopsis root tips. This approach enabled us to more precisely dissect the transcriptional regulatory network of Arabidopsis gene expression under osmotic stress at the single-cell level.


title: G-quadruplex stabilizer CX-5461 effectively combines with ionizing radiation to selectively target ATRX-deficient malignant glioma [CUT&Tag]

first: Sharvari

last: Dharmaiah

summary: Mutational inactivation of ?-thalassaemia/mental retardation X-linked (ATRX) represents a defining molecular feature in large subsets of adult and pediatric malignant glioma. ATRX deficiency gives rise to abnormal G-quadruplex (G4) DNA secondary structures at GC-rich regions of the genome, altering chromatin accessibility and enhancing DNA damage. Building on earlier work, we sought to assess the extent to which pharmacological G4 stabilization selectively enhances DNA damage and cell death in preclinical models of ATRX-deficient glioma. To investigate the effect of G4 stabilization on histone variant H3.3 deposition on the genome, we treated patient-derived glioma stem cells (GSCs) with G4 stabilizer CX-5461 and performed cleavage under targets and tagmentation (CUT&Tag) for H3.3. Our analyses show that G4 stabilizer CX-541 disrupts H3.3 deposition in ATRX-deficient GSCs and likely enhances replication stress and DNA damage.

overall_design: Comparative global genomic profiling analyses of CUT&Tag sequencing data for patient-derived glioma stem cells (GSCs) treated for 48 hours with either Vehicle (DMSO) or G4 stabilizer CX-5461 (1 µM). GSC lines were treated in triplicates for each condition (VEH or CX) and are as follows: TS 543-sh590 (ATRX-/-), TS 543 (ATRX wt).

first: Prit

last: Malgulwar

first: Jason

last: Huse


title: Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution (RNA-Seq)

status: Public on Mar 11 2024

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: Adaptive immunity and the five vertebrate NF-kB/Rel family members first appeared in cartilaginous fish, suggesting that NF-kB family expansion allowed the acquisition of new functions to regulate adaptive immune responses. Transcriptome profiling revealed that, even in macrophages, the NF-kB family member, c-Rel, most potently regulates a cytokine gene linked to adaptive immunity, Il12b, with limiting roles at key regulators of innate immunity. Neofunctionalization of c-Rel to regulate Il12b depends on its unique DNA-binding properties, which we examined using structural, biochemical, functional, and genomic approaches. Among our findings was functional c-Rel homodimer binding to motifs with little resemblance to canonical NF-kB motifs. To determine whether c-Rel’s unique binding properties drove c-Rel-RelA divergence, we compared binding properties in various vertebrate species. c-Rel-RelA binding properties diverged in mammals and amphibians but were comparable in earlier vertebrates, suggesting that divergent DNA binding emerged relatively late during vertebrate evolution to support increasing complexity of adaptive immune regulation.

overall_design: To investigate the role of cRel in macropahge activation, we performed chromatin assosiated RNA-seq on bone marrow derived macropahges (BMDMs). We stimulated wild-type and cRel-/- BMDMs with lipid a for 0.5, 1.0, 2.0, and 6.0 hours.

first: George

last: Yeh

first: Allison

last: Daly


title: Programmed RNA Editing with an Evolved Bacterial Adenosine Deaminase II

first: Hao

last: Yan

first: Yan

last: Hao

first: Tang

last: Weixin


title: Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi

status: Public on Mar 26 2024

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

institute: Ludwig-Maximilians-Universität München

summary: Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution and single-cell RNA-seq CRISPR interference screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct in the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPR interference screen. Hence, we provide valuable resources for performing and further extending CRISPRi screens in human and non-human primates.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: Two human and one cynomolgus KRAB-dCas9 iPS cell line were transduced with species-specific lentiviral gRNA libraries. Using the 10X Genomics platform, gene-expression and CRISPR libraries for capturing the gRNAs were generated and sequenced.

first: Fiona

middle: C

last: Edenhofer

first: Anita

last: Térmeg

first: Mari

last: Ohnuki

first: Jessica

last: Radmer

first: Zane

last: Kliesmete

first: Eva

last: Briem

first: Wolfgang

last: Enard


title: cell lines

status: Public on Mar 13 2024

city: Chengdu

first: Jian

last: Zhang

state: Sichuan

address: Guoxuexiang Road

department: Westchina Hospital

institute: Sichuan University

type: Methylation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level

first: Qing

last: LIU


title: Single nuclei RNA sequencing of skin draining lymph nodes in the setting of skin inflammation and RAG1 fate mapping

status: Public on Apr 28 2024

city: St. Louis

first: Aaron

last: Ver Heul

state: MO

address: 660 S Euclid Ave.

department: Medicine

institute: Washington University School of Medicine

summary: Type 2 inflammation contributes to the pathology of skin diseases such as atopic dermatitis (AD) and urticaria. We previously found that AD-like inflammation induced by calcipotriol in mice is critically mediated by group 2 innate lymphoid cells (ILC2s), while T cells and B cells are dispensable given development of robust AD-like disease in RAG knockout mice. Indeed, we found that in RAG knockout mice AD-like inflammation was worse, with a proportion of ILC2s displaying increased markers of activation. The goal of this study was to characterize transcriptional and epigenomic changes in ILC populations with a history, or not, of expressing RAG1 in the setting of AD-like skin inflammation.

overall_design: Mice expressing a Cre-inducible dimeric dimeric red fluorescent protein (tdRFP) were crossed to mice expressing transgenic Cre under the control of the Rag1 promoter, allowing labeling of any cells that expressed RAG1. These mice were treated with topical calcipotriol to induce atopic-dermatitis-like inflammation and cells from lymph nodes draining the affected skin were collected for sequencing. Since our focus was on ILCs, we used magnetic-activated cell sorting to deplete T cells, B cells and granulocytes. Using a custom reference library including the sequence for tdRFP, we were able to determine which of the cells we sequenced had a history, or not, of expressing RAG1 to enable analysis of any transcriptional or epigenomic differences RAG1 expression might confer on ILCs.

