title: FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [Bisulfite-Seq]

city: Salt Lake City

first: Katherine

last: Gillis

state: UT

address: 2000 CIRCLE OF HOPE DR

institute: Snyder Lab at Huntsman Cancer Institute

summary: The ability of cancer cells to alter their identity is essential for tumor survival and progression. Loss of the pulmonary lineage specifier NKX2-1 within KRAS-driven lung adenocarcinoma (LUAD) enhances tumor progression and results in a pulmonary-to-gastric lineage switch that is dependent upon the activity of pioneer factors FoxA1 and FoxA2; however, the underlying mechanism remains largely unknown. Here, we show that FoxA1/2 reprogram the epigenetic landscape of NKX2-1-negative LUAD to facilitate a gastric differentiation program. Using sequential recombination models, we find that FoxA1/2 are required for demethylation of gastric-defining genes after Nkx2-1 deletion. FoxA1 colocalizes with TET3, an enzyme that mediates DNA demethylation, in NKX2-1-negative tumors. Deletion of Foxa1/2 results in loss of TET3 occupancy at key gastric marker genes, indicating that FoxA1/2 recruit TET3 to lineage-specific sites. H3K27ac ChIP-seq and HiChIP show that FoxA1/2 also control the activity of enhancers and promoters as well as their 3D interactions at gastric target genes following NKX2-1 loss. Furthermore, oncogenic KRAS is required for the FoxA1/2-dependent epigenetic reprogramming in NKX2-1-negative LUAD. This work demonstrates the role of FoxA1/2 in rewiring the methylation and histone landscape and cis-regulatory dynamics of NKX2-1-negative LUAD to drive cancer cell lineage switching.

overall_design:
To identify the FoxA1/2- and KRAS-dependent methylation changes, enzymatic methyl-seq was performed on sorted GFP+, DAPI+ tumor nuclei from each GEMM (K, KN, KNF1F2, N)
To determine whether FoxA1/2 were required to maintain methylation patterns in a gastric differentiation program, enzymatic methyl-seq was performed on 3D organoid lines, KG1A and 22E, in the presence and absence of FoxA1/2.

first: Gabriela

last: Fort

first: Walter

last: Orellana


title: FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [HiChIP]

status: Public on Sep 11 2024

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To identify FoxA1/2-dependent epigenetic interactome changes, HiChIP was performed on sorted GFP+, DAPI+ nuclei from KN and KNF1F2 tumors.

first: Xiaoyang

last: Zhang

first: Emily

last: Wilson


title: YY1-mediated targeting of MSL/MOF

status: Public on Sep 12 2024

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

type: Expression profiling by high throughput sequencing

summary: Msl2 knockout in pre-B cells impaired the expression of genes involved in early B cell differentiation. The  genome-wide occupancy of MSL2 and YY1 in pre-B cells identified a set of YY1-bound genomic sites that are co-occupied by MSL2 and genes that are deregulated in Msl2 knockout pre-B cells.

overall_design: MSL2, YY1 and RNA Polymerase II ChIP-seq were performed in SLP65KO preB cells. A CRISPR/Cas9-mediated Msl2KO was generated in Slp65KO pre-B cells and compared with the wt clone for the gene expression analysis.

first: Yutthaphong

last: Phongbunchoo

first: Haribaskar

last: Ramachandran

first: Gerhard

last: Mittler

first: Rudolf

last: Grosschedl


title: Single cell RNA sequencing of primary human hepatoblastoma tumoroids

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

institute: Cincinnati Children's Hospital Medical Center

summary: Single cell RNA sequencing was used to characterize transcriptional heterogeneity of primary patient-derived hepatoblastoma tumoroids.

overall_design: Single cell RNA sequencing was performed on ten primary human hepatoblastoma tumoroids at early passage (P1-P2) using the 10x Genomics 3' platform.

middle: V

first: Roel

last: Nusse

first: Maurizio

last: Morri

first: Norma

last: Neff


title: Long-term Tolerance to Islet Transplantation via Targeted Reduction of beta cell-specific T cells

first: Jonathan

middle: D

last: Katz

state: Ohio

address: 3333 Burnet Avenue

department: Division of Immunobiology

summary: Type 1 diabetes (T1D) results from insulin insufficiency due to the loss or dysfunction of pancreatic beta cells following T cell-mediated autoimmune attack. Currently, the only long-term therapy is daily exogenous insulin replacement. The ideal curative approach is the durable restoration of functional islets via transplantation with or without immunosuppression or immune modulation. To date, the limiting factors impeding realization of this goal is the lack of a cost effective and limitless source of high-quality islets suitable for transplantation and the ability to provide long-term islet graft acceptance without prolonged need for deleterious immunosuppression. Ongoing clinical trials are testing the suitability of islets derived from human induced pluripotent stem cells (iPSC); however, long-term acceptance of these or any other islet graft will require a clinically effective therapeutic strategy to prevent engrafted islet destruction by pre-existing islet-antigen specific T cells. While current immunomodulatory strategies focus on autologous T regulatory (Treg) cell expansion or the use of broad immunosuppression, here we demonstrate in the NOD mouse model for T1D that autologous islet graft acceptance can be achieved by the targeted elimination of (re)-activated islet-reactive CD4+ and CD8+ T effector (Teff) cells in the initial post-transplantation period by using a short-acting, combination therapy that results in the elimination of islet-reactive Teff cells by exacerbation of their natural DNA damage response (DDR) to drive apoptosis while at the same time maintaining endogenous Treg cell function and reducing the effector function of residual islet-reactive T cells.

overall_design: To investigate the ability to target autoreactive CD4+ and CD8+ T cells in islet transplant in diabetic mice. Using a combination p53 potentiator (MDM2 inhibitior, nutlin-3) and cell cycle disruptor (Wee1 inhibitor, MK-1775), serial treatments of new onset diatic NOD mice were treated daily for 3 days with longitudanal sampling of pancretic infiltrating T cells by scRNA-Seq, 1, 2, and 3 days of therapy to assess changes in CD4+ and CD8+ T cells subsets and gene expression.

first: Michael

last: Kotliar

first: Eileen

middle: E

last: Cianciolo

first: Duc

middle: H

last: Pham

first: Artem

last: Barski

middle: B

last: Jordan


title: The rs6967330 minor allele in CDHR3 increased CRS exacerbations and is associated with an exaggerated interferon response to RV-A and RV-C infections

city: Tucson

first: Eugene

last: Chang

state: Arizona

address: 1501 N Campbell Ave, PO Box 245074

department: Otolaryngology

institute: University of Arizona

summary:
Background: Adults with at least one copy of the minor allele in the rs6967330 SNP (AA/AG) in the rhinovirus (RV) receptor Cadherin related family member 3 gene (CDHR3), have a higher risk for CRS than those with two copies of the major allele (GG).
Objective: To determine if the rs6967330 SNP increased the risk for acute exacerbations of chronic rhinosinusitis (AECRS) in adults and identify if their nasal cells showed a distinct pathophysiologic process activated by RV infection.
Methods: We recruited adults with CRS (AG/AA,n=17; GG,n=37) and at baseline collected sinonasal outcome tests (SNOT-22), objective endoscopy scores, and nasal brushings for cells and RV viral detection. Subjects were contacted every two weeks for AECRS over one year, and if symptomatic this data was re-collected. To determine the effect of the rs6967330 SNP, air-liquid-interface (ALI) cultures were derived from nasal samples (AG/AA,n=19; GG,n=19). Cytokines and RNA transcriptome responses were measured 48 hours-post viral challenge with RV-A, RV-B, and RV-C.
Results:  During AECRS, adults with the AA/AG allele had 1.6x higher SNOT-22 scores, 2x higher endoscopic scores, and were 4x more likely to have RV infections during AECRS than those with the GG allele. (AA/AG) ALI cultures had significantly greater virus replication of RV-A (2.4x) and RV-C (3.5x) but not RV-B, higher levels of inflammatory cytokines, and significantly increased interferon-related pathways compared to (GG) ALI cultures.
Conclusions: The minor allele in the rs6967330 SNP increases the risk for AECRS disease severity and is associated with an aberrant interferon-mediated inflammatory response to both RV-A and RV-C infections.

overall_design: To determine the effect of the rs6967330 SNP, air-liquid-interface (ALI) cultures were derived from nasal samples. RNA transcriptome responses were measured 48 hours-post viral challenge with RV-A and RV-C. A total of 90 samples were submitted for nanostring analyses.

first: Sunny

last: Palumbo

first: Joseph

last: Irish

first: Nirushan

last: Narendran

first: Sophia

last: Volpe

first: Christopher

last: Le

first: Rebekah

last: Starks

first: Anthony

last: Bosco

first: Fernando

last: Martinez


title: Arabidopsis microRNA changes upon Fusarium infection

city: Denton

first: Mauricio

middle: S.

last: Antunes

state: Texas

address: 1155 Union Cir

department: Department of Biological Sciences

institute: University of North Texas

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to identify changes in Arabidopsis thaliana microRNAs during the early stages of infection by the fungal pathogen Fusarium graminearum. This study is relevant to Agriculture, as F. graminearum is a major pathogen of cereal crops; microRNAs provide a rapid and early response by the plant to trigger changes in expression of genes involved in limiting the infection and immunity.

overall_design: Sequencing of miRNAs from Arabidopsis plant infected with the fungal pathogen Fusarium graminearum and control in 3 days and 4 days.

first: Antunes

last: Mauricio S.

first: Bozdag

last: Serdar

first: Ferreira

last: Savio S.

first: Pandey

last: Suman


title: multiomics depicting the immunometabolism landscape of steatotic livers undergoing bariatric surgery and diet intervention

city: Berlin

first: Hanyang

last: Liu

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology (CCM/CVK),

institute: Charité Universitätsmedizin Berlin

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent chronic liver disease worldwide that encompasses a spectrum of steatosis, inflammation, and fibrosis. Evidence suggests that weight loss approaches such as dietary restriction (DR) and sleeve gastrectomy (SG) can lead to remission of hepatic steatosis and inflammation. However, it remains unclear about the effects of weight loss on the hepatic immune mechanisms in MASLD. Therefore, this study aims to elucidate the intricate immunometabolic landscape of steatotic livers following DI and BS by employing the sleeve gastrectomy (a typical BS procedure) and comparable food intake after sham surgery in a rat model of MASLD. Single-cell (sc) and single-nuclei (sn) transcriptome analysis together with spatial metabolomics and immunohistochemistry were utilized to depict immunometabolic landscape, while circulating markers were assessed in serum. Furthermore, artificial intelligence (AI)-based image analysis was introduced to characterize the distribution of hepatocytes, myeloid cells and lymphocytes.

