title: WT and RNE∆IDR mRNA half-life profiling in Sinorhizobium meliloti.

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: WT and RNE∆IDR strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Wild type(WT) was compared to RNE∆IDR strain.

overall_design: WT and RNE∆IDR strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Biological samples were taken before rifampicin treatment (0 minute), then at 1, 3, and 9 minutes after rifampicin treatment.  Two biologycal replicates were performed.


title: Exploring the tumor micro-environment of ovarian cancer histotypes and tumor sites

status: Public on Dec 15 2023

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

country: USA

institute: University of Texas Southwestern medical center

type: Expression profiling by high throughput sequencing

summary: Ovarian cancer is a common, malignant cancer in the female reproductive system. Despite the commonly affected tissue ovary, ovarian cancer is a heterogeneous disease consisting of at least five different histological subtypes and varying clinical features, cells of origin, molecular composition, risk factors, and treatments. With cumulative studies on the tumor microenvironment, a comprehensive landscape of the constituent cell types, and their interactions are yet to be established in ovarian cancer and its histotypes. Further characterization of tumor progression, metastasis, and various histotypes is needed to connect molecular signatures to pathological grading for tailored diagnosis and treatment. In this study, we leveraged high-resolution single-cell RNA sequencing technology to elucidate the cellular compositions on 21 solid tumor samples collected from 12 patients with six ovarian cancer histotypes and both primary (ovaries) and metastatic (omentum, rectum) sites. The diverse collection allows us to zoom in on histotype and tumor site-specific expression patterns of cells in the tumor and identify key marker genes and ligand-receptor pairs that are active in the ovarian tumor microenvironment. Our findings can be used in improving disease stratification and design of customized treatment.

overall_design: scRNA-seq of ovarian cancer cells from 8 ovarian cancer patients with different cancer histotypes, where tumor samples were dissected from both primary and metastatic sites.

first: Susan

last: Olalekan

first: Rebecca

last: Back

first: Naa

middle: A

last: Ashitey

first: Heather

last: Eckart

first: Anindita

last: Basu


title: IFN-γ induced transcriptional profile of A549 cells in absence of key transcriptional regulators IRF1 and NF2

city: St. Louis

first: Sumit

middle: Kumar

last: Matta

state: MO

address: 660 S. Euclid

department: Molecular Microbiology

institute: Washington University in St. Louis

summary: Type-II interferon or IFN-gamma is a critical cytokine in innate immunity that control multitude of intracellular infections. IFN-gamma binds to interferon gamma receptors to phosphorylate and activate STAT1 mediated transcription of interferon stimulated genes (ISGs). We executed a genome-wide CRISPR-Cas9 screen against ~20,000 human genes to identify IRF-1 and NF2 as significant regulators of Toxoplasma infection in A549 lung epithelial cells.  IRF-1 is a key transcription factor immediately downstream of STAT1 induced transcription that amplifies ISG expression in different cell types. NF2 or MERLIN is a tumor suppressor that is known to regulate expression of genes involved with cellular growth and metabolism. Transcriptomic signature of A549 cells lacking IRF-1 and NF2 were measured upon activation with IFN-gamma to find set of genes that may be regulating Toxoplasma infection. A total of 1,046,709,676 reads from 3 independent biological replicates were mapped to human hg38 reference genome. Expression of a ISGs that failed to induced in cells lacking IRF1 were found to be dysregulated in absence of NF2 as well.

overall_design: Wild type, IRF1 KO and NF2 KO A549 cells were left untreated or treated with IFN-gamma treatment (100 U/ml) for 24 h. Total RNA was extracted from 3 independent biological replicates and submitted for next generation sequencing to analyze the role of IRF-1 and NF2 in IFN-gamma induced transcriptional profile of A549 cells.

first: L

middle: D

last: Sibley

middle: K


title: Single cell RNA-sequencing of undifferentiated pleomorphic sarcomas and leiomyosarcomas.

status: Public on Dec 12 2023

city: Stanford

first: Ajay

last: Subramanian

state: CA

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

summary: The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used single cell RNA sequencing to analyze the malignant, immune, and other stromal cells present within soft tissue sarcomas.

overall_design:
Single cell RNA-sequencing was performed on 7 soft tissue sarcomas from 6 patients.

[UPDATE] 05-31-2024: For GSM6534011 and GSM6534013, the titles were swapped and the processed data files were renamed accordingly. The file associations did not change.

first: Everett

last: Moding


title: Single-cell gene expression profiles associated with myxoid liposarcoma scaffold culture compared to xenograft and effect of fusion oncogene FUS-DDIT3

status: Public on Dec 31 2023

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

summary: Myxoid liposarcoma (MLS) is the second most common type of liposarcoma and is characterized by the fusion oncogene FUS‐DDIT3 or the less common EWSR1‐DDIT3. While the presence of FUS-DDIT3 as a driver oncoprotein in most MLS cases has been confirmed, the exact molecular action behind the capacity of FUS-DDIT3 for transformation is still unclear and therefore creates a challenge in finding new treatments against this type of cancer. The importance of the microenvironment for tumor progression have long been accepted and might also influence the effect of the fusion oncoprotein. However, due to a lack of relevant experimental model systems, it has been challenging to examine the microenvironmental impact in myxoid liposarcoma development. Therefore, we have developed a new model system utilizing scaffolds derived from myxoid liposarcoma patient-derived xenograft tumors that are decellularized and then repopulated with sarcoma cell lines. This cell culture system mimics in vivo-like tumor cell growth conditions and induce transcriptional changes within the cells. In order to investigate the effect of the microenvironment as well as the fusion oncogene, we analyzed myxoid liposarcoma cell lines as well as fibrosarcoma cells with and without ectopic FUS-DDIT3 expression cultured in scaffolds and adherent two-dimensional growth conditions. We identified several gene networks and processes that are uniquely associated with FUS-DDIT3 expression and with the microenvironment, respectively. The development of patient-derived scaffolds opens up new possibilities to understand tumor development.

overall_design: Single cell RNA sequencing using 10x Genomics 3' solution of HT1080 fibrosarcoma cells with and without the fusion oncogene FUS-DDIT3.

first: Anders

last: Ståhlberg

first: Stefan

last: Filges


title: An iPSC-derived neuronal model of DNAJC6 parkinsonism reveals neurodevelopmental and synaptic vesicle recycling defects

city: London

first: Manju

last: Kurian

address: Great Ormond Street Institute of Child Health, 30 Guilford Street

department: Developmental Neurosciences

country: United Kingdom

institute: University College of London

summary: Biallelic mutations in DNAJC6 cause a complex, early-onset movement disorder characterized by rapidly progressive parkinsonism-dystonia in childhood. The disease is commonly associated with additional neurodevelopmental, neurological and neuropsychiatric features. Currently, there are no disease-specific treatments for this condition, resulting in significant morbidity and risk of premature mortality. To investigate the underlying disease mechanisms in childhood-onset DNAJC6 parkinsonism, we generated induced pluripotent stem cells (iPSC) from three patients harboring pathogenic loss-of-function DNAJC6 mutations and subsequently developed a midbrain dopaminergic (mDA) neuronal model of disease. DNAJC6 encodes auxilin, a co-chaperone protein involved in clathrin-mediated synaptic vesicle (SV) recycling at the presynaptic terminal. When compared to age-matched and CRISPR-corrected isogenic controls, the neuronal cell model revealed disease-specific auxilin deficiency as well as disturbance of synaptic vesicle recycling and homeostasis. We also observed dysregulation of key neurodevelopmental pathways affecting ventral midbrain pattering and neuronal maturation.

overall_design: An aged-matched healty Control, 3 DNAJC6-related parkinsonism patients and one isogenic control (from Patient 2) iPSCs-derived midbrain dopaminergic neurons (3 biological replicates each)

first: Giada

last: Rossignoli

first: Lucia

last: Abela


title: Human apical-out nasal organoids reveal an essential role of matrix metalloproteinases in airway epithelial differentiation

status: Public on Dec 11 2023

city: Guangzhou

first: Danni

last: FENG

state: Guangdong

address: No. 58, Zhong Shan 2nd Street, Guangzhou, China, 510080

department: Department of Otolaryngology, Department of Allergy

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Extracellular matrix (ECM) assembly/disassembly is a critical regulator for airway epithelial development and remodeling. Airway organoid is widely used in respiratory research, yet there is limited study to indicate the roles and mechanismsof ECM organization in epithelial growth and differentiation by using in vitro organoid system. Moreover, most of current Matrigel-based airway organoids are in basal-out orientation where accessing the apical surface is challenging. We present a novel human apical-out airway organoid using a biochemically defined hybrid hydrogel system. During human nasal epithelial progenitor cells (hNEPCs) differentiation, thegel gradually degraded, leading to the organoid apical surfaces facing outward. The expression and activity of ECM-degrading enzymes, matrix metalloproteinases (MMP7, MMP9, MMP10 and MMP13) increased during organoid differentiation,where inhibition of MMPs significantly suppressed the normal ciliation, resulting in increased goblet cell proportion. Moreover, a decrease of MMPs was found in goblet cell hyperplastic epithelium in inflammatory mucosa. This system reveals essential roles of epithelial-derived MMPs on epithelial cell fate determination, and provides an applicable platform enabling further study for ECM in regulating airway development in health and diseases.

overall_design:
To investige the role of matrix metallo proteinases(MMP) in airway epithelial differentiation accompanied with gel degradation on the surface,we cultured untreated organoids and act-treated organoids in which MMP activity were  inhibited by actinonin(MMP inhibitor). In addition,comparison of molecular characteristics between hANO and ALI model was performed to  to demonstrate their similarity.
We then performed gene expression profiling analysis using data obtained from RNA-seq of organoids  from 3 donors' nasal polyps tissue and ALI of other 3 donors'  nasal polyps at three time points.
Comperative gene expression profiling analysis of RNA-seq data for untreated organoids vs act-treated organoids and untreated organoids vs ALI model.