middle: M

first: Lydia

last: Zamidar

first: Ting-lin

last: Yang

first: Brian

last: Kim


title: Gene expression of PC9 and PC9-OR cell line [JXQ_RNA]

summary: To investigate the abnormal gene expression in Osimertinib Resistance lung cancer cell line, We performed gene expression profiling analysis using data obtained from RNA-seq of PC9 cell line and PC9-OR cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PC9 and PC9-OR cell lines.


title: Silencing of NFYC-AS1 by Gapmer antisense oligonucleotides and CRISPR/Cas9 TSS deletion.

status: Public on Mar 08 2024

city: Milan

first: Paolo

last: Gandellini

state: Milan

address: Via celoria 26

department: Bioscience

country: Italy

institute: University of Milan

summary: NFYC-AS1 is an overlapping antisense RNA transcribed head-to-head to NFYC sense gene, encoding for the subunit C of NF-Y transcription factor, which is known as master regulator of cell cycle and proliferation in normal and tumor cells. Here we performed NFYC-AS1 silencing in lung squamous carcinoma H520 cells by Gapmer antisense oligonucleotides and CRISPR/Cas9 TSS deletion. Afterwards, we performed differentially expressed analysis and gene set enrichement analysis to investigate on NFYC-AS1 function and mechanism of action.

overall_design: RNA sequencing of H520 cells knocked down for NFYC-AS1 by Gapmer antisense oligonucleotides performed in four replicates and for four independent CRISPR edited clones and three independent non-edited clones.

first: Cecilia

last: Pandini

first: Giulia

last: Pagani


title: CHMP5-Mediated Transcriptional Regulation of T-Cell Acute Lymphoblastic Leukemia

status: Public on Feb 26 2024

city: Bethesda

first: Stanley

last: Adoro

state: MD

address: Center Dr

department: CCR

institute: NCI

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Effects of targeting endothelial mTORC1 on metastatic tumor cells

first: Jin

last: Chen

summary: Tumor metastasis, the main cause of death in cancer patients, requires outgrowth of tumor cells after their dissemination and residence in microscopic niches. Nutrient sufficiency is a determinant of such outgrowth. Fatty acids (FA) can be metabolized by cancer cells for their energetic and anabolic needs, thereby supporting metastatic progression. The vascular endothelium serves as a barrier to access of molecules into tissues, but it is unclear how fatty acid delivery to early metastatic tumors is regulated. Using a mouse model of metastatic outgrowth in the lung, we show that tumor endothelium actively promotes tumor growth by transferring FA into developing metastatic tumors. Tumor burden was significantly reduced upon endothelial-specific targeted deletion of Raptor, a unique component of the mTORC1 complex (RptorECKO). The goal of this study was to investigate how endothelial mTORC1 alters metastatic tumor cells.

overall_design: To model metastatic outgrowth, tail vein injection of LLC-GFP-luciferase cells was performed in control (WT) mice or those with a endothelial-targeted Raptor knockout (Raptor ECKO). GFP+ tumor cells were collected by cell sorting and gene expression analysis was evaluated. Four biological replicates were evaluated, which were  generated from independent experiments.

first: Deanna

last: Edwards

first: Shan

last: Wang


title: Bulk RNA sequencing data of rice root sections for Single-cell RNA-seq developmental stage annotation

status: Public on Mar 03 2024

first: Rachel

last: Shahan

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

summary: We report raw bulk RNA sequencing data of rice root sections from Meristem, Elongation and Maturation zones

overall_design: Sections (root tip to end of lateral root cap: Meristem; end of lateral root cap to the start of root hair elongation: Elongation; 1mm each beyond the start of root hair elongation: Maturation1 and Maturation2)were harvested. Samples were frozen in liquid nitrogen and RNA was isolated using the Zymo MagBead RNA Isolation kit. RNA was used as input into the Lexogen QuantSeq 3′ FWD RNA-Seq library preparation procedure. Libraries were indexed and pooled on an Illumina NextSeq. Reads were aligned to Michigan State University Rice genome v7 counted with HTSeq-Count.

first: Mingyuan

last: Zhu

first: Che-Wei

last: Hsu

first: Ogorek

last: Lucas

first: Isaiah

middle: W

last: Taylor

first: Medhavinee

last: Mijar

first: Trevor

last: Nolan

first: Ari

last: Sadanandom

first: Malcolm

last: Bennett

first: Philip

last: Benfey

first: Bipin

last: Pandey


title: CHMP5-Mediated Transcriptional Regulation of T-Cell Acute Lymphoblastic Leukemia (CHIPseq)

summary: Oncogene activity rewires cellular transcription to create new transcriptional networks which cancer cells become addicted to through mechanisms that remain unresolved. Using human and mouse models of T-cell acute lymphoblastic leukemia (T-ALL), we identified an essential requirement of the endosomal sorting complex required for transport (ESCRT) protein CHMP5 in enabling the T-ALL transcriptional program. Loss of CHMP5 impaired recruitment of the bromodomain transcriptional coactivator BRD4 to enhancer and super-enhancers which caused RNA polymerase II stalling, resulting in severe downregulation of key pro-leukemogenic genes, including MYC and MYC-target genes. Mechanistically, CHMP5 facilitated BRD4 interaction with the histone acetyl transferase p300 to promote H3K27 acetylation at pro-T-ALL gene regulatory elements. Validating its importance to T-cell leukemogenesis, CHMP5-deficiency mitigated chemoresistance in human T-ALL cells and abrogated T-ALL initiation by oncogenic NOTCH1 in vivo. Collectively, our results uncover an unexpected transcriptional activity of CHMP5 that is essential for T-ALL pathogenesis.