overall_design: Wild-type rats were administrated with high-fat diet (HFD) for 12 weeks to develop obesity and MASLD. Then, SG (sleeve gastrectomy) was performed on 3 MASLD rats, following by HFD. Simultaneously, 3 rats (DR group) were fed with reduced HFD  comparable to BS group, while 3 rats (Sham group) recieved sham surgery following by uncontrolled HFD. After 8 weeks, rats from each group were sacrificed for the acquisition of liver samples. Last, fresh liver samples were poceeded with sc/sn RNA-seq detection.

first: Shuai

last: Chen

first: Adrien

last: Guillot


title: JOSD1 facilitates colorectal cancer progression via stabilizing YAP

city: Xinxiang

first: Zhongbo

last: li

state: Henan

country: China

institute: Xinxiang medical university

summary: Colorectal cancer is one of the most lethal human malignancies in the world. Although great efforts are put in developing novel therapeutic targets, the effective targeting drugs are still limited. Recent studies reveal the abnormality of Hippo/YAP axis play critical role in the oncogenic process of Colorectal cancer. It is of great importance to demonstrate the regulation of Hippo signaling activity and YAP protein turnover in Colorectal cancer. Besides, the phosphorylation cascade on YAP function, which has been thoroughly investigated, the ubiquitination of YAP is also important in Hippo signaling status. Here, We utilized the DUB (Deubiquitinase) siRNA library to identify critical DUB for Hippo signaling. We discovered JOSD1 as a critical factor to facilitate Colorectal cancer cell stemness and progression, which deubiquitinated and stabilized YAP protein. The clinical data analysis implicated JOSD1 was correlated with YAP activity and poor survival. Molecular studies demonstrated that JOSD1 associated with the YAP protein and enhanced YAP protein stability by blocking the K48-linked polyubiquitination of YAP. Our study revealed a novel deubiquitinase of Hippo/YAP axis and one possible therapeutic target for YAP-driven Colorectal cancer

overall_design: Colorectal cancer mRNA samples were summarized in six samples, divided into two groups, Control and siJOSD1

first: Yanan

last: Sun

first: Jian

last: Zhu

first: Xiaodong

last: Tan


title: Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity

city: Jerusalem

first: Batia

last: Azria

state: Israel

address: Jerusalem

country: Israel

institute: Hebrew university of Jerusalem

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: TGFβ primes alveolar-like macrophages to induce type I IFN following TLR2 activation.

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

summary: Alveolar macrophages (AMs) are key mediators of lung function and are potential targets for therapies during respiratory infections. TGFb is an important regulator of AM differentiation and maintenance but, how TGFb directly modulates the innate immune responses of AMs remains unclear. This shortcoming prevents effective targeting of AMs to improve lung function in health and disease. Here we leveraged an optimized ex vivo AM model system, fetal-liver derived alveolar-like macrophages (FLAMs), to dissect the role of TGFb in AMs. Using transcriptional analysis, we first globally defined how TGFb regulates gene expression of resting FLAMs. We found that TGFb maintains the baseline metabolic state of AMs by driving lipid metabolism through oxidative phosphorylation and restricting inflammation. To better understand inflammatory regulation in FLAMs, we next directly tested how TGFb alters the response to TLR2 agonists. While both TGFb (+) and TGFb (-) FLAMs robustly responded to TLR2 agonists, we found an unexpected activation of type I interferon (IFN) responses in FLAMs and primary AMs in a TGFb-dependent manner. Surprisingly, mitochondrial antiviral signaling protein and the interferon regulator factors 3 and 7 were required for IFN production by TLR2 agonists. Together, these data suggest that TGFb modulates AM metabolic networks and innate immune signaling cascades to control inflammatory pathways in AMs.

overall_design: FLAMs with and without TGFβ were plated in 6-well plates at 1 x 106 cells/well and treated with Pam3 as described for 18 hours. We used the Direct-zol RNA Extraction Kit (Zymo Research, Cat no. R2072) to extract RNA according to the manufacturer’s protocol. Quality was assessed by the MSU Genomics Core using an Agilent 4200 TapeStation System. The Illumina Stranded mRNA Library Prep kit (Illumina, Cat no. 20040534) with IDT for Illumina RNA Unique Dual Index adapters was used for library preparation following the manufacturer’s recommendations but using half-volume reactions. Qubit™ dsDNA HS (ThermoFischer Scientific, Cat no. Q32851) and Agilent 4200 TapeStation HS DNA1000 assays (Agilent, Cat no. 5067-5584) were used to measure quality and quantity of the generated libraries. The libraries were pooled in equimolar amounts, and the Invitrogen Collibri Quantification qPCR kit (Invitrogen, Cat no. A38524100) was used to quantify the pooled library. The pool was loaded onto 2 lanes of a NovaSeq S4 flow cell, and sequencing was performed in a 2x150 bp paired end format using a NovaSeq 6000 v1.5 100-cycle reagent kit (Illumina, Cat no. 20028316). Base calling was performed with Illumina Real Time Analysis (RTA; Version 3.4.4), and the output of RTA was demultiplexed and converted to the FastQ format with Illumina Bcl2fastq (Version 2.20.0). RNAseq analysis was completed using the MSU High Performance Computing Center (HPCC). FastQC (Version 0.11.7) was used to assess read quality. Bowtie2 (Version 2.4.1) with default settings was used to map reads with the GRCm39 mouse reference genome. Aligned reads counts were assessed using FeatureCounts from the Subread package (Version 2.0.0). Differential gene expression analysis was conducted using the DESeq2 package (Version 1.36.0) in R (Version 4.2.1).

first: Sean

middle: M

last: Thomas

first: Laurisa

last: Ankley

first: Alexander

middle: W

last: Rapp

first: Abigail

middle: P

last: McGee

first: Francois

last: LeSage

first: Christopher

last: Tanner

first: Taryn

last: Vielma

first: Eleanor

middle: C

last: Scheeres

first: Joshua

middle: J

last: Obar

first: Andrew

last: Olive


title: Histone demethylase PHF8 promotes prostate cancer metastasis via the E2F1-SNAI1 axis.

city: Chongqing

first: Li

middle: qiu

last: Liu

address: No. 10, Changjiang Road, Daping, Yuzhong District, Chongqing

institute: Chongqing Daping Hospital

summary: We performed the CUT&Tag analysis on the chromatic profiling of PHF8 and E2F1 in prostate cancer.A total of 6589 and 14899 peaks on the promoters were identified in PHF8k's and E2F1's binding results and 81% binding sites on promoters were shared.

overall_design: The chromatic binding profile of PHF8 and E2F1 was performed by CUT&tag analysis.

first: Jun

last: Jiang

first: Qiuli


title: Gene expression signatures for auricular cartilages of microtia patients and controls

city: Shanghai

first: Run

last: Yang

address: No.83 Fenyang Rd.

institute: Eye&ENT Hospital of Fudan University

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

summary: To explore the coding and non-coding gene expression in the auricular cartilage of microtia patients, we have employed RNA microarray expression profiling as a discovery platform to identify the coding and non-coding genes differentially expressed in microtia patients and controls. The discarded auricular cartilage tissue from 10 unilateral Grade III isolated microtia patients during auricular reconstruction surgery and 5 volunteers without ear malformation or other physical abnormalities during tympanoplasty surgery were collected. All fresh tissues were harvested from the tragus and cavum conchae of the auricle.

overall_design: The RNA expression in auricular cartilage tissue was measured by microarray. One independent experiment was performed on each clinical sample.

first: Jing

last: Ma


title: Acyl-coA Binding Protein neutralization improves cancer immunosurveillance

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: The plasma concentrations of acyl coenzyme A binding protein (ACBP, also known as diazepam-binding inhibitor, DBI, or ‘endozepine’) increase with age and obesity, two parameters that are also the most important risk factors for cancer. In mice bearing MCA205 fibrosarcoma, antibody mediated ACBP/DBI neutralization enhanced the anticancer T-cell response in the context of chemoimmunotherapy. T-cells infiltrating MCA205 tumors were sorted and submitting to single-cell TCR sequencing and single-cell RNA sequencing (scRNAseq) to identify the mechanisms driving this improvement.

overall_design: C57Bl/6 mice were injected with 3E5 MCA205 cells subcutaneously. 8 days after injection they were treated intraperitoneally with one cycle of chemotherapy (10 mg/kg oxaliplatin) followed, 8 days later, by immunotherapy (200 µg anti-PD1). Simultaneously, half the mice were treated with anti-ACBP/DBI neutralizing antibody (n = 3), the other half with isotype control (n=3) (2.5 mg/kg every other day, from two days before chemotherapy to the day prior to immunotherapy). Tumors were collected two days after immunotherapy, dissociated and fluorescently labelled to sort CD4+ and CD8+ T cells. A CD4:CD8 ratio of 1:1 was analyzed by TCR/scRNAseq.

first: Léa

last: Montégut

first: Rafael

last: Mena Osuna

first: Isabelle

last: Martins

first: Eliane

last: Piaggio

first: Guido

last: Kroemer


title: FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [ChIP-seq]

first: Katherine

last: Gillis

overall_design:
To identify the FoxA1/2- and KRAS-dependent transcriptional changes, bulk RNA-seq was performed on sorted GFP+, DAPI- tumor cells from each GEMM (K, KN, KNF1F2, N)
To determine whether FoxA1/2 were required to maintain a gastric differentiation program, bulk RNA-seq was performed on 3D organoid lines, KG1A and 22E, in the presence and absence of FoxA1/2.

first: Gabriela

last: Fort

first: Walter

last: Orellana


title: FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [RNA-Seq]


title: Gene expression profile at single cell level of intestine stem cells from mice with graft-versus-host disease

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Intestinal stem cells (ISC) encounter inflammatory insults in immune mediated gastro-intestinal (GI) diseases. It remains unknown whether, and how, they adapt, and if the adaptation leaves scars on the ISCs that affects their subsequent regeneration capacity. We investigated the consequences of inflammation on Lgr5+ISCs in well-defined clinically relevant models of gastro-intestinal acute graft-versus-host disease (GI GHD). Utilizing single cell transcriptomics, organoid, metabolic, epigenomic and in vivo models we found that Lgr5+ISCs undergo metabolic changes that lead to accumulation of succinate, which reprograms its epigenome. Single cells were isolated from small intestine crypts from Allo (BALB/c→C57BL/6) or Syn (C57BL/6→C57BL/6) transplant 7 days after bone marrow transplantation (BMT) and analyzed using scRNA-seq.