first: Liyue

last: Li

first: Linyi

last: Jiao

last: Feng

first: Yizhang

last: Yuan

first: Chun

last: Liu

first: Chunwei


title: Microbiota configuration dictates nutritional immune optimization [16s rRNA-seq]

status: Public on Dec 13 2023

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: Mild or transient dietary restriction (DR) improves many aspects of health and aging. Emerging evidence from us and others has demonstrated that DR also optimizes the development and quality of immune responses. However, the factors and mechanisms involved remain to be elucidated. Here, we demonstrate that DR-induced optimization of immunological memory requires co-operation between memory T cells, the intestinal microbiota, and myeloid cells. Our data indicate that DR enhances the ability of memory T cells to recruit and activate myeloid cells in the context of a secondary infection. Concomitantly, DR promotes expansion of the commensal Bifidobacteria within the large intestine, which supplies the short-chain fatty acid acetate to myeloid cells. Acetate conditioning of the myeloid compartment during DR enhances their capacity to kill pathogens. Enhanced host protection during DR is abolished when Bifidobacteria expansion is prevented, indicating that microbiota configuration and function critically dictates immune responsiveness to this dietary intervention. Altogether, DR induces both memory T cells and the gut microbiota to produce essential, distinct factors that converge on myeloid cells to promote optimal pathogen control. These findings reveal how nutritional cues promote adaptation and co-operation between multiple immune cells and the gut microbiota, which synergize to optimize immunity and protect the collective metaorganism.

overall_design: Examination of murine fecal microbiome in samples with Bifidobacteria and without Bifidobacteria

first: Nicholas

last: Collins


title: NR5A1 and FOXL2 Induce Human Fibroblasts into Steroidogenic Ovarian Granulosa-Like Cells

city: Beijing

first: Kehkooi

last: Kee

address: Shuangqing Road, Haidian District

department: Department of Basic Medical Sciences

institute: Tsinghua University

summary: Granulosa cells provide essential niche for ovarian folliculogenesis by communicating with oocytes and secreting steroids at different follicular stages, but current cellular models for studying human granulosa cells mainly rely on immortal cancer cell lines. Here, we established a reprogramming method to collect early and late granulosa cells with different steroidogenic abilities. We applied AMH-fluorescence-reporter system to screen six candidate factors for cellular reprogramming and generated human induced granulosa like cells (hiGC) by overexpressing FOXL2 and NR5A1. AMH-EGFP+ hiGC resembled human cumulus cells in transcriptome profiling and secreted high levels of estrogen as well as progesterone, similar to late-stage granulosa cells at antral or preovulatory stage. Moreover, we identified a cell surface marker CD55 which can be used to isolate early-stage granulosa cells. CD55+AMH-EGFP- hiGC secreted high levels of estrogen but low levels of progesterone, and the transcriptome profiles were more similar to early-stage granulosa cells. Both types of the hiGC promoted oocyte maturation when cocultured with immature oocytes. More importantly, when CD55+ hiGC were transplanted to mouse model with Polycystic ovary syndrome (PCOS), the number of cystic follicles was significantly reduced, showing alleviation of PCOS. Hence, hiGC provides a cellular model to study developmental program of human granulosa cells and has potential to treat PCOS.

overall_design: comparative gene exspression profiling analysis of AMH-EGFP+ cells, CD55+ cells, CD55+AMH-EGFP- cells, human cumulus granulosa cells, CTRL cells of fibroblast cells, each group has two replicates.

first: Fan

last: Wen

first: Shen

last: Zhang


title: Intestinal tuft cell immune privilege enables norovirus persistence

status: Public on Dec 08 2023

city: New Haven

first: Craig

middle: B

last: Wilen

address: 789 Howard Avenue, Clinic Building Rm 438

department: Immunobiology

institute: Yale University

summary: The persistent murine norovirus strain MNVCR6 is a model for human norovirus and enteric viral persistence. MNVCR6 causes chronic infection by directly infecting tuft cells, rare chemosensory epithelial cells. Although MNVCR6 induces functional MNV-specific CD8+ T cells, these lymphocytes fail to clear infection. To clarify how tuft cells promote immune escape, we interrogated tuft cell interactions with CD8+ T cells by adoptively transferring JEDI (Just EGFP Death Inducing) CD8+ T cells into tuft cell reporter mice (Gfi1b-GFP). Surprisingly, some tuft cells partially resist JEDI CD8+ T cell-mediated killing – unlike Lgr5+ intestinal stem cells and extraintestinal tuft cells – despite seemingly normal antigen presentation. When targeting tuft cells, JEDI CD8+ T cells predominantly adopt a T resident memory phenotype with decreased effector and cytotoxic capacity, enabling tuft cell survival. Importantly, JEDI CD8+ T cells neither clear nor prevent MNVCR6 infection in the colon, the site of viral persistence, despite targeting a virus-independent antigen (e.g., GFP).

overall_design: To investigate the effector function of JEDI CD8+ T cells in the colonic epithelium of mice targeting Gfi1b-GFP+ tuft cells or Lgr5-GFP+ stem cells

first: Madison

middle: S

last: Strine

first: Gabriel

middle: M

last: Barron

first: Michael

middle: R

last: Howitt


title: Next Generation Sequencing Facilitates Quantitative Analysis of control and MILIP Knockdown by siRNA in MDA-MB-231 human triple-negative breast cancer cell line

status: Public on Dec 06 2023

city: Zhengzhou

first: Simin

last: Zheng

address: Huanghe Road, Jinshui District, Zhengzhou City, Henan Province

institute: Henan Provincial People's Hospital

summary: RNA-sequencing analysis revealed that MILIP knockdown downregulated the E2F and G2/M checkpoint hallmark gene sets

overall_design: For RNA-seq analysis of MILIP siRNA versus control siRNA, the MDA-MB-231 cells were transfected with siRNAs for 48 hours before harvesting.

first: Yuchen

first: Xu

first: Jin

middle: N

last: Gao


title: Single cell methylation, RNA, and ATAC sequencing of ventral hippocampal brain tissue from inbred mouse strains

status: Public on Dec 04 2023

city: Los Angeles

first: Patrick

last: Chen

address: 635 Charles E Young Dr S

department: Psychiatry

institute: UCLA

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Despite advances in genetics over the last two decades, relating genetic variants to behavior remains a fundamental challenge. Particularly in mice, progress is frustrated by the low resolution of genetic mapping, and consequently by the thousands of candidate causal variants that must be screened. To assess the utility of DNA methylation marks in discovering causative variants we examined their relationship to genetic variation by generating genome-wide, base-pair resolution maps of multiple cell types from the hippocampus of eight fully sequenced inbred strains of Mus musculus. We find that the impact of sequence variation, as mediated by methylation changes, depends on local CpG sequence density. At CpG sequence densities of less than 40 CpG/Kb, cells compensate for loss of methylated sites by methylating additional sites to maintain methylation levels. At higher CpG sequence densities, the exact location of a methylated site becomes more important suggesting that variants affecting methylation sites in regions of high CpG density will have a greater effect on transcription. We test this hypothesis by assessing the effect of mutations on single cell transcript abundance for two inbred strains (C57BL/6J and DBA/2J). The effect of mutations that alter methylated CpG sites is restricted to regions of high sequence density, and from single cell ATAC-seq data, localizes predominantly to enhancers. With approximately tenfold fewer mutations in high than low sequence density CpG regions, candidate variants affecting transcript abundance, and hence downstream phenotypes, including behavior, can be prioritized based on CpG sequence density. Furthermore, our findings imply that DNA methylation influences the likelihood that mutations occur at specific sites in the genome, supporting the view that the distribution of mutations is not random.

overall_design: Adult male animals (Jackson Laboratories) were euthanized at 10-16 weeks old in an isoflurane chamber and decapitated. The brain was removed and the ventral region of the hippocampus was microdissected, snap frozen in dry ice, and stored at -80oC until processing. Tissue from ~2 animals were combined into a single tube and considered a replicate, with 2 replicates per strain for snmC-seq2, snRNA-seq, and snATAC-seq experiments. snmC-seq2 on microdissected tissue as previously described (Luo et al 2018). We selected for a 75-25 enrichment of neuronal vs non-neuronal nuclei during FACS sorting using NeuN-488/DAPI counterstains. For snRNA-seq, single nuclei suspension and library generation were completed at the Cedars Sinai Applied Genomics, Computation and Translational Core and followed the 10X protocol for the Chromium Next GEM Automated Single Cell 3’ Library and Gel Bead Kit v3.1 (cat# PN-100014) as described except for the following modifications: Suspensions from cell nuclei were generated using the recommended method from the 10X scMultiome protocol (CG000375 Rev C) to lyse cells and obtain nuclei. Following single nuclei suspension generation, nuclei were counterstained for 7-AAD and NeuN-405 antibody (Novus Biologicals, 1:200) and sorted on a MACSQuant Tyto prior to GEM generation. We selected for a 75-25 split of NeuN+/7-AAD+ nuclei for neurons and NeuN-/7-AAD+ for non-neuronal nuclei respectively. We captured ~10,000 nuclei per genotype per region per replicate on a single 10X GEM chip. All downstream library preparation was done according to the 10X protocol (CG000286) and sequenced on a Novaseq 6000 with a target of ~40-50k reads per nucleus. For snATAC-seq, single nuclei suspension and library generation were completed at the Cedars Sinai AGCT core and followed the 10X protocol for Next GEM scATAC-Seq v1.1 (PN-1000175) as described except for the following modifications: Nuclei suspensions were generated using the recommended method from the 10X scMultiome protocol (CG000375 Rev C) to lyse cells and obtain nuclei Following single nuclei suspension generation, nuclei were counterstained for 7-AAD and sorted on a MACSQuant Tyto prior to GEM generation. NeuN was not used for neuronal enrichment due to dye incompatibility between our NeuN antibody and a nuclear counterstain. After the sort, we carried out permeabilization of nuclei as per the protocol. We aimed to capture 10,000 nuclei per well x 8 wells, for a total of 80,000 nuclei over 8 total samples (~10,000 nuclei per genotype per region per replicate). All downstream library preparation was done according to the 10X protocol (CG000209) and sequenced on a Novaseq 6000 with a target of >35k reads per nucleus.

first: Jonathan

last: Flint

first: Chongyuan

last: Luo


title: Red clover (Trifolium pratense L.) extract inhibits ferroptotic cell death by modulating cellular iron homeostasis

status: Public on Dec 01 2023

city: Seoul

first: Junpil

last: Won

state: Seoul

address: 120 Neungdong-ro

department: Food science and biotechnology of animal resources

country: South Korea

institute: Konkuk university

summary: To investigate the mechanisms related to anti-ferroptotic effects of red clover extract, we performed differentially expressed genes analysis using data obtained from the RNA-seq of system xCT knockout mouse embryonic fibroblast cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for system xCT knockout mouse embryonic fibroblast cells with absense or presence of red clover extract.