overall_design: CHIPseq of BRD4, Pol II, and H3K27ac from CUTLL1 cells treated with control shRNA (CT) and CHMP5 shRNA (KD).

first: Katharine

last: Umphred-Wilson

first: Shashikala

last: Ratnayake

first: Qingrong


title: Soluble E-cadherin stimulated EcCAR-MSCs and UTD-MSCs with 3 normal donors

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

summary: Bulk RNAseq was performed across 3 biological donors of MSCs transduced with EcCAR (EcCAR-MSCs) or untransduced (UTD-MSCs)

overall_design: MSCs from normal donors were transduced with a replication-incompetent lentiviral vector expressing a second-generation chimeric antigen receptor (CAR) consisting of an anti-Ecad single chain variable fragment (FMC63) fused to CD28 and CD3ζ intracellular domains as previously described. Cells were then stimulated for 24 hours with soluble E-cadherin fc chimera.

first: Olivia

last: Sirpilla


title: Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient GC B cell responses [ATAC-seq]

status: Public on Feb 14 2024

first: Vipul

last: Shukla

address: 303 E. Superior Street

department: Department of Cell and Developmental Biology

institute: Northwestern University

summary: Differentiating B cells in germinal centers (GC) require tightly coordinated transcriptional and epigenetic transitions to generate efficient humoral immune responses. The mammalian BAF (Brg1/Brm-associated factor) complexes are major regulators of nucleosomal remodeling, crucial for cellular differentiation and development, and are commonly mutated in several cancers, including GC-derived B cell lymphomas. However, the specific roles of distinct BAF complexes in GC B cell biology and the generation of functional humoral immune responses are not well-understood. Here, we show that the Arid1a-dependent canonical BAF (cBAF) complex is indispensable for generatingon of fully mature GCs and high affinity humoral immune responses. While Arid1a-deficient B cells undergo activation to initiate GC responses, they fail to sustain the GC program, resulting incausing premature GC collapse. Mechanistically, Arid1a-dependent cBAF activity establishes permissive chromatin landscapes at several thousand genomic regions during B cell activation and isare concomitantly required to suppress inflammatory gene programs to maintain transcriptional fidelity in early GC B cells. Interestingly, the inflammatory signatures instigated by Arid1a- deficiency in early GC B cells recruits neutrophils and inflammatory monocytes, and eventually disrupts GC homeostasis. Remarkably, dampening of inflammatory cues with anti-inflammatory glucocorticoid receptor signaling rescues GC B cell differentiation of Arid1a-deficient B cells, thus highlighting a critical role of inflammation in impeding GC responses. In sum, our work identifies essential functions of Arid1a-dependent BAF activity in promoting efficient GC responses. These findings further support recent paradigms uncovering a deterministic role of unrestrained inflammation in obstructing GC responses, common in patients with severe bacterial and viral infections.

overall_design: To investigate the changes of chromatin accesibility in Arid1a KO in B cells, using Cd19 or Cg1cre

first: Ajay

last: Abraham

first: Daniela

last: Samaniego-Castruita

first: Jillian

last: Paladino

first: Prathyaya

last: Ramesh

first: Mi

last: Tran

first: Isabella

middle: G

last: Han

first: Rebecca

last: Southern

first: Ashima


title: Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient GC B cell responses [RNA-seq]

overall_design: To investigate the changes of gene expression in Arid1a KO in B cells, using cd19 or Cg1cre


title: Skin immune response of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Rainbow trout (Oncorhynchus mykiss) is one of the economically important cold-water fish cultivated in the world. The outbreak of infectious hematopoietic necrosis (IHN) seriously restricted the development of rainbow trout farming industry and caused huge economic losses. Fish skin is the largest mucosal immune organ, providing the first line of defense against pathogen invasion. However, the immune mechanisms associated with fish skin remain unclear. To systematically identify skin mucosal immune genes induced by infectious hematopoietic necrosis virus (IHNV) infection, trout transcriptome profiles following IHNV challenge were examined. Transcriptome analysis identified 6905 differentially expressed genes (DEGs) and revealed numerous immune-related DEGs involved in cytokine-cytokine receptor interactions, NOD-like receptor signaling, RIG-I-like receptor signaling, Toll-like receptor signaling, JAK-STAT signaling, Chemokine signaling pathway, and TNF signaling pathway, and the expression of these DEGs was significantly up-regulated in T48Skm group, including NOD1, NLRC3, NLRC5, TLR3, TLR7/8, TRIM25, DHX58, IFIH1, IRF3/7, STAT1, TRAF3, MX1, and HSP90A1. Additionally, highly interactive DEGs network involving immune-related terms and pathways was shown using protein-protein interaction network. The expression patterns of 12 DEGs were further verified by quantitative real-time PCR, which confirmed the reproducibility and reliability of transcriptome sequencing data. These findings expand our understanding of the innate immune system of rainbow trout skin infected with IHNV, and lay a foundation for further studies of the immune molecular mechanism and disease resistance breeding.

first: Jinqiang

last: Huang

first: Tongzhen

last: Sun


title: CHMP5-Mediated Transcriptional Regulation of T-Cell Acute Lymphoblastic Leukemia (Murine RNAseq)

first: Stanley

last: Adoro

overall_design: CD45.2 Chmp5f/f CD4cre- (WT) or Chmp5f/f CD4cre+ (KO) bone marrow was transduced with ICN1-NGFR retrovirus and injected into lethally irradiated CD45.1 recipients. After 4 weeks and establishment of T-ALL disease, CD45.2+ NGFR+ cells from the spleen of recipient mice were isolated by FACS and submitted for RNAseq

first: Katharine

last: Chen


title: Single-cell RNA-seq of Kitaake rice roots grown in gel, and non-compacted soil conditions

status: Public on Feb 01 2024

first: Rachel

last: Shahan

summary: We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress

overall_design:
scRNA-seq of 10 wild type (X.kitaake) grown in gel conditions, 2 wilde type grown in non-compacted soil conditions and 2 wild type grown in compacted soil conditions. The supplemtary file (Rice_12S_WT_atlas_seu3.rds.gz) contains another wild type (ZH11) grown in petri dish with wet filter paper from the previously published work: Zhang et al. PMID: 33824350; NCBI accession numbers “PRJNA706435” and “PRJNA706099”.
scRNA-seq of 2 kitaake grown in gel conditions, 2 Kitaake grown in non-compacted soil conditions.