first: Fengju

last: Chen

first: Pavan

last: Reddy

first: Dongchang

last: Zhao


title: Whole genome bisulfite sequencing (WGBS) of intestinal organoids from mice with graft-versus-host disease

first: Tyler

last: Leach

address: One Baylor Plaza

department: Duncan Cancer Center

summary: Intestinal stem cells (ISC) encounter inflammatory insults in immune mediated gastro-intestinal (GI) diseases. It remains unknown whether, and how, they adapt, and if the adaptation leaves scars on the ISCs that affects their subsequent regeneration capacity. We investigated the consequences of inflammation on Lgr5+ISCs in well-defined clinically relevant models of gastro-intestinal acute graft-versus-host disease (GI GHD). We investigated the consequences of inflammation on Lgr5+ISCs in well-defined clinically relevant models of gastro-intestinal acute graft-versus-host disease (GI GVHD). Utilizing single cell transcriptomics, organoid, metabolic, epigenomic and in vivo models we found that Lgr5+ISCs undergo metabolic changes that lead to accumulation of succinate, which reprograms its epigenome. These changes reduced the ability of ISCs to differentiate and regenerate ex vivo in serial organoid cultures demonstrating the persistence of the maladaptive impact of an in vivo inflammatory encounter by the ISCs. Thus, inflammation from GI GVHD leaves a memory of its effects on ISCs that persist and are likely to affect their sensitivity to adapt to future stress or challenges.

overall_design: Small intestine crypts were isolated from Allo (BALB/c→C57BL/6) or Syn (C57BL/6→C57BL/6) transplant 7 days after bone marrow transplantation (BMT) and cultured in matrigel for five days. The genomic DNA was extracted from organoids and analyzed with WGBS-seq.


title: Heterogeneous single-molecule packaging of human mitochondrial nucleoids

city: Boston

first: Thomas

last: Tullius

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: During eukaryotic transcription, RNA polymerases must initiate and pause within a crowded, complex environment, surrounded by nucleosomes and other transcriptional activity. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address these limitations, we employed long-read chromatin fiber sequencing (Fiber-seq) to visualize RNA polymerases within their native chromatin context at single-molecule and near single-nucleotide resolution along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of single-molecule RNA Polymerase (Pol) II and III transcription associated footprints, which, in aggregate, mirror bulk short-read sequencing-based measurements of transcription. We show that Pol II pausing destabilizes downstream nucleosomes, with frequently paused genes maintaining a short-term memory of these destabilized nucleosomes. Furthermore, we demonstrate pervasive direct coordination and anti-coordination between nearby Pol II genes, Pol III genes, transcribed enhancers, and insulator elements. This coordination is largely limited to spatially organized elements within 5 kb of each other, implicating short-range chromatin environments as a predominant determinant of coordinated polymerase initiation. Overall, transcription initiation reshapes surrounding nucleosome architecture and coordinates nearby transcriptional machinery along individual chromatin fibers.

overall_design: PacBio sequencing of exogenously methylated genomic DNA from Drosophila S2 cells

first: Stefan

middle: R

last: Isaac

first: Jane

last: Ranchalis

first: Danilo

last: Dubocanin

first: Andrew

last: Stergachis

first: Stirling

middle: L

last: Churchman


title: FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma


title: ccRNA identification by circularization and miSeq

status: Public on Sep 10 2024

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

summary: Efforts to identify ccRNA by sequencing by gibson circularization after template-switching 5' RACE using a cRNA-end specific primer and subsequent sequencing by Illumina miSeq. Sequencing of wild-type A/WSN/1933 and a variant bearing the mutation T677A in the PB1 subunit.

overall_design: A549 cells were infected with the indicated variants at an MOI of 1, RNA harvested 16hpi, and samples processed using a custom sequencing pipeline.

first: Marisa

last: Mendes


title: Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma

city: GuangZhou

first: Dong-Mei

last: Chi

address: 651 Dongfeng Road East

institute: SYSUCC

summary: Tertiary lymphoid structures are immune cell aggregates linked with cancer outcomes, but their interactions with tumour cell aggregates are unclear. Using nasopharyngeal carcinoma as a model, we analyse single-cell transcriptomes of 343,829 cells from 77 biopsy and blood samples and spatially-resolved transcriptomes of 31,316 spots from 15 tumours to decipher their components and interactions with tumour cell aggregates. We identify essential cell populations in tertiary lymphoid structure, including CXCL13+ cancer-associated fibroblasts, stem-like CXCL13+CD8+ T cells, and B and T follicular helper cells. Our study shows that germinal centre reaction matures plasma cells. These plasma cells intersperse with tumour cell aggregates, promoting apoptosis of EBV-related malignant cells and enhancing immunotherapy response. CXCL13+ cancer-associated fibroblasts promote B cell adhesion and antibody production, activating CXCL13+CD8+ T cells that become exhausted in tumour cell aggregates. Tertiary lymphoid structure-related cell signatures correlate with prognosis and PD-1 blockade response, offering insights for therapeutic strategies in cancers.

overall_design:
We profile 343,829 cells from 77 biopsies and blood samples, and 31,316 spots from 15 nasopharyngeal carcinoma tumours

***Please note that raw data is not provided due to patient privacy concerns***

first: Yang

last: Liu

first: Jin-Xin

last: Bei


title: An improved terminal ribose-modified small RNA sequencing (TRM-sRNA-seq) reveals novel features of miRNA modification and identifies HEN1-independent 2’-O-modified sRNAs derived from tRNAs

first: Susu

address: 1200 Cailun Road, Pudong New District, Shanghai, China

institute: Shanghai University of Traditional Chinese Medicine

summary: Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

sample_organism:
Arabidopsis thaliana
Solanum lycopersicum
Oryza sativa
Zea mays

overall_design: TRM-sRNA-seq relied on the sequential treatment of RNA samples with PBA-PAGE and NaIO4 oxidation.

first: Yuchen

last: Cai

first: Huiru

last: Yang

first: Bin

last: Zhang


first: Li

summary: RNA-seq analysis were applied to elucidate the transcriptional differences between PC-3 cell lines transfected with control-sgRNA (Control) and PHF8-shRNA (PHF8-KD). a total of 1122 DEGs were identified with 775 upregulated and 347 downregulated genes (FDR<0.05, |log2FoldChanges|>1)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PC-3 cells and its KD derivatives (shPHF8).

first: Jun

last: Jiang

first: Qiuli


title: Remdesivir has previously unknown anti-viral immunomodulatory properties through the Adenosine A2A Receptor pathway

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: The COVID-19 pandemic has unveiled an urgent need for new anti-virals to control emerging infectious diseases and potential future pandemics. Classic anti-virals are currently designed to directly interfere with pathogens. However, anti-virals are often insufficient to rapidly clear infections in the absence of an effective immune response. Immunotherapy could complement the use of anti-virals, however its application to infectious diseases remains largely unexplored. In this work, we found that the anti-viral drug remdesivir has previously unknown immunomodulatory properties which contribute to its therapeutic effect against SARS-CoV-2. These properties are due to remdesivir metabolite, GS-441524, acting as an Adenosine A2A Receptor antagonist, a function that is distinct from its intrinsic anti-viral activity. Our findings support a new rationale for the design of next-generation anti-viral agents with dual – immunomodulatory and intrinsic - anti-viral properties. These compounds could represent game-changing therapies to control emerging viral diseases and future pandemics.

overall_design: C57Bl/6J mice treated IP with REM (10mg/kg) before infection with 10^5 PFUs of mouse-adapted SARS-CoV-2 (MA30) under BSL3 conditions. Treatment continued for the duration of the experiment. Mouse lungs were collected, fixed and used for RNA isolation to study differentially expressed genes in response to the infection/treatment.

first: G

last: Monticone

first: Z

last: Huang

first: P

last: Hewins

first: T

last: Cook

first: O

last: Mirzalieva

first: K

last: Larter

first: MD

last: Sanchez-Pino

last: Foster

last: Nichols

first: A

last: Ramsay

first: D

last: Wyczechowska

last: Tauzier

first: E

last: Gravois

first: S

last: Crabtree

first: J

last: Garai

first: L

last: Li

last: Barbier M

last: Del Valle

middle: A

last: Jurado

last: Miele


title: Deep mutational scanning and mobility-based selection for 6 RNA targets

city: Shenzhen

first: Zhe

last: Zhang

state: Guangdong

address: Gaoke Innovation Center

department: Institute of Physical and Systems Biology

institute: Shenzhen Bay Laboratory

summary: RNA mutations are known to change mobility in native gels. What is not known is if mobility can serve as an effective tool to separate structurally similar (structural homologs) from structurally destabilized variants in a deep-mutation library of an RNA. Here we defined the proportion of a mutant in the native band from native polyacrylamide gel electrophoresis (PAGE) as a native-mobility-fitness score. The fitness scores of single and double mutants allowed a unsupervised, RNA-specific analysis to detect key secondary and tertiary base pairs through covariational signals. Subsequent amplification of these signals and their use as restraints for folding led to not only high-accuracy secondary structures with the F1-score > 0.9, but also quality tertiary-structure models between 3.6 Å and 7.7 Å RMSD from their native structures for the best in top 5 models for 6 RNAs tested including two CASP 15 difficult targets. This MobiSeq method should provide a simple and effective method for inferring 2D and 3D structures and improving mechanistic understanding of all structured RNAs.

overall_design: The RNA-MobiSeq pipeline is a method to predict the 3D structure of a target RNA from its sequence by obtaining artificial homologous sequences and their native-mobility-fitness scores from high-throughput sequencing of mobility-selected RNA mutants, followed by a new RNA-specific covariation analysis as restraints for energy-based structure prediction. Error-prone PCRs (or oligo pools) were first employed to obtain randomly mutated sequences, which were assembled into plasmids and then electro-transformed into DH5α for library constructions. The DNA libraries were further in vitro transcribed into RNAs that were subjected to native PAGE separation according to mobility. The band with the same mobility as the wild-type RNA sequence was excised for reverse transcription. Both pre- and post-selection samples were sent for high-throughput sequencing. The obtained sequences along with their fitness scores estimated from mutants’ fractions in the excised band were then analyzed for co-variation to infer the base pairing structures by an RNA-specific method CODA2 and MC simulated annealing. The resulting base pairing structures were employed as restraints for energy minimization to model the 3D structures of the RNA by using the BRiQ statistical energy function and a folding-tree-based folding algorithm.

first: Jinle

last: Tang

first: Yazhou

last: Shi

first: Jian

last: Zhan

first: Yaoqi

last: Zhou


title: Axonal transcriptome reveals upregulation of PLK1 as a protective mechanism in response to increased DNA damage in FUSP525L spinal motor neurons