first: Jun

middle: P

first: Eunsu

last: Kim

first: Jinwoo

last: Hur

first: Hyuk

middle: G

last: Lee

first: Won

middle: J

first: Han

last: Seo


title: Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells

status: Public on Dec 20 2023

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Colorectal cancer tumors are composed of heterogeneous and plastic cell populations, including a pool of cancer stem cells that express LGR5. Whether these distinct cell populations display different mechanical properties, and how these properties might contribute to metastasis is unknown. Using CRC patient derived organoids (PDOs), we found that compared to LGR5- cells, LGR5+ cancer stem cells are stiffer, adhere better to the extracellular matrix (ECM), move slower both as single cells and clusters, display higher nuclear YAP, show a higher survival rate in response to mechanical confinement, and form larger transendothelial gaps. These differences are largely explained by the downregulation of the membrane to cortex attachment proteins Ezrin/Radixin/Moesin (ERMs) in the LGR5+ cells. By analyzing scRNA-seq expression patterns from a patient cohort, we show that this downregulation is a robust signature of colorectal tumors. Our results show that LGR5- cells display a mechanically dynamic phenotype suitable for dissemination from the primary tumor whereas LGR5+ cells display a mechanically stable and resilient phenotype suitable for extravasation and metastatic growth.

overall_design: We sorted the cells based on LGR5 expression into 3 groups expressing high (LGR5+), medium (LGR5med), or low (LGR5-) levels of Tdtomato and performed a transcriptomic characterization of these three populations through bulk RNAseq.

last: Stephan-Otto Attolini

first: Sefora

last: Conti


title: ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

overall_design:
Human telencephalic organoids derived from iPSC lines: control and harboring heterozygous ARID1B mutations.
scRNAseq and scMultiomics (scRNAseq + scATACseq) datasets (processed data).

scRNAseq:
Human telencephalic organoids, at day 120, from 4 different sequencing runs (libraries), as follows (please see cell line clone nomenclature in original publication):
1. Library 177136: Pat.2 ARID1B+/+ clone 2c (2 organoids, E11rep_1, E11rep_2), Pat.2 ARID1B+/- clone 2a (2 organoids: B002orig_1, B002orig_2)
2. Library 178119: Pat.2 ARID1B+/+ clone 2c (3 organoids: E11rep_1, E11rep_2, E11rep_3), Pat.2 ARID1B+/- clone 2a (3 organoids: B002orig_1, B002orig_2, B002orig_3)
3. Library 178120: Pat.2 ARID1B+/+ clone 2d (3 organoids: A3rep_1, A3rep_2, A3rep_3), Pat.2 ARID1B+/- clone 2b (3 organoids: B002_F7_1, B002_F7_2, B002_F7_3)
4. Library 184337: Pat.1 ARID1B+/- clone 1a (3 organoids: B001orig_1, B001orig_2, B001orig_3), HD.1 ARID1B+/+ clone 3a (3 organoids: 176_1, 176_2, 176_3), HD.1 ARID1B+/- clone 3b (3 organoids: F10_1, F10_2, F10_3)

scMultiomics:
Human telencephalic organoids, at day 120, from 3 different sequencing runs (libraries), as follows (please see cell line clone nomenclature in original publication):
1. Library 233269(RNA)/235293(ATAC): Pat.1 ARID1B+/- clone 1a (9 pooled organoids).
2. Library 233270(RNA)/235294(ATAC): HD.1 ARID1B+/+ clone 3a (9 pooled organoids).
3. Library 233271(RNA)/235295(ATAC): HD.1 ARID1B+/- clone 3b (8 pooled organoids).

NOTE FROM SUBMITTER: hosting processed patient single cell data on GEO while raw data are kept at EGA (studies: scRNAseq, EGAS50000000344; scMultiomics, EGAS50000000343)

first: Catarina

last: Martins-Costa

first: Alexander

last: Vogt

first: Jürgen

last: Knoblich


title: Genes and transposons expression profiling of wild-type Bone Marrow Derived Macrophages (BMDMs) after VSV and HSV infection.

status: Public on Nov 30 2023

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging and highly pathogenic coronavirus that causes coronavirus disease (COVID-19), and might even lead to death. The long terminal repeat of the endogenous retrovirus (LTR ERVs), a type of mammalian genome elements derived from ancient viruses which infected the host and now accounts for 8% of human genome, are implicated in multi viral pathogenesis and host immune responses. However, their expression patterns and functions during SARS-CoV-2 infection still remain to be uncover. We first identified that SARS-CoV-2 infection could upregualted the expression of TEs and ERVs from the published RNA-seq data. Then in this study, we also conducted the genome-wide analysis of ERVs from wild-type mice Bone Marrow Derived Macrophages (BMDMs) after VSV and HSV infection. Collectively, these results provides the first glimpse into the expression patterns and potentail roles of ERVs after viral infection, and would serve as a valuable resource for future studies on SARS-CoV-2 infection and pathogenesis.

overall_design:
To investigate whether VSV and HSV infection could induce the expression of ERV and TEs, we separated the BMDMs from wt BALBC/6J mice and induced them with GM-CSF for one week.
We then performed gene expression profiling analysis using data obtained from RNA-seq of WT BMDMs with VSV and HSV infection for 12 hours.
Comparative gene expression profiling analysis of RNA-seq data for VSV, HSV and MOCK group.


title: Genomic changes in response to different doses of early life stress in the developing hippocampus

status: Public on Dec 07 2023

city: NEW HAVEN

first: Arie

last: Kaffman

state: CT

address: 300 GEORGE ST. SUITE 901, SUITE 901

institute: YALE UNIVERSITY

summary: Early adversity in the form of neglect, abuse, and unpredictable stress impairs hippocampal development across diverse mammalian species. Individuals exposed to multiple adversities are more impacted compared to those exposed to a single adversity. However, the mechanisms responsible for this dose-dependent effect are unclear and have not been investigated in animal models. Here we assess the effects of a single stressor (i.e. limited bedding/nesting) abbreviated as LB and unpredictable multiple stressors (limited bedding/nesting, unpredictable maternal separation, and nest disruption) abbreviated as UPS on gene expression in the hippocampus of 17-day old pups (P17).

overall_design: RNA was isolated from the left hippocampus of 17-day old pups raised under control (CTL), limited bedding (LB), or unpredictable postnatal stress (UPS) and sequenced using the Illumina NovaSeq 6000 at an average depth of 73MR per sample. Reads were trimmed, aligned, and gene expression in TPM was calculated using HISAT2. TPM for all samples are shown in the processed data file: ELS_Sex_exp49.txt (TPMS). Low expressing gene (TPM < 3 in all three groups) were removed and the remaining 13,245 genes were analyzed using DESeq2 script in R (Love et al., 2014) to identify genes that are differentially expressed between the three groups. The information is provided in one excel file (Summary DRG 050322) containing CTL_LB, CTL_UPS, and LB_UPS comparisons. Each comparison provides info for gene name, log2 fold change, p-value, and padj (correcting for false discovery rate using Benjamin and Hochberg correction).

first: Rafiad

last: Islam

first: Jordon

last: White

first: Kiran

last: Dayananda

first: Alexa

last: Pugliese

first: Sameet

last: Mehta

first: Daniel

last: Wang

first: Baruh

last: Polis

first: Sahabuddin

last: Ahmed

first: Bryan

last: Pasqualucci

first: Christopher

last: Castaldi


title: Effect of 0,5,10 μM acacetin treatment on activated CD4+ T cells

first: yang

last: lu

address: Zhengzhou

institute: The First Affiliated Hospital of Zhengzhou University

summary:
To investigate the function of Acacetin in regulating CD4+ T cell activation, we activated CD4+ T cells from normal BALB/c mice with CD3/CD28 antibody and treated them with different concentrations of acacetin.
Then, we performed gene expression profiling using data obtained by RNA-seq of three different concentrations of acacetin.

overall_design: Comparative gene expression profiling of RNA-seq data from activated CD4+ T cells treated with different concentrations of acacetin.

first: Yang

last: Lu

first: Yuwei

last: Wu

first: Jiu

last: Pu

first: Qiongfeng

first: Qian

last: Qian Dong

first: Ning

last: Zhao

first: Guirong

last: Li

first: Yimei

last: Du


title: A single-cell atlas of the aging murine ovary

status: Public on Nov 27 2023

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. However, the field lacks a cellular map of the transcriptomic changes in the aging ovary to identify drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with T and B lymphocyte proportions increasing most. We also discovered an age-related upregulation of alternative macrophage and downregulation of collagenase pathways in stromal fibroblasts. Overall, follicular cells (especially granulosa and theca) display stress response, immunogenic, and fibrotic signaling pathway inductions with aging. These changes are more exaggerated in the atretic granulosa cells but are also observed in healthy antral and preantral granulosa cells. Moreover, we did not observe age-related changes in markers of cellular senescence in any cellular population with advancing age, despite specific immune cells expressing senescence-related genes across both timepoints. This report raises several new hypotheses that could be pursued to elucidate mechanisms responsible for ovarian aging phenotypes.

overall_design: scRNA-Seq from dissociated ovaries from young (3 months old; n=4) and reproductively aged (9 months old; n=4) wild-type C57BL/6j mice

first: José

middle: V

last: Isola

first: Sarah

last: Ocañas

first: Chase

last: Hubbart

first: Sunghwan

last: Ko

first: Samim

last: AliMondal

first: Jessica

last: Hense

first: Augusto

last: Schneider

first: Susan

last: Kovats

first: Willard

last: Freeman


title: Full-length RNA profiling of Mycobacterium tuberculosis with SEnd-seq

status: Public on Dec 10 2023

city: Newyork

first: Xiangwu

last: Ju

address: 1230 York Avenue

institute: The Rockefeller University

summary: Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that inflicts major health and economic costs around the world. Mtb encounters diverse environments during its lifecycle and responds to these changes by reprogramming its transcriptional output. However, the mechanisms and regulation of Mtb transcription remains poorly understood. In this work, we simultaneously determine the 5' and 3' ends of individual RNA molecules in Mtb cells using the SEnd-seq method, which enables us to profile the Mtb transcriptome at high resolution. Unexpectedly, we find that most Mtb transcripts are incomplete, with their 5' ends aligned at transcription start sites and 3' ends located 200-500 nucleotides downstream. Using native elongating transcript sequencing, we show that these short RNAs are mainly associated with paused RNA polymerases (RNAPs) rather than products of premature termination. We further show that the high propensity of Mtb RNAP to pause early in transcription is dependent on the binding of the sigma factor. Finally, we show that a translating ribosome promotes transcription elongation, suggesting a role for transcription-translation coupling in Mtb gene expression. In sum, our findings depict a mycobacterial transcriptome that prominently features incomplete transcripts resulting from RNAP pausing. We propose that the pausing phase constitutes an important transcriptional checkpoint in Mtb that allows the bacterium to adapt to new environments and could be exploited for TB therapeutics.