first: Mingyuan

last: Zhu

first: Che-Wei

last: Hsu

first: Ogorek

middle: P

last: Lucas

first: Isaiah

last: Taylor

first: Medhavinee

last: Mijar

first: Trevor

last: Nolan

first: Ari

last: Sadanandom

first: Malcolm

last: Bennett

first: Philip

last: Benfey

first: Bipin

last: Pandey


title: Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient GC B cell responses

first: Vipul

last: Shukla


title: Single cell transcriptome analysis of the THY-Tau22 mouse model of Alzheimer's disease reveals sex-dependent dysregulations

status: Public on Feb 09 2024

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary: Alzheimer's disease (AD) is characterized by the accumulation of amyloid-beta and tau proteins in vulnerable brain regions. While the main pathological hallmarks of AD are shared across the sexes, a diverse array of sex differences have been documented for both AD-associated symptoms and molecular characteristics. To gain insights into AD-associated molecular changes and their sex-dependence for tau pathology in the cortex as one of the most severely affected brain regions, we performed single-cell gene activity profiling for the THY-Tau22 mouse model. By studying cell-type specific and cell-type agnostic AD-related changes and their sex-dimorphism for single genes, pathways and cellular sub-networks, we aimed to identify both statistically significant alterations and interpret the upstream mechanisms that control them.

overall_design: The study used the THY-Tau22 transgenic mouse model of Alzheimer's disease, which overexpresses a mutant human tau protein. Single-cell RNA-seq was performed on brain cortex samples from 7-month old THY-Tau22 mice and wildtype control mice (5 mice per genotype and sex). The experimental conditions compared were: THY-Tau22 transgenic males (n=5), Wildtype control males (n=5), THY-Tau22 transgenic females (n=5), and Wildtype control females (n=5).

first: Muhammad

last: Ali

first: Pierre

last: Garcia

first: Laetitia

last: Lunkes

first: Alessia

last: Sciortino

first: Melanie

last: Thomas

first: Tony

last: Heurtaux

first: Kamil

last: Grzyb

first: Rashi

last: Halder

first: Djalil

last: Coowar

first: Alex

last: Skupin

first: Luc

last: Buée

first: David

last: Blum

first: Manuel

last: Buttini


title: CHMP5-Mediated Transcriptional Regulation of T-Cell Acute Lymphoblastic Leukemia (Human RNAseq)

first: Stanley

last: Adoro

overall_design: RNAseq of CUTLL1 cells treated with control shRNA (CT) and CHMP5 shRNA (KD).

first: Katharine

last: Umphred-Wilson

first: Shashikala

last: Ratnayake

first: Qingrong

last: Chen


title: Functional consequences of impaired linc-GALNTL6-4 in adipocytes

status: Public on Jan 31 2024

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute


title: High-throughput mRNA-seq atlas of human placenta at first and third trimester, all live births

first: Margareta

last: Pisarska

address: 8635 West Third Street Suite 160

department: Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

summary: Human placenta bulk mRNA-sequencing from n=124 first trimester (59 female, 65 male) and n=43 third trimester (18 female, 25 male) tissue samples. A subset of 23 pregnancies has matched placenta tissue collected at both first and third trimester. Tissue was collected at Cedars-Sinai Medical Center in Los Angeles, California, USA. First trimester placenta was collected at gestational ages of 70-100 days from leftover tissue from chorionic villus sampling for prenatal genetic diagnosis, after cleaning to remove maternal decidua. Third trimester placenta was collected after delivery at gestational ages 254-290 days from the fetal side near the umbilical cord insertion site beneath the amnion. Tissue was stored in RNAlater RNA Stabilization Solution (Invitrogen) at -80C until further processing. All pregnancies were conceived without fertility treatments, were normal karyotype, and resulted in live singleton births. Mothers with pre-existing diabetes or hypertension were excluded from the study, but not excluded if complications developed during pregnancy, though most pregnancies were uncomplicated. The average parental age was advanced (over 35 years old) but principal components analysis did not show clustering by either maternal or paternal age. RNA extraction was performed with physical homogenization of tissue followed by the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN), then 1 ug of the total RNA elution was used for library construction using the Illumina TruSeq Stranded mRNA library preparation kit (Illumina), with polyA mRNA selection then cDNA synthesis using SuperScript II reverse transcriptase (Invitrogen) and random primers. The cDNA was converted into double stranded DNA and PCR-amplified, then purified with Agencourt AMPure XP beads (Beckman Coulter). Sample libraries were multiplexed and sequenced on a NovaSeq 6000 platform (Illumina) using 75bp single-end mRNA-sequencing, with average 30 million reads per sample. Differential expression analysis was performed with DEseq2 to compare first versus third trimester placenta, adjusted for fetal sex [PubMed ID: 38271627]. Subanalyses were also performed to identify sex differences.

overall_design: Human placenta was analyzed for differential gene expression across gestation (first versus third trimester, adjusted for fetal sex) using the DESeq2 R package. Subanalyses were also performed for first trimester placenta sex differences, third trimester placenta sex differences, female cohort first versus third trimester differences, and male cohort first versus third trimester differences.