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

institute: University Medical Center Rostock

summary: Mutations in the gene fused-in-sarcoma (FUS) have been implicated in the motor neuron disease Amyotrophic lateral sclerosis (ALS). However, it is poorly understood how these gene mutations lead to selective motor neuron (MN) degeneration and if there are common pathomechanisms across disease etiology. To address the biological impact of the FUS-P525L mutation on the transcriptome of neurons, we applied RNA-sequencing (RNA-seq) method, using microfluidic chambers, to generate axonal as well as soma compartment specific profiles from isogenic induced pluripotent stem cells (iPSCs)-derived motor neurons. We demonstrate high purity of axonal and soma fractions, and further show that the axonal transcriptome is very specific from somas with fewer number of transcripts. Notably, functional enrichment analysis revealed a unique and distinct transcriptional landscape in both axonal and soma compartments including specific transcript types, most of which were required for RNA metabolism and DNA damage/cell cycle related processes, that were likely altered by FUS mutation. Among altered transcripts, we identified robust upregulation of polo-like kinase 1 (PLK1), a master regulator of cell cycle-related events, in FUS-P525L mutant MNs and confirmed that inhibition of PLK1 increases late apoptotic or necrosis-induced neuronal cell death in mutant neurons compared to healthy controls. Taken together, our findings provide insights into compartment-specific transcriptomics in FUS-ALS neuronal model and we propose that PLK1 activation is a consequence of MN-specific upregulation, possibly contributing to the DNA-damage response and other associated pathways including cell cycle and cytoskeleton machinery.

overall_design: Patient-derived isogenic spinal motoneurons (MNs) expressing either normal (FUS WT) or mutant P525L FUS-eGFP (FUS P525L) were matured for 14 DIV using microfluidic chambers, where somas (n=6)  and axons (n=6) were harvested and total RNA was isolated for RNA-sequencing. The main cell model used in this study were neurons derived from FUS-WT-EGFP and FUS-P525L-EGFP that were generated as a part of previous study (Naumann, Pal et al. 2018). Briefly, fibroblasts carrying R521C FUS mutation obtained from a 58-year-old female were reprogrammed into iPSC using cDNA of OCT4, SOX2, KLF4 and cMYC delivered via retroviral vectors. Next, CRISPR/Cas9 genome editing was used to i) correct the R521C mutation into WT FUS and to tag it with EGFP to generate the FUS WT EGFP line or ii) replace the R521C mutation into P525L FUS mutation and to tag it with EGFP to generate FUS P525L EGFP line. Differentiation of hiPSC into spinal motor neurons (MNs) was carried out based on the protocol from Reinhardt et al. 2013. RNA-sequencing was performed on 2 cell lines (isogenic control and FUSP525L) resulting in the following 4 groups:control somas (n=3), control axons (n=3), FUSP525L somas (n=3) and FUSP525L axons (n=3). A total of 12 samples were analyzed here.

first: Vitaly

last: Zimyanin

first: Banaja

last: Dash

last: Petzold

first: Mathias

last: Lesche


title: Dnmt3a Controls Hematopoietic Stem Cells via DNA Methylation-Independent Regulation of Telomeres

city: SAINT LOUIS

first: Daofeng

state: MO

address: 4515 McKinley Avenue

institute: Washington University in St. Louis

summary: Dnmt3a is the most recurrently mutated gene in clonal hematopoiesis (CH) and it is a critical regulator of hematopoietic stem cells (HSCs). Conditional deletion of Dnmt3a in mouse HSC results in enhanced self-renewal but impaired differnetiation. Dnmt3a encodes for a de novo DNA methyltransferase enzyme but both mouse and human cells with loss of Dnmt3a show minimal change in DNA methylation levels which do not correlate with gene expression differences. To understand if these changes are due to non-canonical function of Dnmt3a, we generated varying levels of DNA methyaltion-impared Dnmt3a mouse models. Our data depicts that DNA methyaltion-impaired Dnmt3a phenocopy wild-type in serial transplant. And Dnmt3a methyltransferase-deficient HSCs showed differntially methylated regions (DMRs) and gene expression  pattern that overlapped with Dnmt3a-null HScs. Suggesting that Dnmt3a has important non-canonical function that partially regulates HSC fate. Dnmt3a-null HSC increased HSC self-renwal and can be transplanted indefinitely and increase longevity with no erosion of telomere length. Dnmt3a-null HSCs showed increased telomere at baseline and maintained overa serial transplant and increased telomerase activity. The role of Dnmt3a in telomere maintenance was not strictly linked to elongated telomere length but in regulation of DNA damage response that occurs at stressed telomeres. These data show a unidentified role of Dnmt3a in HSC telomere maintenance that is note related to DNA methylation function.

overall_design: To investigate the diffential DNA methylation and gene expression patterns in hematopoietic cells expressing Dnmt3a-variants with varying DNA methyltransferase activity, we established Cre-mediated knockin mouse models. Competitive HSC transplantation was performed.  Post-transplant cells were isolated 18-weeks post transplant for analysis of gene expression patterns by RNA sequencing and DNA methylation patterns by whole genome bisulfite sequencing.

first: Infencia

middle: X

last: Raj

first: Won

middle: K

last: Koh

first: Christine

first: Jessica

last: Harrison

first: Barbara

last: Soares

first: Nancy

last: Issa

first: Hassan

last: Bjeije

first: Tyler

last: Parsons

first: Wentao

last: Han

first: Ting

last: Wang

first: Luis

middle: F

last: Batista

first: Grant

last: Challen


title: Metabolic Reprogramming of Iron Endows the Function of ISCA2-TET Interaction During Peri-implantation Development (EM-Seq)

first: Xinyu

address: Siping Road 1239

institute: Tongji University

summary: Metabolic reprogramming plays important roles in embryo development. However, the metabolic network has still not been systematically investigated during the processes. In this study, we develop MFE, a metabolites flux estimation tool, to predict metabolite abundances and their regulons, highlighting the role of Fe(II) and its regulon-ISCA2, in the inner cell mass (ICM) of human and mouse blastocysts. By introducing Isca2-/-, Isca2G77S/G77S and Isca2C144S/C144S mice, we find ISCA2 binding with iron, but not Fe-S cluster, is indispensable for mouse peri-implantation development. Mechanistically, nuclear ISCA2 interacts with TET, and Fe(II) is important for the interaction by triggering the enzymatic activity of TET. The partnership safeguards promoters of epiblast-specific genes from hypermethylation and is essential for epiblast development in mouse peri-implantation embryos. The study provides insights into how iron metabolism modulates embryo development, and suggests a manner of Fe(II)-dependentenzymes to achieve activity under physiological conditions.

overall_design: RNA-seq, small RNA-seq, EM-seq of mouse Isca2 WT and KO pre-implantation embryos. To collected pre-implantation embryos, Isca2+/- female mouse intraperitoneal with 6.5 international unit of pregnant mares’ serum gonadotropin and, 45 to 47 h later, with 5 IU of human chorionic gonadotropin and crossed to Isca2+/- males.

first: Jiaming

last: Zhang

first: Weibo

last: Hou

first: Qingran

last: Kong


title: SARS-CoV-2 viral RNA disseminates to hamster toes and associates with localized IFN-I production: mechanistic footprints of an abortive COVID-19 infection in pandemic-associated pernio

city: New York

first: Justin

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

summary: SARS-CoV-2 infection generates a systemic immune response mediated by type I interferons. Pernio is a rare cutaneous manifestation of disorders characterized by excessive IFN-I signaling. Pernio increased in incidence during the pandemic but lacks direct evidence of SARS-CoV-2. We characterized clinical pernio samples and mechanistic feasibility in a rodent model which phenocopies human SARS-CoV-2 infection. Golden hamsters infected with SARS-CoV-2 experienced rapid dissemination of viral RNA to both lungs and toes. Interferon responses at both sites coincided with detection of viral RNA, which cleared within 10 days post-infection. Live virus could not be detected at acral sites. In two cohorts of clinical biopsies of affected skin, we detected SARS-CoV-2 RNA in 20-30% of cases, plasmacytoid dendritic cell activation, and a robust IFN-I response across all samples. Our data suggest footprints from SARS-CoV-2 exposure in a subset of cases that can produce a sustained localized IFN-I response-- even in the absence of serconversion.

sample_organism:
Homo sapiens
Mesocricetus auratus

platform_organism:
Homo sapiens
Mesocricetus auratus

overall_design: Hamsters were intranasally infected with 1000 PFU of SARS-CoV-2 (Washington strain) and sacrificed at 3 days-post infection (dpi). Hamsters were intracardially perfused with 60 mL PBS, and toes were harvested into Trizol. RNA was extracted from toes, poly-A enriched, and sequenced for transcriptional analysis. Human PBMC samples were taken from a group of control donors as well as donors affected by pandemic associated pernio (PAP), alternatively known as COVID-associated pernio (CAP) or COVID toes, at various points post-presentation in clinic. These PBMCs were frozen following isolation using Ficoll gradient. PBMCs were thawed, and then RNA was isolated and sequenced for transcriptional analysis. RNA-seq data was aligned to the Mesocricetus Auratus MesAur1.0 genome or GRCH38 Homo Sapiens genome as appropriate using Salmon. Salmon output files were further analyzed for differential expression via DESeq2 where necessary.

first: Lisa

last: Arkin

first: Anne

last: Singh

first: Jacqueline

last: Mays

first: Benjamin

last: tenOever


title: Decoding the occupancy of RNA polymerase I  on rDNA

city: Guangzhou

first: Jianyou

last: Liao

address: Guangzhou

institute: Medical Research Center, Sun Yat-sen Memorial Hospital,  Sun Yat-sen University

summary: In order to deeply analyze the role of ribosome biogenesis associated proteins (RiBPs) in the development of breast cancer, we used chromatin immunoprecipitation combined with high-throughput sequencing (CHIP-seq) to detect the occupancy of RNA polymerase I on rDNA under the condition of RiBP knockout. In order to confirm the regulatory effect of RiBP on the transcriptional activity of pol I, the molecular mechanism of ribosome biogenesis associated proteins in promoting the malignant progression of breast tumors was further elaborated.

overall_design: Chromatin immunoprecipitation DNA-sequencing (CHIP-seq) for RPA194 in MDA-MB-231 cells.