sample_organism:
Mycolicibacterium smegmatis
Mycobacterium tuberculosis

overall_design: SEnd-seq and NET-SEnd-seq methods were employed to investigate the transcriptome of Mtb cells under different growth conditions. These included wild-type cells in both log and stationary phases, Mtb cells after Rho knockdown, and cells subjected to treatments with linezolid, rifampicin, streptomycin, and clarithromycin separately at different time points. Additionally, the genomic occupancy of RpoB and SigA in Mtb was further profiled using ChIP-seq.

first: Shixin

last: Liu


title: Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in tank culture environment

status: Public on Nov 20 2023

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Channel catfish and blue catfish represent two economically important freshwater aquaculture species in the United States. Our study aims to investigate the gene expression differences between these two catfish species by high-throughput RNA sequencing to understand their associated phenotypic differences in growth and disease resistant. Our transcriptomic analyses provide some insights into gene function differences between the two species and the molecular basis of channel catfish growth advantage in the tank culture environment.

sample_organism:
Ictalurus punctatus
Ictalurus furcatus

platform_organism:
Ictalurus punctatus
Ictalurus furcatus

overall_design: Muscle, liver, intestine, mucus, and heart of channel catfish and blue catfish with three replicates were collected for RNA sequencing to identify the differentially expressed genes and tissue-specifically expressed genes.


title: Effects of ECM rigidity on normal and keloid dermal fibroblasts

status: Public on Nov 02 2023

first: John

last: Connelly

state: London

address: 4 Newark Street

department: Blizard Institute

institute: Queen Mary University of London

summary: This study investigated the effects of extracellular matrix (ECM) rigidty on gene expression patterns in normal dermal fibroblasts (NDFs) and keloid dermal fibroblasts (KDFs).  Cells were cultured on collagen coated polyacrylamide hydrogels with elastic moduli mimicking normal skin (8 kPa) or keloid scar tissue (214 kPa), and changes in gene expression were profiled using next-generation RNA-sequencing.  Differential gene expression analysis identified overall significant differences in gene expression between the NDF and KDF populations.  Despite high levels of inter-patient heterogeneity in the KDF samples, further principal components analysis revealed a subset of genes (PC5) that were specifically regulated by ECM rigidity.  Gene set enrichment analysis of the PC5 genes identified classic pathways associated with mechanotransduction, including Hippo Signalling and Regulation of the Actin Cytoskeleton, as well as genes associated with the Autophagy pathway.  Additional in vitro studies and human tissue staining confirmed the biomechanical regulation of autophagic flux in NDFs and KDFs and differential remodelling of the lysosome in KDFs and keloid scars.  Together, these findings implicate autophagy and lysosomal remodelling as biomechanically dysregulated pathways in keloid fibroblasts, and these mechanisms may contribute to scar pathogenesis.

overall_design: NDFs and KDFs from three different donors were cultured on polyacrylamide gels coated with type I collagen for 24 hours.   Total RNA was isolated for each sample and sequenced using the Illumina NextSeq platform.  Subsequent differential gene expression and pathway analysis was performed using the SeqMonk and Webgestalt platforms

first: Rosie

last: Ross


title: Myeloid cells interact with a subset of thyrocytes to promote their migration and follicle formation through NF-κB.

status: Public on Nov 16 2023

city: Shanghai

first: Ruifeng

last: Yang

address: Zhi Zao Ju Road

department: Molecular Diagnostics & Endocrinology

institute: Shanghai Ninth People's Hospital

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

overall_design: Refer to individual Series.


title: Functions of STE12 in Trichoderma reesei

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

institute: Austrian Institute of Technology

summary: We investigated the function of the transcription factor STE12 and found an involvement in gene expression and growth in light and darkness

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei QM6a (WT) and deletion mutant QM6aΔste12

first: Monika

last: Schmoll


title: Binding-site resolution structure and dynamics of Cebpa regulatory regions during macrophage-neutrophil differentiation

status: Public on Nov 08 2023

city: Grand Forks

first: Manu

last: Manu

state: ND

address: 10 Cornell Street, Stop 9019

department: Biology

institute: University of North Dakota

summary: During hematopoiesis, multipotential progenitors differentiate into all the types of cells found in blood by the action of complex gene regulatory networks (GRNs) comprising transcription factor (TF) genes that regulate each other’s expression. The gene regulatory logic—by which we mean the identities of the TF regulators, where they bind, whether they activate or repress, and how they interact with each other—remains unknown for most hematopoietic genes. Here, we utilize high coverage ATAC-Seq and reporters integrated in a site-specific manner to investigate binding-site resolution chromatin accessibility dynamics of Cebpa enhancers during macrophage-neutrophil differentiation. Reporter genes were integrated into the ROSA26 locus using CRISPR/Cas9 in PUER cells, which can be differentiated into neutrophils or macrophages in vitro. Time series reporter data showed an upregulation of two enhancers during the first 48 hours of neutrophil differentiation, which mirrored the temporal expression pattern of the endogenous Cebpa gene. Chromatin accessibility was also profiled at several time points by high coverage (300 million reads per sample) ATAC-Seq. The accessibility patterns were highly correlated between time points, allowing us to pool the data and achieve approximately 50x coverage after filtering. These data revealed that the enhancers had many protected regions of low accessibility interspersed with short high-accessibility islands. All previously characterized TF binding sites and centers of ChIP-Seq peaks overlapped protected regions, indicating that they are TF footprints. Surprisingly, while the total accessibility of the enhancers increased during differentiation, this increase occurred after gene expression had peaked, implying that the total accessibility of the enhancers was not driving gene expression. However, Tn5 counts at the high-accessibility islands adjacent to TF footprints, especially for Cebp sites, increased at earlier time points, suggesting that TF occupancy may drive the upregulation in gene expression as well as the later increase in the total accessibility of the enhancers. Our high coverage accessibility maps reveal a complex regulatory architecture, with 5-7 TFs binding up to 20 sites in a single Cebpa enhancer. Furthermore, the temporal dynamics of accessibility and gene expression do not support a causal role for total accessibility in gene expression. More generally, these results show that profiling gene expression and accessibility at high temporal- and genomic-resolution have the potential to reveal the causal drivers of gene expression changes during development.

overall_design: Time series of Assay for Transposase Accessible Chromatin using sequencing (ATAC-Seq) during the differentiation of a mouse cell-line, PUER, into macrophages and neutrophils. ATAC-Seq was performed in duplicate in undifferentiated PUER cells, at 5 timepoints in GCSF conditions (neutrophil) and 2 timepoints in IL3 conditions (macrophage).

first: Trevor

middle: E

last: Long Jr

first: Tapas

last: Bhattacharyya

first: Andrea

last: Repele

first: Madison

last: Naylor

first: Sunil

last: Nooti

first: Shawn

last: Krueger


summary: The pathogenesis of thyroid dysgenesis (TD) is not well understood. Here, using a combination of single-cell RNA and spatial transcriptome sequencing, we identify a subgroup of NF-κB-activated thyrocytes located at the center of thyroid tissues in postnatal mice, which maintained a partially mesenchymal phenotype. These cells actively protruded out of the thyroid primordium and generated new follicles in zebrafish embryos through continuous tracing. Suppressing NF-κB signaling affected thyrocyte migration and follicle formation, leading to a TD-like phenotype in both mice and zebrafish. Interestingly, during thyroid folliculogenesis, myeloid cells played a crucial role in promoting thyrocyte migration by maintaining close contact and secreting TNF-α. We found that cebpa mutant zebrafish, in which all myeloid cells were depleted, exhibited thyrocyte migration defects. Taken together, our results suggest that myeloid-derived TNF-α-induced NF-κB activation plays a critical role in promoting the migration of vertebrate thyrocytes for follicle generation.

overall_design: Thyroid cells of C57 mice from different stages of postnatal days were isolaated and analyzed using scRNAseq.

first: Rui-Meng

first: Shi-Yang

last: Song

first: Feng-Yao

last: Wu

first: Rui-Feng

first: Yan-Ting

last: Shen

first: Ping-Hui

last: Tu

first: Zheng

first: Jun-Xiu

last: Zhang

first: Feng

last: Cheng

first: Guan-Qi

last: Gao

first: Jun

last: Liang

first: Miao-Miao

last: Guo

first: Liu

first: Yi

last: Zhou

first: Shuang-Xia

last: Zhao

first: Ming

last: Zhan

first: Huai-Dong


title: Microsporidian EnP1 alters host cell H2B monoubiquitination and prevents ferroptosis facilitating microsporidia survival

status: Public on Nov 21 2023

city: Jinan

first: Jingyu

last: Guan

address: No. 44 Wenhuaxi Road

institute: Shandong university

summary: Microsporidia are intracellular eukaryotic pathogens that pose a substantial threat to immunocompromised hosts. The way these pathogens manipulate host cells during infection remains poorly understood. Using a proximity biotinylation strategy we established that microsporidian EnP1 is a nucleus-targeted effector that modifies the host cell environment.   EnP1's translocation to the host nucleus is meditated by nuclear localization signals (NLSs). In the nucleus, EnP1 interacts with host histone H2B. This interaction disrupts H2B monoubiquitination (H2Bub), subsequently impacting p53 expression. Crucially, this inhibition of p53 weakens its control over the downstream target gene SLC7A11, enhancing the host cell's resilience against ferroptosis during microsporidian infection. This favorable condition promotes the proliferation of microsporidia within the host cell. These findings shed light on the molecular mechanisms by which microsporidia modify their host cells to facilitate their survival.

overall_design:
In order to investigate the impact of the overexpression of the microsporidian secreted protein EnP1 on host cell gene expression, we generated stable cell lines expressing EnP1 and GFP.
We then utilized the RNA-seq data obtained from the stable cell lines expressing EnP1 and GFP for the analysis of gene expression profiles, with three biological replicates for each group.