first: Tania

middle: L

last: Gonzalez

first: Sahar

last: Wertheimer

first: Amy

middle: E

last: Flowers

first: Yizhou

last: Wang

first: Chintda

last: Santiskulvong

first: Ekaterina

last: Clark

first: Caroline

last: Jefferies

first: Kate

last: Lawrenson

first: Jessica

last: Chan

first: Nikhil

middle: V

last: Joshi

first: Yazhen

last: Zhu

first: Hsian-Rong

last: Tseng

first: S

last: Karumanchi

first: John

last: Williams III


title: Angelica dahurica Polysaccharides Ameliorates Colitis

status: Public on Jan 26 2024

city: Nanjing

first: Jingyi

last: Hu

state: Jiangsu

address: Hanzhong road No155.

institute: Affiliated Hospital of Nanjing University of Chinese Medicine

summary: ImP was further identified as an inhibitor of the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which may contribute to the development or exacerbation of colitis.

overall_design: Colitis were treated with or without ImP for 7 days. The colonic tissues were collected for further study.


title: Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability

status: Public on Mar 09 2024

city: Wuhan

first: Rui

last: Xiao

state: Hubei

address: Medical Research Institute, Wuhan University

department: Medical Research Institute

institute: Wuhan University


title: Supermajority of Chlamydia trachomatis genes are activated during the first hour of infection

status: Public on Jan 30 2024

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary:
The obligate intracellular bacterium Chlamydia has a unique developmental cycle that alternates between two contrasting cell types. With a hardy envelope and highly condensed genome, the small elementary body (EB) maintains limited metabolic activities yet can survive in an extracellular environment and is infectious. After entering host cells, EBs differentiate into larger and proliferating reticulate bodies (RBs). Progeny EBs are derived from RBs in late developmental stages and eventually exit host cells. How the expression of the chlamydial genome consisting of nearly 1000 genes governs the chlamydial developmental cycle is unclear. A previous microarray study identified only 29 immediately early genes, defined as genes activated by the first hour postinoculation, in C. trachomatis. By performing RNA sequencing analysis for C. trachomatis cultures with high multiplicities of infection (i.e., MOI of 50 and 200), we observed that 730 C. trachomatis genes underwent 2- to 900-fold activation within one hour postinoculation. By conducting quantitative reverse transcription real-time PCR (qRT-PCR) analysis for 48 of the 730 genes using an MOI of 1, we confirmed the expression increases in 46 genes. Our results demonstrate that the immediate early transcriptome is tens of times more extensive than previously realized. Gene ontology analysis indicates that the activation spans across all functional categories. We conclude that a supermajority of the C. trachomatis genes are activated almost immediately after EBs are inside host cells to initiate the differentiation toward RBs and to establish an intracellular niche conducive for chlamydial development and growth.
RNA-Seq analysis was performed for Chlamydia trachomatis L2

overall_design: Total RNA was prepared at 0 and 1 hpi.

first: Wurihan

last: Wurihan

first: Huizhou

last: Fan

first: Yi

last: Zou

first: Zhao

last: Lai


title: Prolong elevation of prolactin and sex-depnendt regulation of pain chronicity

status: Public on Feb 27 2024

summary: Prolong elevation of prolactin sex-dependently regulate pain resolution via inflammatory mechanisms

overall_design: Paw tissue from 4 males and 4 females

first: Priscilla

last: Barba-Escobedo

first: Jennifer

last: Mecklenburg

first: Andi

last: Wangzhou

first: Vincent

last: Goffin

first: Anahit

last: Hovhannisyan

first: Alexei

last: Tumanov

first: Gregory

last: Dussor

first: Theodore

last: Price

first: Armen

last: Akopian


title: High-resolution analysis of mononuclear phagocytes reveals clinically relevant markers in human colo-rectal liver metastasis - Visium Spatial Transcriptomics

status: Public on Jan 29 2024

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

institute: IRCCS Humanitas Research Hospital

summary: Macrophages (Mf) are the most abundant mononuclear phagocytes in tumor tissues and hold promise as therapeutic targets and indicators of disease progression. In this work, we mapped by single-cell analysis the distinct Mf populations infiltrating the invasive margin and normal adjacent regions of human colo-rectal liver metastasis (CLM), and we exploited this information to identify non redundant markers with clinical relevance. Different populations were enriched in the invasive margin, including early-mature, inflammatory Mf (MoMf) expressing the monocytic markers S100A12 and SERPINB2, and a more mature population (TAMs) expressing CD68, GPNMB and TREM2. TAMs were enriched in pathways of matrix degradation, angiogenesis and lipid metabolism, similarly to dysfunctional macrophages described in other tumors. Cell-cell interaction analysis with CD8+ T cells defined opposing roles of MoMf, predicted to interact via IL-15, and TAMs, engaging T cells via IL-20 and IL-10. By multiplex immunofluorescence in CLM sections, we confirmed that SERPINB2 and GPNMB are expressed by different Mf subsets, with distinct topographical distribution and opposite association with patient clinical outcome.

overall_design: Four-μm FFPE tissue sections were stained with hematoxylin and eosin (H&E) and the appropriate tissue regions (inclusive of tumor and IM) were selected for further processing.