first: Jian-you

first: Dong

last: Yin

first: Zhi-zhi

last: Yang

first: Bing


title: Epigenetic changes from ATAC-seq of intestine stem cells from mice with graft-versus-host disease

first: Chad

last: Creighton

summary: Intestinal stem cells (ISC) encounter inflammatory insults in immune mediated gastro-intestinal (GI) diseases. It remains unknown whether, and how, they adapt, and if the adaptation leaves scars on the ISCs that affects their subsequent regeneration capacity. We investigated the consequences of inflammation on Lgr5+ISCs in well-defined clinically relevant models of gastro-intestinal acute graft-versus-host disease (GI GVHD). Utilizing single cell transcriptomics, organoid, metabolic, epigenomic and in vivo models we found that Lgr5+ISCs undergo metabolic changes that lead to accumulation of succinate, which reprograms its epigenome. We performed transposase-accessible chromatin sequencing (ATAC-seq) in sorted Lgr5+ISCs harvested from the BALB/c→B6-GFP-Lgr5 model of GVHD.

overall_design: Fifty thousand Lgr5+ISCs were sorted by FACS from Allo- and Syn-recipients seven days following bone marrow transplantation (BMT) and analyzed by ATAC-seq

first: Fengju

last: Chen

first: Pavan

last: Reddy

first: Dongchang

last: Zhao


title: Effect of vehicle or drug treatment on gene expression in p53-null and p53Y220C stable cell lines

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

summary: To investigate the effect of mutant p53 Y220C acetylation in gene expression, we treated NCI-H1299 (WT) and (p53Y220C-stable) cell lines with either DMSO or MS78.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DMSO vs MS78 treatment in NCI-H1299 and NCI-H1299 (p53Y220C) cell lines

first: Kabir

last: Md

first: Martin

last: Tiphaine


title: An epigenome-wide DNA methylation study conducted on 96 patients six months after COVID-19 infection reveals biological age acceleration and increased epigenetic drift.

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

type: Methylation profiling by genome tiling array

summary: We performed a whole-genome DNA methylation analysis using EPIC Illumina BeadArrays on blood samples of a cohort of 96 individuals collected six months after COVID-19 infection.

overall_design: Genome-wide DNA methylation analysis of a cohort of post-COVID-19 patients (6 months) (n=96) using Illumina Human Methylation EPIC Beadchips.

first: Davide

last: Gentilini

first: Gianfranco

last: Parati


title: Transcriptome sequencing of ARPE-19 cells treated with cinobufagin

first: Songbin

last: Wu

address: 89 Taoyuan Rd., Nanshan District,

department: Department of Pain Medicine

institute: Huazhong University of Science and Technology Union Shenzhen Hospital

summary: This study investigates the alterations in the transcriptomic landscape of cells following treatment with cinobufagin.

overall_design: The experimental procedure was conducted as follows: ARPE-19 cells were cultured in 6-well plates one day prior to treatment, during which they were exposed to cinobactin (320 nM) or DMSO for 24 hours. Following this exposure, the cell pellet was collected and dissolved in Trizol reagent to extract total RNA from the sample. Transcriptome sequencing was performed after confirming that the RNA quality met the necessary standards. Ultimately, the transcriptome data expression profiles of ARPE-19 cells treated with cinobufagin (experimental group) and DMSO (control group) were obtained.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo ChIP-seq]

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

summary: X chromosome inactivation (XCI) triggers a drastic reprogramming of gene activities and chromosome architecture. However, how the 3D organization of the inactive X chromosome (Xi) is de novo established in vivo in mammals remains poorly understood. By comprehensive stage- and lineage- specific Hi-C mapping, we identified a unique Xist-separated megadomain structure (X-megadomains) on the Xi in mouse early embryos. X-megadomains emerge in extraembryonic lineages during imprinted XCI, in derived extraembryonic endoderm (XEN) cells, and transiently in the embryonic lineages during random XCI, before Dxz4-delineated megadomains (D-megadomains) occur at later stages in a strain-specific manner. Mechanistically, the emergence of X-megadomain boundary coincides with developmentally regulated enhancer activities and cohesin binding in a regulatory region near Xist (XRR). We pinpointed a subregion XRRa that is critical for the X-megadomain boundary. X-megadomains are impaired when XRRa is removed or cohesin is degraded in XEN cells. Importantly, this is accompanied by ectopic activation of regulatory elements and genes near Xist, suggesting that cohesin loading at regulatory elements promotes X-megadomains and confines local gene activities. Finally, the knockout of XRRa in mouse preimplantation embryos severely impairs the activation of Xist and the initiation of XCI. Hence, our data not only reveal stepwise chromosome folding during de novo XCI in vivo, but also support a model that regulatory element-dependent gene activation and cohesin loading simultaneously promote essential transcription activities and subsequent self-insulation amid global silencing during the early stage of XCI.

overall_design: STAR ChIP-seq for H3K27ac in E6.5 extraembryonic tissues

first: Zhuoning

last: Zou

first: Liangjun

last: Hu

first: Zihan

last: Li

first: Wei

last: Xie


title: Effect of isolated neutrophils from Cd177 knockout mice post-SCI on microglia in a co-culture system

city: Nanjing

first: Siming

last: Dai

address: No. 300, Guangzhou Road, Nanjing

department: Department of Orthopedic

institute: The First Affiliated Hospital of Nanjing Medical University

summary: To investigate the transcriptional effects of CD177+ neutrophils on microglia in spinal cord injuries (SCI), we adapted a co-culture system containing isolated neutrophils from Cd177 WT or KO mice post-SCI and isolated microglia. Each group had a biological repeat (n=3).

overall_design: Briefly, we isolated neutrophils in injured lesions at 3 dpi from Cd177 KO or WT mice by magnetic-activated cell sorting (MACS) and co-cultured them with microglia. After co-culturing for 24h, We isolated microglia by fluorescence-activated cell sorting (FACS, gated on Ly6G-) for further testing.

first: Ziyang

last: Zheng

first: Shujie

first: Guoyong

last: Yin


title: KIAA1429 promotes cell proliferation by regulating MYC messenger RNA in clear cell renal cell carcinoma

city: Nantong

first: Zhan

last: Chen

state: Jiangsu

address: No. 666 Shengli Road

department: Urology Surgery

institute: The Second Affiliated Hospital of Nantong University

summary: KIAA1429 is an integral component of the m6A methyltransferase complex, essential for facilitating the interaction between the catalytic core components METTL3 and METTL14. However, the mechanisms by which KIAA1429 influences clear cell Renal cell carcinoma (ccRCC) remain incompletely elucidated. Analysis of the TCGA and GEO database confirmed that KIAA1429 was significantly upregulated in ccRCC samples, which correlated with poor survival. Additionally, qRT-PCR, Western Blot and IHC detection revealed significantly upregulated levels of KIAA1429 in ccRCC tissues. Moreover, multivariable Cox regression analysis showed that patients with ccRCC with high KIAA1429 expression had a poor clinical prognosis. Notably, silencing KIAA1429 significantly inhibited the proliferation, migration and invasion of ccRCC cells. Similarly, KIAA1429 knockdown also significantly inhibited the growth of ccRCC cells in nude mice. Mechanistically, KIAA1429 silencing significantly reduced the overall level of m6A in, the stability of MYC mRNA and the mRNA and protein expressions of MYC in ccRCC cells. Furthermore, RIP-qRT-PCR experiments showed that KIAA1429 could directly bind to MYC mRNA. MeRIP assay revealed that KIAA1429 knockdown resulted in a significant decrease in the m6A level of MYC mRNA in ccRCC cells. In conclusion, KIAA1429 regulates the proliferation, migration and invasion of ccRCC cells by stabilizing MYC mRNA in an m6A-dependent manner. Therefore, targeting the KIAA1429-MYC signalling pathway emerges as a potential strategy for the treatment of renal cell carcinoma.

overall_design: KIAA1429 knockout ACHN cells and Negative Control ACHN cells


title: Effect of isolated neutrophils from Cd177 knockout mice post-SCI on macrophages in a co-culture system

summary: To investigate the transcriptional effects of CD177+ neutrophils on macrophages in spinal cord injuries (SCI), we adapted a co-culture system containing isolated neutrophils from Cd177 WT or KO mice post-SCI and bone marrow-derived macrophages (BMDMs). Each group had a biological repeat (n=3).

overall_design: Briefly, we isolated neutrophils in injured lesions at 3 dpi from Cd177 KO or WT mice by magnetic-activated cell sorting (MACS) and co-cultured them with BMDMs. After co-culturing for 24h, We isolated macrophages by fluorescence-activated cell sorting (FACS, gated on Ly6G-) for further testing.

last: Zhao


title: Transcriptomics profiling reveal the heterogeneity of white and brown adipocytes

city: Changchun

first: Tongjian

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

summary: The marker genes associated with white adipocytes and brown adipocytes have been previously identified; however, these markers have not been updated in several years, and the differentiation process of preadipocytes remains relatively fixed. Consequently, there has been a lack of exploration into alternative differentiation schemes. In this particular study, we present a transcriptional signature specific to brown adipocytes and white adipocytes. Notably, our findings reveal that ZNF497, ZIC1, ZFY, UTY, USP9Y, TXLNGY, TTTY14, TNNT3, TNNT2, TNNT1, TNNI1, TNNC1, TDRD15, SOX11, SLN, SFRP2, PRKY, PAX3KLHL40, PAX3, INKA2-AS1, SOX11, and TDRD15 exhibit high expression levels in brown adipocytes. XIST, HOXA10, PCAT19, HOXA7, PLSCR3, and AVPR1A exhibited high expression levels in white adipocytes, suggesting their potential as novel marker genes for the transition from white to brown adipocytes. Furthermore, our analysis revealed the coordinated activation of several pathways, including the PPAR signaling pathway, focal adhesion, retrograde endocannabinoid signaling, oxidative phosphorylation, PI3K-Akt signaling pathway, and thermogenesis pathways, in brown adipocytes. Moreover, in contrast to prevailing culture techniques, we conducted a comparative analysis of the differentiation protocols for white preadipocytes and brown preadipocytes, revealing that the differentiation outcome remained unaffected by the diverse culture schemes employed. However, the expression levels of certain marker genes in both adipocyte types were found to be altered. This investigation not only identified potential novel marker genes for adipocytes but also examined the impact of different differentiation methods on preadipocyte maturation. Consequently, these findings offer significant insights for further research on the differentiation processes of diverse adipocyte subtypes.

overall_design: The present study reveals notable disparities in the transcriptional profiles of white adipocytes and brown adipocytes. Furthermore, we conducted a comparative analysis of various culture techniques for white and brown preadipocytes, and determined that the differentiation outcome remained unaltered. Nevertheless, the culture methods did exert an influence on the expression levels of specific marker genes in both adipocyte types. These findings underscore the substantial dissimilarities in the transcriptomic profiles of brown and white adipocytes, thereby enhancing our comprehension of gene functions in the context of brown adipose tissue thermogenesis.