first: Bing

last: Han


title: Enhanced CTLA-4 blockade anti-tumor immunity with APG-157 combination in a murine head and neck cancer

status: Public on Nov 01 2023

city: Houston

first: Arjun

last: Bhattacharya

state: TX

address: 1155 Pressler Street

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

summary: We evaluated APG-157 and immune checkpoint inhibitors combination treatment using syngeneic mouse head and neck cancer cell line model, SCCVII. The study demonstrated best tumor control with APG-157+ anti-CTLA-4 antibody combination treatment and RNA-seq of the tumor revealed up-regulation of various genes related to T cell activity and down-regulation of various genes related to poor prognosis of head & neck cancer.

overall_design: The tumors were collected from 10 groups of mice treated with following treatment groups. 1) Control 2)APG-157 3)anti-PD-1, 4)anti-CTLA-4, 5) APG-157 + anti-PD-1, 6) APG-157 + anti-CTLA-4, 7) APG-157 + anti-PD-1 + anti-CTLA-4, 8) Anti-PD-1 + anti-CTLA-4, 9) anti-CD8 antibody 10) anti-CD8 antibody + APG-157 + anti-CTLA-4.

first: Shin

last: Daniel

first: Bhattacharya

last: Arjun


title: to investigate the changes of the gene of glioma mice after Bifidobacterium administration

status: Public on Oct 31 2023

city: chengdu

first: Huali

last: Fan

email: hanmingyy@126.com, hwari_f@163.com

address: West China School of Pharmacy, Sichuan University, No. 17, Section 3, Southern Renmin Road. Wuhou District, Chengdu 610041, China

institute: Sichcuan University

summary: Differentially expressed genes (DEGs) between the Glioma and BIF groups were identified based on P < 0.05 and |log2 (fold change)| ≥1, among which 441 were up-regulated and 520 were down-regulated

overall_design: glioma tissues were collected in TRIzol reagent.UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication generated by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was quantified as fragments per kilo base of exon per million fragments mapped (FPKM). The threshold of significantly differential expression was set at P < 0.05 and |log2(fold change)| ≥1.

first: Fu

last: Peng


title: Genome-wide map of Acetyl-H3K27 marked chromatin in pancreatic cancer cells treated with vehicle and acetate under low pH condition

first: Pankaj

last: Singh

address: 940 Stanton L. Young Blvd., BMSB 332A

department: Oncology Science

institute: OUHSC

summary: We report the application of ChIP sequencing technology for high-throughput profiling of histone modification in pancreatic cancer cells. We obtained 49.7 million reads from acetylated-H3K27 modified chromatin immunoprecipitated DNA from vehicle and acetate-treated pancreatic cancer cells. We find that lysine 27 acetylation effectively discriminates genes that are expressed, or stably induced upon acetate treatment. We identified genes involved in ribosome biogenesis, oxidative phosphorylation, and various metabolic pathways to be differentially acetylated in acetate-treated cells. The identification of these pathways provides link between cellular metabolism and chromatin status in the cells that can alter the pathophysiology of pancreatic cancer progression.

overall_design: Examination of acetyl-H3K27 histone modification in pancreatic cancer cells. Two samples were analyzed.

first: Divya

last: Murthy

first: David

middle: L

last: Klinkebiel


title: Dysregulated neuroimmune interactions and sustained type I interferon signaling after human immunodeficiency virus type 1 infection of human iPSC derived microglia and cerebral organoids

status: Public on Oct 25 2023

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Human immunodeficiency virus type-1 (HIV-1) associated neurocognitive disorder (HAND) affects up to half of HIV-1 positive patients with long term neurological consequences, including dementia. There are no effective therapeutics for HAND because the pathophysiology of HIV-1 induced glial and neuronal functional deficits in humans remains enigmatic. To bridge this knowledge gap, we established a model simulating HIV-1 infection in the central nervous system using human induced pluripotent stem cell (iPSC) derived microglia combined with sliced neocortical organoids. Upon incubation with two replication-competent macrophage-tropic HIV-1 strains (JRFL and YU2), we observed that microglia not only became productively infected but also exhibited inflammatory activation. RNA sequencing revealed a significant and sustained activation of type I interferon signaling pathways. Incorporating microglia into sliced neocortical organoids extended the effects of aberrant type I interferon signaling in a human neural context. Collectively, our results illuminate the role of persistent type I interferon signaling in HIV-1 infected microglial in a human neural model, suggesting its potential significance in the pathogenesis of HAND.

overall_design: RNA-Seq was used to identify differentially-expressed genes in iPSC-derived microglia at 15 days after infection with HIV strain JR-FL

first: Andrew

last: Boreland

first: Hsin-ching

last: Lin

first: Peng

last: Jiang

first: Arnold

last: Rabson

first: Zhiping

last: Pang


title: Vagus nerve stimulation limits the germinal center B cell response via CD4+ T cell-derived acetylcholine

city: Manhasset

first: Izumi

last: Kurata-Sato

address: 350 Community Drive

institute: the Feinstein Institutes for Medical Research

summary: Neural signals are known to contribute to immune regulation and modulation of the innate immune response downstream of the vagus nerve has been well studied. The effects of vagus nerve activity on antibody production, however, have been largely unexplored. Here we use a chronic vagus nerve stimulation (VNS) mouse model to study the effect of vagal activation on T-dependent B cell responses. We observed lower titers of high-affinity serum IgG and fewer antigen-specific germinal center (GC) B cells in the spleen. GC B cells from chronic VNS mice expressed more active caspase-3 and exhibited an altered gene expression profile suggesting increased susceptibility to apoptosis and impaired maturation. Follicular dendritic cell (FDC) cluster dispersal and altered FDC gene expression suggested poor FDC function. These alterations were diminished in the absence of a subset of acetylcholine-producing CD4+ T cells. In vitro studies revealed that α7 and α9 nicotinic acetylcholine receptors (nAChRs) directly regulated B cell production of TNF, a cytokine crucial to FDC clustering. Engagement of the α4 nAChR subunit on B cells impaired Akt phosphorylation, presumably decreasing B cell survival. Thus, VNS-induced GC impairment can be attributed, at least in part, to the effect of acetylcholine on B cell intrinsic pathways, resulting in hindered B cell survival and maturation and leading to an alteration in FDC function. Our findings identify a potential therapeutic target to prevent immunosuppression in conditions associated with increased vagal activity.

overall_design: NP-specific activated B cell of chronic vagus nerve stimulation and sham mice immunized with NP-CGG were isolated from the spleens by fluorescence-activated cell sorting (FACS) according to B220 and GL7 signals and binding to NP antigen and analyzed using scRNAseq.

first: Ibrahim

middle: T

last: Mughrabi

first: Minakshi

last: Rana

first: Michael

last: Gerber

first: Yousef

last: Al-Abed

first: Barbara

last: Sherry

first: Stavros

last: Zanos

first: Betty

last: Diamond


title: HRS mediates tumor immune evasion by regulating proteostasis-associated interferon pathway activation

status: Public on Oct 30 2023

city: PHILADELPHIA

first: Wei

last: Guo

state: PENNSYLVANIA

address: 433 S. University Avenue

institute: University of Pennsylvania

summary: By sorting receptor tyrosine kinases into endolysosomes, the endosomal sorting complexes required for transport (ESCRTs) are thought to attenuate oncogenic signaling in tumor cells. Paradoxically, ESCRT members are upregulated in tumors. Here, we show that disruption of hepatocyte growth factor-regulated tyrosine kinase substrate (HRS), a pivotal ESCRT component, inhibited tumor growth by promoting CD8+ T cell infiltration in melanoma and colon cancer mouse models. HRS ablation led to misfolded protein accumulation and triggered endoplasmic reticulum (ER) stress, resulting in the activation of the type I interferon pathway in an inositol-requiring enzyme-1α (IRE1α)/X-box binding protein 1 (XBP1)-dependent manner. HRS was upregulated in tumor cells with high tumor mutational burden (TMB). HRS expression associates with the response to PD-L1/PD-1 blockade therapy in melanoma patients with high TMB tumors. HRS ablation sensitized anti-PD-1 treatment in mouse melanoma models. Our study shows a mechanism by which tumor cells with high TMB evade immune surveillance and suggests HRS as a promising target to improve immunotherapy.

overall_design: To study the consequence of HGS inhibition, we performed shRNA knock-down (KD) experiments targeting several ESCRT members in B16 melanoma cell lines or mouse xenograft. We did RNA-seq for gene expression quantification. The B16 cell line samples consist of two batches. In the first batch, we constructed two groups: (1) control and (2) Hrs KD; each group has two replicates. In the second batch, we constructed two groups: (1) Hrs KD, and (2) control; each group has two replicates. The B16 tumor xenograft samples consist of two groups: (1) Hrs KD, and (2) control; each group has 5 replicates.

last: Zhang

first: Jiegang

last: Yang

first: Beike

last: Wang

first: Jingbo

first: Wenqun

last: Zhong

first: Yi

middle: Y

last: Ma

first: Ravi

last: Amaravadi

first: Meenhard

last: Herlyn

first: Xiaowei

last: Xu


title: The evolution of the naked mole-rat T cells

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

address: 1170 Veterans blvd

institute: Calico

summary: The immune system consists of a network of specialized cells and processes that protect the organism from diseases and regulates tissue repair. Natural killer (NK) cells and the αβ and γδ T cells comprise the cytotoxic arm of the immune system and have evolved to detect and eradicate cells infected with pathogens and affected by malignancies, in order to prevent their spread and subsequent tissue damage. The naked mole-rat (NMR; Heterocephalus glaber) exhibits an unusually long lifespan relative to its body size, remarkable cancer resistance, and a surprising absence of NK cells, likely lost during its evolution. So far, little is known about NMR T cells in terms of the subsets they comprise, the evolution of the genes that regulate their function, the diversity of their clonotypes, and the organ in which they mature – the thymus. Using single-cell RNA sequencing (scRNA-seq), we find that NMRs have a large population of circulating γδT cells, comprising two subsets, one with an activated cytotoxic profile. Using comparative genomics, we find that the NMR genome maintains a large diversity of γ and δ variable T-cell receptor (TCR) regions, relative to that in other mammalian genomes. We devise a novel TCR scRNA-seq approach, which reveals that the NMR cytotoxic γδT-cell subset harbors a dominant clonotype, and that, in contrast to mouse, the clonotypic diversity of NMR CD8 αβT cells is significantly lower than that of its CD4 αβT cells. The latter suggests that NMRs have evolved under a relaxed intracellular pathogenic selective pressure, consistent with the loss of their NK cells. We corroborate this by showing that the genomic diversity of NMR MHC-I genes, relative to that of MHC-II genes, is considerably smaller than in other mammalian genomes. In line with these findings, we further show that NMR thymi in early life are considerably smaller compared to mouse thymi, yet by middle age thymi of both species show equivalent signs of involution. Our study thus sheds significant light on NMR T cells and moves us one step closer towards understanding the contributions of the immune system to the remarkable longevity and cancer resistance of this species.