first: R

last: Carriero

first: A

middle: R

last: Putignano

first: N

last: Cortese

first: P

last: Kunderfranco

first: F

last: Marchesi

last: Mantovani


title: Med12 cooperates with multiple differentiation signals to facilitate efficient lineage transitions in embryonic stem cells

status: Public on Jan 25 2024

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

institute: University Leiden

overall_design: Refer to individual Series


title: 6 h FGF4 stimulation of Fgf4-mutant mESCs [bulkRNA-seq]

summary: Cell differentiation results from coordinated changes in gene transcription in response to combinations of signals. FGF, Wnt, and mTOR signals regulate the differentiation of pluripotent mammalian cells towards embryonic and extraembryonic lineages, but how these signals cooperate with general transcriptional regulators is not fully resolved. Here, we report a genome-wide CRISPR screen that reveals both signaling components and general transcriptional regulators for differentiation-associated gene expression in mESCs. Focusing on the Mediator subunit Med12 as one of the strongest hits in the screen, we show that it regulates gene expression in parallel to FGF and mTOR signals. Loss of Med12 is compatible with differentiation along both the embryonic epiblast and the extraembryonic primitive endoderm lineage, but pluripotency transitions are slowed down, and the transcriptional separation between epiblast and primitive endoderm identities is enhanced in Med12-mutant cells. These cellular phenotypes correlate with reduced biological noise upon loss of Med12. These findings suggest that Med12 regulates cellular plasticity through the priming of transcriptional changes during differentiation, thereby modulating the effects of a broad range of signals.

overall_design: To investigate FGF4 target genes in mESCs, we used a Fgf4-mutant line and stimulated cells for 6h with different concentrations of FGF4.

first: Christian

last: Schröter


title: 6 h FGF4 stimulation in Fgf4-mutant and Fgf4; Med12 double mutant mESCs [bulkRNA-seq]

overall_design: We generated Med12 mutations in an Fgf4-mutant ESC line, which allowed us to specifically compare the effects on gene expression of FGF signaling, induced by supplementation of FGF4, between Med12 wild-type and-mutant cells. We included three independent biological experiments and three independent Med12-mutant lines.


title: Primitive endoderm differentiation in wild-type and Med12-mutant mESCs [scRNA-seq]

overall_design: Single cell sequencing of two Med12 wild-type and three independent Med12-mutant cell lines in the pluripotent state and after PrE differentiation. To minimize batch effects, samples were multiplexed and pooled before mRNA capture and library preparation


title: 24 h differentiation in N2B27 of wild-type and Med12-mutant mESCs [bulkRNA-seq]

overall_design: Gene expression in wild-type and Med12 mutant mESCs was compared in pluripotency and after 24h of differentiation in N2B27. Triplicates were obtained by seeding different passages on different days


title: RORγ modulates the extracellular matrix to facilitate hepatocellular carcinoma growth and metastasis

status: Public on Jan 24 2024

city: Guangzhou

first: Qianqian

last: Liu

state: State...

address: Guangzhou City, Guangdong Provinc

institute: Sun Yat-Sen university

summary: Approximately 80%-90% of hepatocellular carcinomas (HCC) occur in a premalignant environment of fibrosis and abnormal extracellular matrix (ECM), predicting an essential role of abnormal matrix in the tumorigenesis and progress of HCC. However, the determinants of ECM in HCC are poorly defined. Here, we show that nuclear receptor RORγ is highly expressed and amplified in HCC tumors. RORγ functions as an essential activator of the matrisome program via directly driving the expression of major ECM genes in HCC cells. The elevated RORγ increased Fibronectin-1 deposition, cell-matrix adhesion, collagen production and cross-linkling, creating a favorable microenvironment to boost liver cancer metastasis. Moreover, RORγ antagonists effectively inhibit tumor growth and metastasis via ECM remodeling in multiple HCC xenografts and immune-intact models, and they effectively sensitize HCC tumors to sorafenib therapy in mice. Notably, the elevated RORγ expression is associated with ECM remodeling and metastasis in patients with HCC. Taken together, we identify RORγ as a key player in HCC progression by remodeling ECM and as an attractive therapeutic target for advanced HCC.

overall_design: RNA-Seq in two conditions were investigated: (1) control HepG2 cells, (2) HepG2 cells treated with RORγ antagonists GSK805 (10µM).

first: Junhua

last: Wang

first: Zhenhua

last: Zhang

first: Hong


title: DNMT3B PWWP mutations cause hypermethylation of heterochromatin (ChIP-seq)

status: Public on Jan 22 2024

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

summary: The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies through its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here we find that knockout of DNMT3B causes losses of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1-alpha and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminus through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.

overall_design: This series contains ChIP-seq for histone modifications from human cancer cell lines. HCT116 cells and derivatives lacking DNMT3B were grown before chromatin was extracted and histone modification levels analysed by ChIP-seq.


title: Memory B cell subsets to their proliferating precursors

status: Public on Jan 07 2024

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

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


title: Masseter muscle treatment with complete Freund's adjuvant or collagenase type 2

status: Public on Jan 02 2024

first: YI

last: ZOU

summary: Specific genes for treated masseter muscle are identified

overall_design: Masseter muscle was dissected and RNA isolated

first: Anahit

last: Hovhannisyan

first: Sergei

last: Belugin

first: Jennifer

last: Mecklenburg

first: Yi

last: Zou

first: Zhao

last: Lai

first: Yu

middle: S

last: Kim


title: ATAC-seq analysis of various murine B cell subsets resulting from different immunogens.

summary:
Purpose: We aimed to link different variations of memory B cell subsets to their proliferating precursors via shared epigenetic features.
Methods : Spleens were processed according to the manuscript. Cells were sorted and DNA was isolated using a protocol adapted from Corces et al. Samples were sequenced to obtain 20M 2x75 bp paired-end reads using an Illumina NextSeq 550 sequencer (Illumina, Inc, California, USA).
Results: Memory cells have many DARs in comparison to FO naïve cells. However, differences between memory cells themselves can be attributed to imprinting by their respective proliferating precursors. A germinal center B cell program may be required to establish some DARs in GC-derived memory cells.

overall_design: We used differentially accessible regions between DN and DPs to establish similarity between putative precursors. We used these regions to further address effects of proliferation and CD40 signals on DAR accessibility.