first: Zhongxiao

last: Zhang

first: Jianfang

last: Gao


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo RNA-seq]

overall_design:
RNA-seq data for female embryos in various stages

Please note that in the rna_embryo_all_stages_merged_allelic_FPKM.txt file of "GEO_embryo_data", the "_m" and "_p" columns contain the FPKM values of genes in the maternal allele and in the paternal allele, respectively.


title: Olfactory Receptor 2 in Monocytes Exacerbates Myocardial Ischemia-Reperfusion Injury via Drp1-Dependent Mitochondrial Fission Mediated by NR4A1

first: Yahao

address: 87 Dingjiaqiao

institute: Zhongda Hospital Southeast University

summary: Myocardial ischemia-reperfusion (I/R) injury represents a major clinical challenge with limited therapeutic options. This study examines the role of Olfactory Receptor 2 (Olfr2) in monocytes during myocardial I/R injury. We utilized RNA sequencing to analyze monocytes isolated from the spleens of wild-type (WT) mice, investigating their response to low-dose LPS priming and subsequent treatment with octanal (Oct), a specific agonist of Olfr2. Principal component analysis (PCA) revealed distinct clustering among experimental groups, highlighting significant gene expression changes in pathways related to cAMP/PKA signaling and inflammasome activation. Notably, the low-dose LPS+Oct treatment induced substantial upregulation of genes such as Adcy, Pka, Nlrp3, Pycard, Casp4, Gsdmd, and Nr4a1. Moreover, monocytes subjected to low-dose LPS+Oct exhibited increased expression of pro-inflammatory cytokines (IL-1β, IL-12a, IL-18, and TNF), chemokines (CCL3, CCL4, CXCL1, CXCL2, and CXCL3), and demonstrated enrichment in pathways associated with oxidative stress, positive chemotaxis, and the production and secretion of inflammatory cytokines (IL-1β, IL-8, TNF).

overall_design: To elucidate the role of Olfr2 in monocytes during myocardial I/R injury, we subjected mouse spleen-derived monocytes to three treatment conditions: (1) low-dose LPS stimulation (40 ng/ml for 5 hours), (2) low-dose LPS priming followed by octanal administration (20 µM for 18 hours), and (3) an untreated control with DMSO (1:1000).

first: Wenbin

last: Lu

first: Jiandong

last: Ding

first: Genshan

last: Ma


title: PD1-mediated microglia assisted cerebrovascular pruning during vascular development.

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To further explore the mechanism of cerebrovascular pruning by PD1 in microglia, we analyzed RNA isolated from Pd1fl/fl and Pd1cKO-Cx3 cerebral cortical microglia at P11 using RNA-seq to identify genome-wide changes.

overall_design: mRNA from P11 isolated microglia of Pd1fl/fl and Pd1cKO-Cx3 mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics

first: Mengtian


title: Cardiac assembloids from human pluripotent stem cells model the atrioventricular conduction axis.

city: Amsterdam

first: Alexandra

last: Wiesinger

state: Amsterdam

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: In this study, we aimed to differentiate atrioventricular (AV) canal-like cardiomyocytes (AVCM) from hiPSCs to facilitate the study of disorders that affect the AV conduction axis. hiPSC-derived AVCM preferentially expressed AV canal-associated genes MSX2, TBX2 and TBX3. Single cell RNA sequencing and comparative analysis with mouse heart further validated their AV canal-like identity. In addition, hiPSC-AVCM demonstrated sensitivity to ivabradine and carbachol, indicating the presence of key nodal currents If and IKACh. To model the AV conduction axis, we created an organoid-based tissue model. These so-called “assembloids” consisted of atrial, AVC, and ventricular organoids, which exhibited spontaneous contractions and unidirectional conduction with impulses initiated predominantly at the atrial end. Remarkably, we observed slower conduction in the AVC region of the assembloid, effectively recapitulating the “fast-slow-fast” conduction pattern found in the early heart tube. Our results demonstrate that hiPSC-derived AVCM recapitulate molecular and electrophysiological properties of in vivo AV canal cardiomyocytes and tissue models incorporating this cell type enhance our ability to evaluate complex cardiac conduction disorders.

overall_design: single cell RNA sequencing of human induced pluripotent stem cell-derived atrioventricular canal-like cells. Single cell collection was performed at day 19 of differentiationand and 768 cells were collected in total.

first: Harsha

middle: D

last: Devalla


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo genomic DNA]

first: Zhenhai

last: Du

overall_design: Genomic DNA libraries for various genotypes of morula embryos.

first: Zhuoning

last: Zou

first: Liangjun

first: Zihan

first: Wei


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells CUT&RUN]

overall_design: CUT&RUN for CTCF and SMC3 in WT and mutant XEN cells

last: Hu

last: Li


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF Cut&Run]

summary: X chromosome inactivation (XCI) triggers drastic reorganization of chromatin architecture, which in turn facilitates XCI. However, how the 3D organization is de novo established during XCI in vivo remains poorly understood. Mouse embryos present an ideal model, as they undergo imprinted XCI, X chromosome reactivation (XCR) and subsequent random XCI. Using low-input Hi-C, we revealed a unique chromatin structure of the inactive X chromosome (Xi) during both imprinted and random XCI in early mouse embryos. A bipartite structure featured by two megadomains separated by Xist (X-megadomains), emerges in extraembryonic lineages, derived extraembryonic endoderm (XEN) cells, and also transiently in embryonic lineages. X-megadomains then diminish in adult tissues, where previously reported Dxz4-delineated megadomains (D-megadomains) appear in a strain-specific manner. Mechanistically, X-megadomains coincide with developmentally controlled activities of regulatory regions near Xist (XRRs), and loss of XRR disrupts X-megadomains. CUT&RUN revealed strong enrichment of CTCF and cohesin near Xist, despite global depletion, on Xi in embryos and XEN cells. X-megadomains are also impaired when Xist is silenced, accompanied by global cohesin restoration, or when residual cohesin is degraded, suggesting that X-megadomain formation is promoted by both global cohesin depletion and local cohesin loading. Importantly, the loss of cohesin leads to ectopic activation of regulatory elements and genes near Xist. Hence, these data reveal programming of chromatin architecture during de novo establishment of mammalian XCI in vivo, and suggest that cohesin mediates self-insulation of gene activity of essential escapees amid global silencing.

overall_design: CUT&RUN for CTCF and SMC3 in MEF cells

last: Xie


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF HiC]

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) for MEF cell lines.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF RNA-Seq]

overall_design: RNA-seq data for MEF cell lines.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells RNA-seq]

overall_design:
RNA-seq data for WT and mutant XEN cells

Please note that, in the *allelic_FPKM.txt.gz files, the "_Xa" and "_Xi" columns contain the FPKM values of genes in the active X chromosome and in the inactive X chromosome, respectively.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF ChIP]

overall_design: STAR ChIP-seq for H3K27ac in MEF cells


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells ChIP-seq]

overall_design: STAR ChIP-seq for H3K27ac in WT and mutant XEN cells


title: Gene expression changes in bone marrow dendritic cell progenitors upon acute and chronic LCMV infection

city: Berkeley

first: Yeara

last: Jo

address: 485 Weill Hall

institute: University of California, Berkeley

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

overall_design: Refer to individual Series


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells HiC]

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) for WT and mutant XEN cells


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo CUT&RUN]

overall_design: CUT&RUN for CTCF and SMC3 in various stages of embryos


title: Gene expression changes in bone marrow dendritic cell progenitors upon acute and chronic LCMV infection [RNA-seq]

summary: Dendritic cell (DC) subsets are critical for immune responses, but their development  from progenitors and maturation are often altered during infection, and the mechanisms  underlying these changes remain unclear. To address this problem, we investigated the  transcriptomes of bone marrow DC progenitors from mice infected with lymphocytic choriomeningitis virus (LCMV).

overall_design: 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Armstrong 53b or Clone-13 or left uninfected. Bone marrow cells from 4-5 pooled mice were harvested to generate one single replicate per group. Bone marrow cells were harvested in triplicates from uninfected control mice and infected mice at 8 days post infection and DC progenitors defined as Lin-c-Kitint/loFlt3+ cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, and CD8), NK cells (NK1.1), red  blood cells (Ter119), granulocytes (Gr-1), and monocytes (CD11b)) were purified by using fluorescence-activated cell sorting (FACS). Samples were subsequently analyzed on a HiSeq 4000 instrument using a single read 100bp RNAseq protocol.

first: Kai

first: Trever

middle: T

last: Greene

first: Simone

last: Dallari

first: Nuha

last: Marooki

last: Wang

first: Elina

middle: I

last: Zuniga


title: Gene expression changes in bone marrow dendritic cell progenitors upon acute and chronic LCMV infection [ATAC-seq]

summary: Dendritic cell (DC) subsets are critical for immune responses, but their development  from progenitors and maturation are often altered during infection, and the mechanisms  underlying these changes remain unclear. To address this problem, we investigated the  Chromatin landscapes of bone marrow DC progenitors from mice infected with lymphocytic choriomeningitis virus (LCMV).

overall_design: 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Armstrong 53b or Clone-13 or left uninfected. Bone marrow cells from 4-5 pooled mice were harvested to generate one single replicate per group. Bone marrow cells were harvested in triplicates from uninfected control mice and infected mice at 8 days post infection and DC progenitors defined as Lin-c-Kitint/loFlt3+ cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, and CD8), NK cells (NK1.1), red  blood cells (Ter119), granulocytes (Gr-1), and monocytes (CD11b)) were purified by using fluorescence-activated cell sorting (FACS). Samples were subsequently analyzed on a HiSeq 4000 instrument using a single read 100bp protocol.

last: Zhang


title: Targeted DNA and surface protein sequencing at single cell level of BM MNCs and PB MNCs from CCUS patients

status: Public on Sep 09 2024

city: Houston

first: Yijune

last: Kim

address: 1901 East Rd

institute: MD Anderson

summary: We performed high-throughput single-cell targeted DNA and surface protein sequencing (scDNA + protein-seq) using the Mission Bio Tapestri Platform to analyze NK cells isolated from five patients with CCUS exhibiting different genetic alterations. Our analysis revealed that the NK cells were part of the mutant clone population, displaying a clonal burden comparable to that observed in the myeloid cells of the same patients. This dataset provides valuable insights into the clonal architecture of NK cells in the context of CCUS.

overall_design: BM and PB MNCs were isolated by Fluorescence-activated cell sorting and analyzed using scDNA + protein-seq


title: Increased Matrix Rigidities Modulate Interleukin Gene Signatures in ER+ Breast Cancer