sample_organism:
Mus musculus
Heterocephalus glaber

platform_organism:
Mus musculus
Heterocephalus glaber

overall_design: Single-cell short-read RNA-seq 10X samples of adult and old naked mole-rat and mouse anti-CD3 sorted splenocytes (hence T cells), adult naked mole-rat and mouse bone-marrow cells, adult naked mole-rat and mouse thymocytes; Single-cell long-read RNA-seq PacBio samples of adult and old naked mole-rat and mouse anti-CD3 sorted splenocytes (hence T cells)

first: Tzuhua

last: Lin

first: Nicole

last: Fong

first: Megan

last: Smith

first: Wendy

last: Craft

first: Baby

last: Martin-McNulty

first: Margaret

middle: A

last: Roy

first: Rochelle

last: Buffenstein


title: Human telencephalic organoid development in the presence and absence of exogenous extracellular matrix

first: Catarina

last: Martins-Costa

address: Dr.-Bohr-Gasse 3

institute: IMBA - Institute of Molecular Biotechnology of the OeAW

summary: Long-term culture of human telencephalic organoids cultured in the presence or absence of exogenous ECM. To evaluate how ECM supplementation influences organoid development, we supplied exogenous ECM in the form of Matrigel at the beginning of neuroepithelialisation (day 10, D10), either as a solid droplet that provides long-term exposure to a polymerized network of ECM proteins (droplet embedding - condition "drop" in the metadata table), or transiently dissolved in the culture medium (concentration of 2%V/V ) from D10 to D13 (liquid embedding - "liq"). These protocols were compared to one without exposure to exogenous ECM ("no"). Organoids were processed at 120 days of culture, when mature cortical tissue is present.

overall_design:
scRNA-Seq; Human telencephalic organoids; 3 replicates per condition of exogenous ECM supplementation (in the metadata file: orgid 1 to 9; condition "drop", "liq", "no").
bulkRNA-Seq: Human telencephalic organoids; 5 replicates per condition of exogenous ECM supplementation (each sample is a single organoid).

first: Vincent

last: Pham

first: Alexander

last: Vogt

first: Jürgen

last: Knoblich


title: Modeling and modulation of RHO signaling in human iPSC-derived retinal organoids from patients with RHO-CNV

status: Public on Oct 22 2023

city: San Francisco

first: Deepak

last: Lamba

address: 35 Medical Center Way, Rm1024

institute: University of California, San Francisco

summary:
To investigate the effects of RHO-CNV in human iPSC-derived retinal organoids. Furthermore Photoregulain3 (PR3) was added to media for 7 days to modulate RHO levels.
We then performed gene expression profiling analysis D300+ retinal organoids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for organoids with RHO-CNV, control and PR3 treated RHO CNV retinal organoids.


title: Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos

status: Public on Oct 19 2023

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

overall_design: Refer to individual Series


title: Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos [RNA-Seq]

summary: In mammals, many retrotransposons are de-repressed during zygotic genome activation (ZGA). However, their functions in early development remain elusive largely due to the challenge to simultaneously manipulate thousands of retrotransposon insertions in embryos. Here, we employed epigenome editing to perturb long terminal repeat (LTR) MT2_Mm, a well-known ZGA and totipotency marker that exists in ~2667 insertions throughout the mouse genome. CRISPR interference (CRISPRi) robustly targeted and repressed 2485 (~93%) MT2_Mm insertions and 1090 (~55%) insertions of the closely related MT2C_Mm in 2-cell embryos. Remarkably, such perturbation caused down-regulation of hundreds of ZGA genes at 2C stage and embryonic arrest mostly at morula stage. Mechanistically, MT2_Mm/MT2C_Mm primarily served as alternative ZGA promoters activated by Obox proteins. Thus, through large-scale epigenome editing, we addressed to what extent MT2_Mm/MT2C_Mm regulates ZGA and preimplantation development. Our approach could be adapted to systematically perturb retrotransposons in other mammalian embryos as it doesn’t require transgenic animals.

overall_design: RNA-seq were performed for mouse embryos injected with dCas9-KRAB mRNA in combination with either non-targetting control sgRNA or MT2_Mm sgRNAs.

first: Jian

last: Yang

first: Lauryn

last: Cook


title: K562 and human brain transcriptomes, and various epigenomes from K562 and human/mouse brain curated from public databases and re-analyzed for comparison with the single-stranded DNA open-chromatin detected by CHEX-seq

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

summary: To study the association of CHEX-seq with transcriptional activity, we downloaded and re-analyzed K562 bulk RNA-seq, single-cell RNA-seq, and GRO-seq data, as well as human brain single-cell RNA-seq data. To study the association of CHEX-seq with DNA replication, we downloaded and re-analyzed K562 replication origin data. To study the association of CHEX-seq with epigenomes, we downloaded and re-analyzed ATAC-seq, DNase-seq, FAIRE-seq, RRBS-seq, DRIP-seq, ChIP-seq and super-enhancer data from K562, human and/or mouse brain. To study the association of CHEX-seq with DNA strand conformation, we downloaded and re-analyzed human and mouse non-B-form DNA regions.

overall_design: We downloaded human and mouse transcriptomes, epigenomes and DNA strand conformation data from GEO, ENCODE, UCSC Genome Browser and non-B DB. They are: K562 bulk RNA-seq, RNA-seq and single-cell RNA-seq samples; 88 human astrocyte and 100 human neuron single-cell RNA-seq samples; K562 ATAC-seq, DNase-seq, FAIRE-seq, RRBS-seq, DRIP-seq, replication origins and super-enhancer samples; 258 K562 TF binding ChIP-seq samples; 11 K562 narrow or broad histone modification samples; one human brain ATAC-seq sample; 5 human brain DNase-seq samples; one human brain FAIRE-seq sample; 2 mouse brain ATAC-seq samples; 3 mouse brain DNase-seq samples; 10 mouse brain narrow or broad histone modification samples; 7 human non-B-form DNA region samples; 7 mouse non-B-form DNA region samples.


title: FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

status: Public on Oct 18 2023

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary:
Experimental methods for discovering RNA Binding Protein (RBP) binding sites on target RNAs have recently emerged which employ fusions of RBPs to RNA-editing enzymes (such asAPOBEC1 or  ADAR) to “label” mRNA.
However, off-target editing, genetic variants and sequencing errors can lead to false positives when using data derived from such approaches, and highlight a need for a robust, statistical approach to prioritizing confident binding sites.

overall_design: Transiently transfected RBFOX2-APOBEC1 fusion construct expression was induced in HEK293 cells using doxycycline for 72 hours before samples were prepared for RNA sequencing. We present FLagging Areas of RNA-editing Enrichment (FLARE),  a Snakemake-based pipeline that uses a statistical approach to determine regions of enriched RNA editing, using SAILOR-derived editing sites as a starting point.

first: Hugo

last: Medina

first: Eric

last: Kofman


title: PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape [RNA-seq]

status: Public on Nov 18 2023

city: Chicago

first: Alexandra

last: Bradu

state: IL

address: 924 East 57th Street

department: Pathology

institute: University Of Chicago

summary: T cells trigger non-specific signaling pathways to elicit specialized effector functions to eliminate pathogens and cancers. Chromatin accessibility at T effector loci prior to antigen encounter poises cells to couple antigen recognition to the activation of lineage-specific responses. Here, by tracing the chromatin accessibility profiles unique to T effector functions during development, we find that the majority of T effector loci become accessible prior to antigen receptor expression. Epigenomic feature analysis, biochemical studies, and inducible perturbations identified two mechanistic linchpins: the physical association of the mSWI/SNF remodeling complex to the pleiotropic transcription factor (TF) RUNX1, and the cooperativity between RUNX1 and lineage-defining TFs PU.1 and BCL11B that respectively facilitate the establishment and maintenance of chromatin accessibility at T effector loci in early thymocyte progenitors. These findings reflect a design principle that allows distinct cell types to use the same signaling pathways to execute disparate roles which collectively orchestrate the immune response.

overall_design: RNA-seq profiling was performed on at various stages of development in wild-type untreated, wild-type FK506-treated, Smarca4 cKO, Bcl11b cKO, and Runx1 cKO murine thymocytes.

first: Noah

last: Gamble

first: Jason

last: Caldwell

first: Joshua

last: McKeever

first: Olubusayo

last: Bolonduro

first: YeEun

first: Benjamin

last: Parks

first: Sandy

last: Klemm

first: William

last: Greenleaf

first: Gerald

last: Crabtree

first: Andrew

last: Koh


title: Single-cell RNA-seq of astrocytes and neurons from primary culture of the mouse brain and of acute slice of interneurons from Patch-clamp pipette [RNA-seq mouse brain]

summary: To investigate the relationship between single-cell transcriptional activity and single-strand open-chromatin landscape in mouse brain, we performed single-cell RNA-seq.

overall_design: We did single-cell RNA-seq for 8 single astrocytes and 12 single neurons from mouse brain primary cultures. We also did single-cell RNA-seq for 8 interneurons collected from acute slice of mouse brain using Patch-clamp pipette.

first: Youtao

last: Lu

first: Jaehee

last: Lee

first: Jifen

last: Li

first: Srini

last: Allu

first: Jinhui

last: Wang

first: Hyun-Bum

first: Kevin

last: Bullaughey

first: Stephen

last: Fisher

first: C

last: Nordgren

first: Jean

last: Rosario

first: Stewart

last: Anderson

last: Ulyanova

first: Steven

last: Brem

first: H

middle: I

last: Chen

first: John

last: Wolf

first: M

last: Grady

first: Sergei

last: Vinogradov

first: James

last: Eberwine


title: Myeloid cells interact with a subset of thyrocytes to promote their migration and follicle formation through NF-κB.