first: Derrick

last: Callahan

first: Shuchi

last: Smita


title: ribosome frofiling with or without 16 mg/L azithromycin treated in pseudomonas aeruginosa UCBPP-PA14

status: Public on Jan 01 2024

city: tianjin

first: congjuan

last: xu

address: weijin load

institute: nankai university

summary: Azithromycin binds to the nascent peptide exit tunnel (NPET) close to the peptidyltransferase center (PTC) of the ribosome, which obstructs the NPET and subsequently induces ribosome stalling and depletion of intracellular pools of tRNAs. To understand the mechanism through which azithromycin represses the transcription of mutation promoting genes, we utilized ribosome profiling to analyze azithromycin caused redistribution of ribosomes on the cellular mRNAs. Wild type PA14 was treated with 16 mg/L azithromycin for 3 hours.

overall_design: Examing 2 conditions, each with 2 replicates,wt indicates without azithromycin treated,A indicates with 16 mg/L azithromycin treated

first: Congjuan

last: Xu

first: Huan

last: Ren

first: Weihui

last: Wu

first: Xiaolei

last: Pan


title: DPYSL5 is Highly Expressed in treatment-induced Neuroendocrine Prostate Cancer and Promotes Lineage Plasticity via EZH2/PRC2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a lethal subtype of castration-resistant prostate cancer resistant to androgen receptor (AR) inhibitors. Our study unveils that AR suppresses neuronal development protein dihydropyrimidinase-related protein 5 (DPYSL5), providing a mechanism for neuroendocrine transformation under androgen deprivation therapy. Our unique CRPC-NEPC cohort with 157 patient samples, including 55 t-NEPC patient samples, shows a high expression of DPYSL5 in t-NEPC patients, and that DPYSL5 correlates with neuroendocrine markers and inversely with AR and PSA. DPYSL5 overexpression in prostate cancer cells induces neuron like phenotype, enhances invasion, proliferation, and upregulates stemness and neuroendocrine related markers. Mechanistically, DPYSL5 promotes prostate cancer cell plasticity via EZH2-mediated PRC2 activation. Depletion of DPYSL5 halts proliferation, induces G1 phase cell cycle arrest, reverses neuroendocrine phenotype and upregulates luminal genes. In conclusion, DPYSL5 plays a critical role in regulating prostate cancer cell plasticity, and we propose the AR/DPYSL5/EZH2/PRC2 axis as a novel driver of t-NEPC progression.

overall_design:
Gene expression profiling by RNA-seq from LNCaP and C42B cells overexpressing (OE) plvx-CTRL or DPYSL5. Gene expression profiling by RNA-seq from enzalutamide resistant (EnzR) LNCaP and C42B cells treated with non-targeting siRNA or DPYSL5 targeting siRNA. All sequencing was done with Illumina NextSeq 500.

UPDATE [May 15, 2025] The treatment time was changed from 48 h to 72 h for Samples GSM4578030-GSM4578032 and GSM5399328-GSM5399331.

first: Roosa

last: Kaarijärvi

first: Marjo

last: Malinen

first: Kirsi

last: Ketola


title: RNA-seq analysis of various murine B cell subsets

first: Mark

last: Shlomchik

summary:
Purpose: We aimed to link different variations of memory B cell subsets to their proliferating precursors via shared transcriptomic features.
Methods : Spleens were processed according to the manuscript. Cells were collected via FACS, washed twice in PBS + 1% FCS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C.
Results: Memory cells have many DEGs in comparison to FO naïve cells. However, differences between memory cells themselves can be attributed to imprinting by their respective proliferating precursors. DP MBCs are split into two major subsets based on transcriptional state. A germinal center B cell program may be required to establish some DEGs in GC-derived memory cells.

overall_design: We used DEGs between DN and DPs, as well as EMPs and GCs, to establish similarity between putative precursors.

last: Challahan


title: Circulating miRNA levels in HIV infection vs non-infected controls

status: Public on Dec 31 2023

first: Júlia

last: Perera-Bel

summary: HIV infection produces a chronic inflammation which leads to early aging of people living with HIV. Even though antiretroviral treatments (ART) have significantly increased HIV patient survival, an underlying chronic inflammation persists leading to HIV-related comorbidities. In this context, changes in microRNAs (miRNAs) expression may contribute to this inflammatory response. This study aims to detect differential expression of circulating miRNAs in treatment-naïve HIV individuals compared to uninfected controls and evaluation of altered miRNAs after one year of ART. Serum miRNAs from patients and controls were analysed using next generation sequencing.

overall_design: SmallRNAs were analyzed by NGS from serum samples of 25 HIV patients and 10 controls

first: Natalia

last: Garcia-Giralt

first: Roberto

last: Fernández


title: scRNA-seq analysis of murine MBC subsets

summary:
Purpose: We wanted to explore further heterogeneity of MBC subsets that were previously defined by our lab.
Methods: MBC subsets were sorted and stained with unique anti-mouse HTO antibodies (CITE-seq).
Results: We found that heterogeneity among MBC subsets was most prominent among DP MBC subsets, which could be separated by extrafollicular or germinal center transcriptional signatures, whereas DN and SP MBCs mostly exhibited an extrafollicular signature.

overall_design: MBCs were generated using our novel Balb/c transfer system. At 10 weeks, MBC subsets were sorted, assigned HTOs, and sequenced using Illumina NovaSeq 6000

first: Florian

last: Weisel


title: Early weaning induces programmed obesity in rats at adulthood through impairing fatty acid β-oxidation and cholesterol metabolism, which can be mitigated by leucine supplementation

city: Harbin

first: Yuchen

last: Sun

state: Heilongjiang

address: Changjiang Street No. 600

institute: Northeast Agricultural University

summary: To examined the underlying variation between early-weaned rats and normal rats, we identified differentially expressed genes using RNA-seq.

overall_design: Wistar rats (Age 23: CON, control group; EW, early weaned group. Age 63: CH, control group; EH, early weaned group) SD rats (Age 211: Con, control group; Ew, early weaned group; EW_Leu, early weaned group with 1.5% leucine in drinking water.)