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

summary: Metastases of breast cancer is a prevalent problem with over 25% of patients suffering with metastatic disease. Of the patients that present with metastatic disease, the majority are estrogen receptor positive (ER+) and have skeletal metastases. These skeletal metastases can cause several issues including pathological fractures, chronic pain, and hypercalcemia. Currently, there are not any cures for metastatic breast cancer in bone and only therapies to mediate the osteolysis caused by breast cancer. The bone microenvironment presents various physical forces that can act on the tumor cell that has been studied in ER- cells, however, the physical forces on ER+ tumor cells have not been widely evaluated. In this study, we explored the transcriptional changes that occur at different matrix rigidities associated with the bone microenvironment (bone marrow:  0.5 kPa to 32 kPa; cortical and trabecular bone – 2 x 107 kPa). We observed that lower stiffnesses contributed to increased gene signatures associated with interleukin signaling. Additionally, we observed that downstream estrogen signaling outputs were modified. These interesting findings give us insights on what may be changing when ER+ tumor cells encounter rigidities associated with the bone microenvironment.

overall_design: CytoSoft® Rigidity Plates were purchased from Advanced BioMatrix. The plate wells were coated with 4 ug/mL of fibronectin (Advanced Biomatrix) for 1 hour before use. MCF7s were cultured in phenol-red free DMEM (Gibco) and phenol-red free RPMI (Gibco), respectively, and supplemented with 10% charcoal-stripped fetal bovine serum and 1% penicillin-streptomycin. After 24 hours in culture, cells were plated at 0.2 x 106 on CytoSoft® Rigidity Plates  which were purchased from Advanced BioMatrix. The plate wells were coated with 4 ug/mL of fibronectin (Advanced Biomatrix) for 1 hour before use. MCF7s were supplemented with 10 nM 17-B estradiol (Invitrogen) and cultured at 37 C for 48 hours at 5% CO2.

first: Northcutt

last: Logan

first: Bennett

last: Natalie

first: Rhoades

last: Julie


title: CRISPRi with barcoded expression reporters dissects regulatory networks in human cells

first: Nicholas

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

summary: Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy and potential of CiBER-seq for dissecting genetic networks in mammalian cells with superior time resolution.

overall_design: Sequencing of expressed barcode reporters from SFFV control promoters and synthetic NF-κB reporters, comparing the effects of CRISPRi induction (between matched SFFV promoters) and TNF-α treatment (between NF-κB and SFFV control)

first: Jinyoung

first: Ryan

middle: Y

last: Muller

first: Eliana

last: Bondra


title: Dietary protein defends lean mass and maintains metabolic benefits of glucagon receptor agonist G108 in mice

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

summary: Glucagon has long been proposed as a component of multi-agonist obesity therapeutics due to its ability to induce energy expenditure and cause weight loss. However, chronic glucagon-receptor agonism has been associated with a reduction in circulating amino acids and loss of lean mass. Importantly, it is currently not known whether the metabolic benefits of glucagon can be maintained in contexts that permit the defence of lean mass.

overall_design: We investigated the effects of the long-acting glucagon receptor agonist, G108, when administered to obese mice at low-doses, and with dietary protein supplementation.

first: Jose

first: Tatiana

last: Lopes

first: Bryn

last: Owen


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo HiC]

first: Zhenhai

last: Du

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) for various stages of embryos or tissues.

first: Zhuoning

last: Zou

first: Liangjun

last: Hu

first: Zihan

last: Li

first: Wei

last: Xie


title: Analysis of endometrial mRNA in patients with different pregnancy outcomes after immunotherapy: A cohort study

city: beijing

first: Yumeng

last: Ren

address: Xicheng District

institute: Peking university people’s hospital

summary: Purpose: The efficacy of immunomodulators in improving pregnancy outcomes in infertile patients is controversial, with some reports finding improvements in pregnancy outcomes and some studies finding lack of efficacy in unselected patient populations. Therefore, the aim of this study was to identify people who could benefit from immunotherapy. Methods: 29 patients who had at least one previous embryo transfer failure and planned to undergo another frozen-thawed embryo transfer (FET) cycle were included. Peripheral blood of the patients was collected for detection of serum cytokines, T cell subsets at D3-D9 days of menstrual cycle before FET, mRNA was extracted from endometrial tissues during the window of implantation (WOI) for analysis. All patients began treatment with immunomodulators, including prednisone, hydroxychloroquine, cyclosporine, on the first day of the FET cycle. They were divided into pregnant group and non-pregnant group according to clinical pregnancy. Results: There were no differences in cytokines and T cell subsets between the two groups. Functional annotation of endometrial mRNA revealed functional enrichment in leucocyte mediated immunity, innate immune response, regulation of T cell receptor (TCR) signaling, T cell activation and positive T cell selection. Conclusion: The cytokines and immune cell subsets of peripheral blood cannot accurately predict the outcome of pregnancy after immunotherapy, and endometrial biopsy on the WOI may be a target to identify people who benefit from immunotherapy.

overall_design: A cohort study，29 patients who had at least one previous embryo transfer failure and planned to undergo another frozen-thawed embryo transfer (FET) cycle were included. mRNA was extracted from endometrial tissues during the window of implantation (WOI) for analysis. They were divided into pregnant group and non-pregnant group according to clinical pregnancy.

first: Hongjing

last: Han

first: Fumei

last: Gao

first: Yi

last: Zhu


title: Normal breast scDNA-ATAC coassay sequencing dataset

first: Nicholas

last: Navin

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: MD anderson Cancer Center

summary: In this dataset, we applied high-throughput nanowell single cell DNA-ATAC co-assay sequencing to profile copy number alterations and chromatin accessibility in 31,176 epithelial cells isolated from breast tissues of 19 disease-free women.

overall_design:
Here we include the scATAC-seq data from the co-assay experiments.

Grant ID: RP180684
Grant title: Integrated Single Cell Genomics Core Facility
Funding agency: Cancer Prevention & Research Institute of Texas
Grantee: Nicholas Navin


title: Inflammation promotes stomach epithelial defence by stimulating the secretion of antimicrobial peptides in the mucus

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary:
Mucus is a protein-based gel   secreted by specialized epithelial cells that protects the gastrointestinal mucosa from microorganism attack and irritating agents. Experiments in mice have demonstrated that when the mucosa is infected or inflamed, the mucus becomes enriched with broad-spectrum bactericidal compounds known as antimicrobial peptides (AMPs). Although AMP gene expression has been identified in both immune and epithelial cells, how inflammation regulates AMP secretion in the mucus remains unclear, and the efficacy of AMP-enriched mucus in defending against microorganisms has not been assessed. We have developed a “mucosoid”  culture model that simulates the healthy human stomach epithelium. In these cultures, epithelial cells form a barrier and can differentiate into mucus-secreting cells. The accumulation of mucus on the apical side facilitates the detection of AMPs and the assessment of their bactericidal properties.
We report that cytokines TNFa, IL1b and IFNg enhance the secretion of the AMPs lactotransferrin, lipocalin2, C3A, and CXCL9 into the mucus. The mucus from inflamed cells which contains the aforementioned AMPs partially kills Helicobacter pylori, the sole stomach pathogen. However, H. pylori can inhibit this defence by reducing AMP gene expression in inflamed epithelial cells.  These results reveal that secreted mucus is a relevant effector of epithelial immunity but pathogens like H. pylori can subvert these defences to persist in the mucosa.

overall_design: Trascriptomic profile of gastric mucosoids treated with TNFɑ, IL1β and IFNɣ and with every single cytokine were analyzed and compared to non treated samples on Agilent-8x60k Human custom arrays as single-color hybridizations.

first: Francesco

last: Boccellato


title: RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [day 14 total_RNA-seq-Nu_Cy]

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: Exosome is the main RNA surveillance and degradation pathway during oocyte growth. To figure out specific roles of RNA surveillance in oocyte growth, the pathway was destroied by deleting MTR4, the only known RNA helicase in exosome pathway. Total RNA-seq was performed using samples after nucleus-cytoplasm separation to examine the global subcellular transcriptional changes.

overall_design: The  total RNA-seq was performed with 10 nuclei or cytoplasms per sample. WT and MTR4-null oocytes were extracted and then nucleus-cytoplasm separation were performed with micromanipulation. Duplicates were conducted. Each sample was sequenced 5G.

first: Yunwen

last: Wu

first: Yuke

first: Hengyu


title: The NRF2 inducer CDDO-2P-Im provokes a reduction in amyloid beta levels in Alzheimer’s disease model mice

city: Sendai

first: Akira

last: Uruno

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: Alzheimer’s disease (AD) is the most common etiology of dementia. The transcription factor NF-E2-related factor 2 (NRF2) induces the expression of genes encoding phase II detoxification and antioxidant genes. NRF2 is regulated by Kelch-like ECH-associated protein 1 (KEAP1), and the KEAP1-NRF2 system is the key regulatory system involved in cytoprotection. To examine whether pharmacological induction of NRF2 expression alleviates AD phenotypes in vivo, we employed two AD mouse models, i.e., AppNL-G-F/NL-G-F (AppNLGF) and APPV717I::TAUP301L (APP/TAU) mice. As the synthetic oleanane triterpenoid 1-[2-cyano-3,12-dioxooleana-1,9(11-dien-28-oyl)] (CDDO)-4(-pyridin-2-yl)-imidazole (CDDO-2P-Im) exhibits strong NRF2-inducing activity, in this study, we treated AD model mice with CDDO-2P-Im.

overall_design: To determine NRF2 inducers exerts therapeutic effects in Alzheimer's disease, a NRF2 inducer the synthetic oleanane triterpenoid 1-[2-cyano-3,12-dioxooleana-1,9(11-dien-28-oyl)] (CDDO)-4(-pyridin-2-yl)-imidazole (CDDO-2P-Im) was administered to Alzheimer's disease model AppNL-G-F/NL-G-F (AppNLGF) and APPV717I::TAUP301L (APP/TAU) mice at 30 micromol/kg body weight per os. We also 10%DMSO/10% Chremophol EL/PBS was used as a vehicle control. After treatment the mice 3 times per week, for 2 weeks to APP/TAU mice or for 4 weeks to AppNLGF mice. brain tissues were collected for sequencing analysis.