first: Ruifeng

last: Yang

address: Zhi Zao Ju Road

overall_design: Thyroid cells of C57 mice from 10 days after birth were isolaated and analyzed using scRNAseq (spatial).

first: Rui-Meng

first: Shi-Yang

last: Song

first: Feng-Yao

last: Wu

first: Rui-Feng

first: Yan-Ting

last: Shen

first: Ping-Hui

last: Tu

first: Zheng

first: Jun-Xiu

last: Zhang

first: Feng

last: Cheng

first: Guan-Qi

last: Gao

first: Jun

last: Liang

first: Miao-Miao

last: Guo

first: Liu

first: Yi

last: Zhou

first: Shuang-Xia

last: Zhao

first: Ming

last: Zhan

first: Huai-Dong


title: Light-Assisted Single-Stranded Open-Chromatin Analysis in K562 and Spatially Localized Neuronal Single Cells

first: Junhyong

last: Kim

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: STAT3 Modulates CD4+ T Mitochondrial Dynamics and Function in Aging

status: Public on Oct 17 2023

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Aging promotes numerous intracellular changes in T cells that impact their effector function. Our data shows that aging promotes an increase in localization of STAT3 to the mitochondria (mitoSTAT3), which promotes changes in mitochondrial dynamics and function and has a mechanistic link to T cell cytokine production. More specifically, mitoSTAT3 increased activity of aging T cell mitochondria due to STAT3’s effect on complex II.  Limiting mitoSTAT3 using a mitochondria targeted curcuminoid, Mtcur-1, lowered complex II activity, prevented age-induced changes in mitochondrial dynamics and function, and reduced proinflammatory Th17 inflammation. Exogenous expression of the constitutively phosphorylated form of STAT3 in T cells from young adults mimicked changes in mitochondrial dynamics and function in T cells from older adults and partially recapitulated aging-induced cytokine profiles. Our data shows the mechanistic link among mitoSTAT3, mitochondrial dynamics,function and T cell cytokine production.

overall_design: Human CD4+ T cells were isolated from peripheral blood of normoglycemic young and old adults  and analyzed using scRNA-seq.

first: Emelia

last: Zukowski

first: Marco

last: Sannella

first: Jack

last: Donato Rockhold

first: Gabriela

last: Pugh

first: Madison

last: Kuhn

first: Nasun

last: Hah

first: Ling

last: Ouyang

first: Tzu-Wen

last: Wang

first: Micah

last: Drummond

first: Elizabeth

last: Proctor

first: Hatice

last: Hasturk

first: Barbara

last: Nikolajczyk

first: Leena

last: Bharath


title: Cortex-specific epigenetic profiling of chromatin accessibility after deeper cerebral hypoperfusion in mice

first: Zengyu

last: Zhang

state: Shanghai

address: Dong'an Road

department: Neurology

institute: Fudan University

summary:
Efforts to understand genetic variability involved in cortex damage and glial activation support a role for upstream regulation by epigenetic mechanisms.
To investigate cortex-specific epigenetic profiling after severe cerebral hypoperfusion in mice

overall_design: Cortex-specific epigenetic profiling analysis was performed using data obtained from ATAC-seq of 4 biological replicates in sham and BCAS mice after hypoperfusion

first: Shaungxing

last: Hou

first: Pengpeng

last: Jin


title: Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures [ATAC-seq]

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary:
Acute lymphoblastic leukemia (ALL) is the most common malignancy in pediatric patients and represents about a quarter of all pediatric malignancies. Past work has characterized B-cell lineage ALL (B-ALL) into molecular subtypes spanning a range of aberrant chromosomal rearrangements and chimeric fusions driving malignancy. While transcriptional and DNA methylation profiling of these subtypes has been extensively examined, the accompanying chromatin landscape and corresponding gene regulatory repertoire is not well characterized for many B-ALL subtypes. To better understand the B-ALL epigenome and gene regulatory network we mapped chromatin accessibility for 11 B-ALL molecular subtypes using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) across 154 primary patient samples. We uncovered extensive chromatin reprogramming between B-ALL and primary B-cells that drive oncogenic signaling pathways and perturb normal B-cell functions. Strikingly, we also identified 42,457 accessible chromatin sites which exhibit strong subtype enrichment. Subtype enriched sites were shown to have a subtype prediction cross-validation accuracy of nearly 90% within a PCA-LDA classification model framework. Transcription factor (TF) footprint profiling and transcriptomic information further identified candidate subtype-specific driver TFs as well as unique gene regulatory networks among B-ALL subtypes. To better understand how genetic variation impacts chromatin accessibility, we identified 9080 variants that act as ATAC-seq chromatin accessibility quantitative trait loci (ATAC-QTLs) and contribute to chromatin accessibility variability among patient samples. Overall, this large dataset and associated analyses offer a unique window into the gene regulatory landscape of B-ALL that highlight the complexity and heterogeneity of chromatin accessibility among B-ALL molecular subtypes.

Keywords: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Fast-ATAC-seq was performed on purified leukemia cells from human patients. 10,000 cells were used for library preparation.


title: Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos [ChIP-Seq]

first: Zhiyuan

last: Chen

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) data of dCas9 and HA in mouse embryonic stem cells. Control cells only express dCas9 whereas the treatment group express both dCas9 and MT2_Mm sgRNAs.

first: Jian

last: Yang

first: Lauryn

last: Cook


title: Fast and robust characterization of RNA targets of RNA-binding proteins by RNA-editing strategy coupled with machine learning in human embryonic stem cells

status: Public on Oct 10 2023

city: Haining

first: Huanchang

last: Tu

address: 718 East Haizhou Rd., Haining, Zhejiang

institute: Zhejiang University

summary: RNA-binding proteins (RBPs) paly critical roles in regulating the maintenance and differentiation of embryonic stem cells. A critical step in understanding the functions of RBPs is the identification of their bound RNA transcripts. Towards this aim, we developed an inducible strategy named as RNA-Editing-Based-RNA-seq (REB-seq) to capture the potential RNA targets bound by the RBPs-of-interest. Fused with the catalytic domain of ADAR or APOBEC1 that mediate the A to I (A to G) or C to U (C to T) editing, respectively, REB-seq identifies the bound RNAs by transcriptome profiling without the necessity of high-performance antibodies for the RBPs. Using REB-seq, we characterized the mRNAs bound by the m6A readers IGF2BP1, IGF2BP2, and IGF2BP3 in human embryonic stem cells. We also incorporated machine learning strategy to the analysis of REB-seq data to improve the accuracy of target RNA characterization. Furthermore, REB-seq identifies associated single nucleotide polymorphisms that may affect the RBP binding and imply the disease pathogenesis. Collectively, REB-seq coupled with machine learning can be applied to capture RNA transcripts bound by RBPs-of-interest easily and robustly.

overall_design: hESCs were cultured with Nuwacell® ncTarget hPSC Medium on Matrigel-coated plates. Control hESCs, hESCs with tetON-overexpression of ADAR, hAPOBEC, rAPOBEC, ADAR-IGF2BP1, hAPOBEC-IGF2BP1, rAPOBEC-IGF2BP1, ADAR-IGF2BP2, hAPOBEC-IGF2BP2, rAPOBEC-IGF2BP2, ADAR-IGF2BP3, hAPOBEC-IGF2BP3, rAPOBEC-IGF2BP3 were induced with doxcycycline for 24 hours before extracting total RNA for RNA-seq.

first: Jin

first: Jilai

last: Xie

first: Shuo

last: Cai


title: Checkpoint Kinase 2 Controls Insulin Secretion and Glucose Homeostasis

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: After the discovery of insulin a century ago, extensive work has been done to unravel the molecular network regulating insulin secretion. Here, we performed a chemical screen and identified AZD7762, a compound that potentiates glucose-stimulated insulin secretion (GSIS) of human β cell line, healthy and type 2 diabetic (T2D) human islets, and primary cynomolgus macaque islets. In vivo studies in diabetic mouse models and cynomolgus macaques demonstrated that AZD7762 enhances GSIS and improves glucose tolerance. Furthermore, genetic manipulation confirmed that ablation of CHEK2 in human β cells results in increased insulin secretion. Consistently, high-fat-diet fed Chk2-/- mice show elevated insulin secretion and improved glucose clearance. Finally, an untargeted metabolic profiling demonstrated the key role of the CHEK2-PP2A-PLK1-G6PD-PPP pathway in insulin secretion. This study successfully identifies a previously unknown insulin secretion regulating pathway that is conserved across rodents, cynomolgus macaques and human β cells in both healthy and T2D conditions.

overall_design: To assess changes in transcriptome of EndoC-βH1 cells treated with 1uM AZD7762 during glucose-stimulated insulin secretion experiment

first: Angie

last: Chong

first: Xiaohua

last: Duan

first: Tuo


title: SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans [sin-3(syb2172) and hda-3(ok1991)]

status: Public on Oct 04 2023

city: Lyon

first: Cecile

last: Bedet

address: 46 allée d'Italie

department: Bilogie

country: France

institute: ENS de Lyon

summary: The SIN3 transcriptional coregulator influences gene expression through multiple interactions that include histone deacetylases (HDACs). Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability (ID)/autism syndromes, emphasizing its key role in development. However,  little is know on its complexity of interactions and functions in developmental processes. Here we show that loss of SIN-3, the single SIN3 homologue in Caenorhabditis elegans, results in maternal effect sterility associated with deregulation of the germline transcriptome, including derepression of X-linked genes. Using proteomics analysis we identify at least two SIN3 complexes containing distinct HDACs and differentially contributing to fertility. Single cell smFISH reveals that loss of sin-3 stochastically derepresses X linked genes in individual germ cells. We further identify acetylation marks whose abundance depends on SIN3. Together, this work provides a powerful paradigm for the in vivo study of SIN3 and associated proteins.

overall_design: gene expression profiling of Smart-seq data  of germlines from young adults  sin-3(syb2172) and hda-3(ok1991) versus wild-type (wt)

first: Matthieu

last: Caron

first: Valerie

last: Robert

first: Loic

last: Gely

first: Adrait

last: Annie

first: Victoria

last: Pakulska

first: Yohann

last: Coute

first: Manon

last: Chevalier

first: Christian

last: Riedel

first: Francesca

last: Palladino


title: RNA binding of DDX20 in the testis of postnatal 7-day-old C57BL/6 mice.