first: Bo


title: DNMT3B PWWP mutations cause hypermethylation of heterochromatin.

first: Duncan

last: Sproul


title: Investigating the role of p16 and cellular senescence in Alzheimer’s disease pathogenesis

city: Worcester

first: Hong

last: Zhang

state: MA

address: 55 Lake Avenue North

department: Pediatrics

institute: University of Massachusetts Chan Medical School

summary: Advancing age is the greatest risk factor for Alzheimer’s Disease (AD), as most AD patients are age 65 and older. However, the mechanistic contribution of aging to AD is unclear. Cellular senescence, one of the major hallmarks of aging, is recently implicated as an aggravator of AD pathogenesis. The critical senescence regulator p16 is increased in neurons of AD patients and mouse models. Eliminating p16-expressing senescent cells attenuates AD pathologies in AD mouse models. However, what p16 does in post-mitotic neurons and how p16 contributes to AD pathogenesis remains unknown. As clinical trials continually fail to improve cognitive decline in AD patients, it is increasingly important to develop a better human cell-based model system to advance our understanding of the impact of aging in AD pathogenesis. Induced pluripotent stem cell (iPSC) technology has revolutionized human disease modeling, enabling differentiation to relevant brain cell types for the study of AD pathogenesis in a human cell-based culture environment. AD iPSC-derived neurons exhibit higher levels of Amyloid beta secretion and tau phosphorylation compared to non-demented control iPSC-derived neurons. Nevertheless, iPSC-derived neurons are “fetal-like” and fail to recapitulate the aging process in AD pathogenesis. Thus, we have developed a robust human iPSC-based neuron model to investigate the contribution of p16 expression to cellular senescence and AD pathogenesis. We found that inducible p16 expression leads to senescence phenotypes in AD as well as non-demented control iPSC-derived neurons. The impact of p16 and induced senescence in neurons on the cellular pathologies of AD is investigated. Our study provides a novel approach to investigate aging-associated cellular changes that potentially influence AD patient-derived differentiated neurons to age and become more permissive to AD pathogenesis in culture.

overall_design: To investigate the consequence of p16 expression in activation of senescence, we established human iPSC lines with an inducible expression of p16. Two iPSC lines were used. Cells were treated with or without doxycycline (DOX) for 2 or 4 days. We performed gene expression profiling analysis of RNA-seq data obtained from untreated and Dox-treated iPSCs at two different treatment points with 8 samples in total.

first: Kristopher

last: Holloway

first: Kashfia

last: Neherin

first: Yingduo

last: Song

first: Kazuhito

last: Sato

first: Andrew

last: Houston

first: Feng

last: Chen

first: Li

last: Ding


title: Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion

city: Cambridge

first: Yiqun

last: Wang

address: 1414 Massachusetts Avenue

institute: Harvard University

summary: During differentiation, cells become structurally and functionally specialized, but comprehensive views of the underlying remodeling processes are elusive. Here, we leverage scRNA-seq developmental trajectories to reconstruct differentiation, using two secretory tissues as a model system – the zebrafish notochord and hatching gland. First, we present an approach (MIMIR) to integrate expression and functional similarities for gene module identification, revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second, we focused on the unfolded protein response (UPR) transducer module to study how general versus cell-type specific secretory functions are regulated. By profiling loss- and gain-of-function embryos, we found that the UPR transcription factors creb3l1, creb3l2, and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program, while xbp1 partners with bhlha15 to activate a gland-specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions.

overall_design: scRNA-seq experiments were conducted to study the regulatory roles of the unfolded protein response (UPR) pathway transcription factors (TFs) during zebrafish embryogenesis. We focused on the four UPR TFs (xbp1, atf6, creb3l1, and creb3l2) that are expressed during the early differentiation of the notochord and/or the hatching gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs, we performed scRNA-seq of UPR TF loss-of-function embryos at 12 hours post fertilization (hpf), when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatching gland. Loss-of-function embryos were generated by CRISPR-mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide RNAs (gRNAs) into 1-cell stage embryos. We additionally raised a stable mutant line for creb3l1. Co-injecting Cas9 with gRNA targeting multiple genes in wild-type or the stable mutant embryos allowed testing for redundant functions by generating double, triple, and quadruple loss-of-function embryos. Tyrosinase (tyr) crispants, which do not exhibit developmental defects, were generated as the control. Using this loss-of-function dataset, we defined target genes for UPR TFs as the genes whose expression levels changed in corresponding crispants and/or mutants. Next, we performed scRNA-seq on UPR TF gain-of-function embryos to test the sufficiency of the UPR TFs in regulating their endogenous targets. To generate gain-of-function embryos, we globally mis-expressed each UPR TF by injecting mRNAs encoding their activated forms into 1-cell stage embryos. We then performed scRNA-seq on the resulting embryos at 8hpf, when 1) a sizable population of transcriptionally distinct notochord and hatching gland cells are detectable, and 2) the endogenous UPR TFs and secretory pathway genes are not yet highly expressed (except for xbp1). Since xbp1 can be activated by UPR TFs including creb3l1, creb3l2, and atf6, and atf6 can be activated by xbp1, we mis-expressed the UPR TFs in xbp1 or xbp1+atf6 double crispants to reduce potential indirect effects. Single-cell transcriptomes were obtained for mCherry control, the activated forms of xbp1 (xbp1-s), creb3l1 (creb3l1-N), creb3l2 (creb3l2-N), and atf6 (atf6-N), as well as the non-activated, full-length creb3l2 (creb3l2-full). All scRNA-seq was performed using the 10x genomics platform (V3 and V3.1).

first: Jeffrey

middle: A

last: Farrell

first: Jialin

last: Liu

first: Lucia

middle: Y

last: Du