first: Shiori

last: Kadoguchi-Igarashi

first: Ritsumi

last: Saito

first: Shohei

last: Koiso

first: Daisuke

last: Saigusa

first: Ching-Tung

last: Chu

first: Takafumi

last: Suzuki

first: Takashi

first: Takaomi

last: Saido

first: Antonio

last: Cuadrado

first: Masayuki

last: Yamamoto


title: Gene expression changes in bone marrow dendritic cell progenitors upon acute and chronic LCMV infection [ATAC-seq_IFNARblockade]

first: Yeara

last: Jo

summary: IFN-I suppresses the number of pre-pDCs and pDC development after infection, and the mechanisms  underlying these changes remain unclear. To address this problem, we investigated the  chromatin landscapes of bone marrow DC progenitors from mice infected with lymphocytic choriomeningitis virus (LCMV) after IFN-I receptor blockade with neutralizing antibodies.

overall_design: 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Clone-13. C57BL/6J mice were intraperitoneally (i.p.) injected with 500ug/mouse of neutralizing antibody (nAb) against IFNAR or anti-mouse IgG1 isotype control on days -1 and 0 post LCMV Cl13-infecteion. Mice were then treated with 250ug/mouse anti-IFNAR nAb or isotype control i.p. on days 2,4, and 6 post-LCMV Cl13 infection. Bone marrow cells from 3-4 pooled mice were harvested to generate one single replicate per group. Bone marrow cells were harvested in triplicates at 8 days post infection and DC progenitors defined as Lin-c-Kitint/loFlt3+ cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, and CD8), NK cells (NK1.1), red blood cells (Ter119), granulocytes (Gr-1), and monocytes (CD11b)) were purified by using fluorescence-activated cell sorting (FACS). Samples were subsequently analyzed on a HiSeq 4000 instrument using a single read 100bp protocol.

first: Kai

last: Zhang

first: Trever

last: Greene

first: Simone

last: Dallari

first: Nuha

last: Marooki

first: Wei

last: Wang

first: Elina

last: Zuniga


title: Transcriptomic profiling at single nucleus level of adult rat auditory cortex (AC)

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: We performed single nucleus RNA sequencing (snRNAseq) to provide foundational insights into the transcriptional landscape of the adult AC.

overall_design: Tissue punches containing the auditory cortex were obtained from homecage adult rats (n=2) for single nuclei isolation.

first: Aysegul

last: Gungor Aydin

first: Alex

first: Kasia

middle: M

last: Bieszczad


title: The use of ectopic volar fibroblast to modify skin identity IV [Xenium]

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

summary: The modification of skin identity, such as the conversion of residual limb/stump (non-volar) skin of amputees to pressure-resistant palmoplantar skin to enhance prosthesis use and minimize skin breakdown, has tremendous clinical potential. Recognizing the capacity of fibroblasts to modify keratinocyte differentiation, we hypothesized that volar fibroblast injections might induce ectopic volar characteristics. First, we observed pressure-responsive volar fibroblast resulting in increased limb development after pressure treatment, then we confirmed this in using a bioprinted skin construct, and later in a clinical trial that showed increased volar measures in non-volar skin after volar fibroblast injections. Bulk and single cell RNA seq demonstrate gene ontology categories of cornified envelope, keratinization and morphogenic pathways. Thus, the long-term engraftment of volar fibroblasts creates a platform for the therapeutic development

overall_design: Autologous scalp or sole fibroblasts were injected into the non-volar dermis. A total of 10 million cells were injected. Skin biopsies from the injected sites were collected at 2-month post-injection time points and processed for Xenium.


title: Protective effects of Ganoderma lucidum spores on estradiol benzoate-induced TEC apoptosis and compromised double-positive thymocyte development

first: wang

last: my

address: Cangqian Street, Cangxing Street

institute: BoYu Intelligent Health Innovation Laboratory, Hangzhou, 311100, P. R. China.

summary: Thymic atrophy is the initial event of immune aging and leads to developmental disorders of T cell . Invariant natural killer T (iNKT) cells are a distinctive subset of innate-like T cells, which are involved in the occurrence and development of various diseases, such as tumor, obesity and diabetes. Cell therapy targeting iNKT cells has become an emerging therapy after PD-1/PD-L1, CTLA-4 and CAR-T therapy. However, the scarcity of iNKT cells in the body limits its application in clinical therapy. A large number of clinical studies and preclinical studies have demonstrated that Ganoderma lucidum spores (GLS) regulates traditional T cell development. Nevertheless, whether GLS regulates iNKT cell development and its underlying mechanisms remains unknown.

overall_design: We used droplet based single-cell RNA sequencing (scRNA seq) method to analyze the transcriptome patterns of thymus in mice from the control group, estradiol benzoate (EB)-induced group, and EB plus high-dose sporoderm-removed GLS (RGLSH) group.

first: Mengyao

first: Jihong

last: Yang


title: Stepwise de novo establishment of inactive X chromosome architecture in early development

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

overall_design: Refer to individual Series


title: Single-cell profiling of remyelination in the LPC model

city: Cambridge

first: Evan

last: Macosko

address: 75 Ames St

institute: Broad Institute

summary: Remyelination is reparative process by which axons that have lost their supportive insulation are re-encased in myelin. Multiple cell types are known to participate in this process, but their transcriptional dynamics from initial injury to full repair remain poorly characterized. Here, we combined high-throughput single-nucleus RNA-seq with Slide-seq, a high-resolution spatial transcriptomics technology, to densely reconstruct the cellular processes that coordinate remyelination after lysolecithin injection. First, we found extensive transcriptional diversity of glia and monocyte-derived macrophages from damage to repair. Second, we identified a population of infiltrating peripheral immune cells-- mostly CD8 T-cells and natural killer cells--that are enriched specifically during remyelination. Thirdly, we identified a concerted Interferon-response signature that is shared across several glial cell types--microglia, astrocytes, and oligodendrocyte lineage--just prior to reestablishment of myelin

overall_design: To model successful remyelination we used the lysophosphatidylcholine (LPC) injection model, delivering a demyelinating agent into the corpus callosum. This results in myelin loss and remyelination in a rapid and stereotyped manner over 3 weeks, enabling dense reconstruction of this reparative process. We chose four time points representing distinct phases of repair: initial myelin damage (3 days post injection, dpi), oligodendrocyte differentiation (7dpi), early (12 dpi) and late (18dpi) remyelination. To profile the gene expression of cells during remyelination we developed an optimized extraction protocol to maximize the yield of nuclei from small white matter samples and performed single-nucleus RNA sequencing (snRNAseq) at all four time points with matched saline-injected controls (n=3 per time point and condition) (Fig. 1a), avoiding isolation aftefacts.

first: Michael-John

last: Dolan

first: Aleksandrina

last: Goeva

first: Naeem

last: Nadaf

first: Sang

last: Lin

first: Beth

last: Stevens

middle: Z


title: RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [polyA_RNA-seq-Nu_Cy]

first: Heng-yu

last: Fan

summary: Exosome is the main RNA surveillance and degradation pathway during oocyte growth. To figure out specific roles of RNA surveillance in oocyte growth, the pathway was destroied by deleting MTR4, the only known RNA helicase in exosome pathway. Poly(A) RNA-seq was performed using samples after nucleus-cytoplasm separation to examine the global subcellular transcriptional changes.

overall_design: The poly(A) RNA-seq was performed with 10 nuclei or cytoplasms per sample. WT and MTR4-null oocytes were extracted and then nucleus-cytoplasm separation were performed with micromanipulation. Duplicates were conducted. Each sample was sequenced 5G.

first: Yunwen

last: Wu

first: Yuke

first: Hengyu


title: RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [total_RNA-seq-Nu_Cy]


title: RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [polyA_RNA-seq]

summary: Exosome is the main RNA surveillance and degradation pathway during oocyte growth. To figure out specific roles of RNA surveillance in oocyte growth, the pathway was destroied by deleting MTR4, the only known RNA helicase in exosome pathway. Poly(A) RNA-seq was performed to examine the global transcriptional changes.

overall_design: The poly(A) RNA-seq was performed with 10 oocytes per sample. WT and MTR4-null oocytes were extracted and duplicates were conducted. Each sample was sequenced 5G.


title: SPP1 represents a therapeutic target that promotes the progression of esophageal squamous cell carcinoma by driving M2 macrophage infiltration

city: Zhengzhou

first: Renle

address: No.40 Daxue North Road

department: Henan Institute of Medical and Pharmaceutical Sciences

institute: Zhengzhou University

summary: Background: Tumor-associated macrophages (TAMs) are an important component of the tumor microenvironment (TME). However, the crosstalk between esophageal squamous cell carcinoma (ESCC) cells and TAMs remains largely unexplored. Methods: Clinical samples and the TCGA database were used to evaluate the relevance of SPP1 and TAM infiltration in ESCC. Mouse models were constructed to investigate the roles of macrophages educated by SPP1 in ESCC. Macrophage phenotypes were determined using qRT‒PCR and immunohistochemical staining. RNA sequencing was performed to elucidate the mechanism. Results: Increasing expression of SPP1 correlated with M2-like TAM accumulation in ESCC, and they both predicted poor prognosis in the ESCC cohort. Knockdown of SPP1 significantly inhibited the infiltration of M2 TAMs in xenograft tumors. In vivo mouse model experiments showed that SPP1-mediated education of macrophages plays essential roles in the progression of ESCC. Mechanistically, SPP1 recruited macrophages and promoted M2 polarization via CD44/PI3K/AKT signaling activation and then induced VEGFA and IL6 secretion to sustain ESCC progression. Finally, blockade of SPP1 with RNA aptamer significantly inhibited tumor growth and M2 TAM infiltration in xenograft mouse models.  Conclusions: This study highlights a SPP1-mediated crosstalk between ESCC cells and TAMs in ESCC. SPP1 could serve as a potential target in ESCC therapy.

overall_design: Total RNA from THP1-derived macrophages educated with conditioned medium from KYSE150shSPP1#2 or KYSE150shNC cells for 48 h was harvested using TRIzol reagent for RNA extraction. Deep RNA sequencing (RNA-seq) was performed and analyzed on the BGI seq500 platform (BGI-Shenzhen, China).

first: Chen

last: Wang

first: Yutong

last: Li

first: Linhong


title: RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [CUT&Tag]

summary: Exosome is the main RNA surveillance and degradation pathway during oocyte growth. To figure out specific roles of RNA surveillance in oocyte growth, the pathway was destroied by deleting MTR4, the only known RNA helicase in exosome pathway. Accumulation of waste RNAs in nucleus seriously effect chromatin status and establishment of histone modifications like H3K4me3. Thus CUT&Tag experiments targeting at H3K4me3 were performed.

overall_design: The H3K4me3 CUT&Tag was performed with 120 oocytes per sample. WT and MTR4-null oocytes were extracted and duplicates were conducted. Each sample was sequenced 8G.

first: Guowei

last: Bu