status: Public on Oct 01 2023

city: beijing

first: dingfeng

last: zou

state: 北京

address: Beijing, Dong Dan San Tiao 5

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

summary: RNA immunoprecipitation assay followed by Next-Generation Sequencing (RIPseq) to identify RNAs bound by DDX20 in testis of postnatal 7-day-old C57BL/6 mice.

overall_design: The assay was performed in the cells separated from 7-day-old C57BL/6 mice testis with DDX20 antibody(Proteintech, #11324-1-AP ).10% of total RNA was used as input.

first: Dingfeng

last: Zou

first: Luying

last: Su


title: RNA-seq reveals an abnormal transcriptome as a result of DDX20 loss in spermatogonia.

summary: To investigate the role of DDX20 in spermatogenesis, we generated Ddx20 flox/flox Ddx4-Cre mice to make a germ cell-specific Ddx20 knockout, and isolated spermatogonia from four-day-old mouse testes by THY1 magnetic beads.We then performed gene expression profiling analysis using data obtained from RNA-seq of THY1 + spermatogonia.

overall_design: THY1-positive cells isolated from Ddx20 knockout mice and littermate controls were sequenced using smart-seq2 based technique.


title: Light-Assisted Single-Stranded DNA Open-Chromatin Analysis in Single Spatially Localized Neuronal Cells Identifies the Capacity of Endogenous DNA to Act Catalytically [CHEX-seq]

first: Junhyong

last: Kim

summary: We report a novel chromatin structure analysis technique, named "CHEX-seq" (CHromatin EXposed), which couples oligonucleotide random annealing and nucleus-resolution photoactivation such that the single-stranded open-chromatin DNA is copied, reverse transcribed, amplified and sequenced.

overall_design:
We applied CHEX-seq to a variety of cell types and treatments, including K562 cell line culture, cultured human astrocytes and neurons, cultured mouse astrocytes and neurons, and in situ tissue section of mouse neurons. For K562, we performed 12-O-tetradecanoylphorbol-13-acetate (TPA) perturbation and measured by CHEX-seq the single-stranded open-chromatin landscape at pre-treatment, 15min, 1hr, 2hr and 24hr post-treatment.

GSM7304391..GSM7304409: NOTE FROM SUBMITTER: we are depositing the raw data files of the human clinical samples to dbGaP

first: Youtao

last: Lu

first: Jaehee

last: Lee

first: Jifen

last: Li

first: Srini

last: Allu

first: Jinhui

last: Wang

first: Hyun-Bum

first: Kevin

last: Bullaughey

first: Stephen

last: Fisher

first: C

last: Nordgren

first: Jean

last: Rosario

first: Stewart

last: Anderson

first: Alexandra

last: Ulyanova

first: Steven

last: Brem

first: H

last: Chen

first: John

last: Wolf

first: M

last: Grady

first: Sergei

last: Vinogradov

first: James

last: Eberwine


title: Cis-regulatory control of transcriptional timing and noise in response to estrogen [RNA-Seq]

status: Public on Oct 12 2023

city: Salt Lake City

last: Richey

state: UT

address: 2000 Cir of Hope Dr

department: Biomedical Engineering

institute: University of Utah

summary: Cis-Regulatory Elements (CREs) precisely control transcription levels, temporal dynamics, and cell-cell variation - often referred to as transcriptional noise. However, the combination of regulatory proteins and epigenetic features necessary to control different transcription attributes is not fully understood. Here, single-cell RNA-seq (scRNA-seq) is conducted during a time course of estrogen treatment to identify genomic predictors of expression timing and noise. We find that multiple active enhancers predict faster temporal responses. Synthetic modulation of enhancer activity verifies that activating enhancers accelerates expression responses, while inhibiting enhancers results in a delayed response. Noise is controlled by a balance of promoter and enhancer activity. Active promoters are found at genes with low noise levels, whereas active enhancers are associated with high noise. Finally, we observe that co-expression across single cells is an emergent property dependent on chromatin looping, timing, and noise levels. Overall, our results indicate a fundamental tradeoff between a gene’s ability to quickly respond to incoming signals and maintain low variation across cells.

overall_design: RNA-seq was used to study gene expression during a timecourse of estrogen treatment

first: Jason

last: Gertz


title: Analysis of gene expression signatures for Met knockdown by siRNA

status: Public on Oct 15 2023

city: Suita

first: Aasa

last: Shimizu

state: Osaka

address: 2-2, Yamadaoka

country: Japan

institute: Osaka University

summary: To comprehensively detect differential gene expression between ovarian cancer cell lines (ES-2) transfected with fibroblast-derived exosomes only or Met targetting siRNA containing fibroblast-derived exosomes, total RNA was extracted and cDNA microarray analyses were performed.

overall_design: ovarian cancer cell lines (ES-2) transfected with fibroblast-derived exosomes only or Met targetting siRNA containing fibroblast-derived exosomes. One experiment was performed at each sample.

first: Kenjiro

last: Sawada


title: Nuclear Organization of Lens Epithelium and Fiber Cells in Newborn Lens

status: Public on Oct 16 2023

city: Bronx

first: William

last: Chang

address: 1301 Morris Park Ave

department: Ophthalmology

institute: Albert Einstein College of Medicine

summary: Cellular differentiation is marked by temporally and spatially coordinated gene expression regulated at multiple levels within the nucleus. Sequence-specific DNA-binding transcription factor CTCF EDIT. Topologically associated domains (TADs). Using Hi-C, we investigated changes in chromatin organization between newborn (P0.5) mouse lens fiber and epithelium and compared them to embryonic stem (ES) cells. Compartments A and B. Using ChIP-seq, we determined localization of CTCF in both lens tissues Formation of lens-specific TADs is demonstrated via comparative studies of chromatin at Pax6, Prox1, Gata3, Hsf4, and crystallin loci (to be updated) between lens and ES cell nuclei. Our study has generated the first data on nuclear organization in lens epithelium and lens fibers and directly compared these data with ES cells.

overall_design: Hi-C of newborn mouse lens epithelium, fiber, and mouse embryonic stem cells; CTCF chromatin immunoprecipitation DNA sequencing (CHiP-seq) of newborn mouse lens epithelium, fiber cells

middle: K

first: Michael

last: Camerino

first: Ales

last: Cvekl


title: Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

status: Public on Sep 28 2023

city: Huaibei

first: Mengmeng

last: Liu

state: Anhui

address: Dongshan Street

department: College of Life Science

institute: Huaibei Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon due to high temperatures, resulting in a significant reduction in yield. The molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata under heat stress and room temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, catalytic and binding activity. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed in two test conditions.  According to the analysis, genes and miRNAs associated with regulation of transcription, DNA-templated, transcription factor activity and sequence-specific DNA binding pathway, may play a major role in the resistance to heat stress in P. ternata. Integration of expression data of transcriptome and miRNAome determined high confidence 41 miRNA-mRNA pairs forming 25 modules. MYB-like protein and calcium-responsive transcription coactivator may play an integral role in the resistance to heat stress in P. ternata. In addition, the candidate genes and miRNAs were subjected to quantitative real-time PCR to evaluate their expression patterns. These results offer a foundation for future studies exploring the mechanism and critical genes of resistance to heat stress in P. ternata.

overall_design:
In order to examine the gene expression patterns of P. ternata under heat stress, six libraries were constructed from two leaf samples, with three biological replicates each (C: control, G: heat stress).
To comprehensively evaluate how heat stress influenced transcript profiles, six small RNA libraries were also constructed.

first: Chen

last: Bo

first: Tao

last: Xue


title: Circadian rhythms in mouse choroid plexus identified by time-resolved RNAseq require clock in the suprachiasmatic nucleus

status: Public on Sep 30 2023

city: Prague 4

first: Martin

last: Sládek

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology of the Czech Academy of Sciences

summary: The aim of our study was to investigate the circadian regulation of cellular processes in mouse choroid plexus (ChP) and to determine their dependence on signals from the clock in the suprachiasmatic nuclei (SCN). We performed time-resolved transcriptomics of ChP samples from C57Bl6J mice with intact (Ctrl) or surgically removed SCN (SCNx) collected every 4 h over 2 days in constant darkness and from FoxJ1-ERT2-Cre+/-; Bmal1fl/fl mice with ChP-specific clock disruption (Bmal1-KO) collected at 2 time points. We found widespread circadian gene expression in Ctrl mice that was not present in SCNx mice, and the SCNx day/night ratios were reduced similarly to Bmal1-KO.

overall_design:
ChP samples were collected every 4 h over 2 days in constant darkness from 12 Ctrl and 12 SCNx mice, and at 2 time points (day, night) from 2 Bmal1-KO mice. Total RNA was purified and submitted for sequencing.
We performed gene expression profiling, comparing time-resolved transcriptome of Ctrl and SCNx samples after circadian rhythmicity analysis.
We also compared day-night differences of top rhythmic genes between Ctrl, SCNx and Bmal1-KO samples.

first: Pavel

last: Houdek

first: Jihwan

last: Myung

first: Alena

last: Sumová


title: Expression profiling of ankle joint of a mouse model of gouty arthritis uncovers potential mechanisms involved in pain and inflammation

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

summary: Gout arthritis (GA) is a prevalent and painful inflammatory arthritis, and its global burden continues to rise. Intense pain induced by gout attacks is a major complication of gout. Treatment and long-term management for gout patients remain challenging. However, the pathogenesis of GA still remained largely unknown. The purpose of this study is to perform an expression profiling to identify genes related with GA in an animal model.  Using a monosodium urate (MSU) crystals-induced GA model, we performed RNA-sequencing for the ankle joint of gout mice in different time points. Our results revealed transcriptional changes in  the joint. We provided by far the first study to profile gene expression changes and pathway analysis of ankle joint in different time for investigating GA mechanisms.    This work may provide novel insights into understanding the mysterious mechanisms underlying GA.

overall_design: Mice were euthanized at 8 h or 24h post-injection of MSU or vehicle. The injected ankle joints were collected collected and RNA-sequencing (RNA-seq) was performed.

first: Boyu

first: Yushuang

last: Pan

first: Boyi


title: SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans

first: Cecile

last: Bedet

overall_design: Refer to individual Series


title: Genomic annotation of a non-coding region deleted on 4q25

city: nantes

first: Julien

last: Barc

address: 8 quai moncousu

institute: INSERM


title: The MODY-associated TALK-1 L114P mutation causes islet α-cell overactivity and β-cell inactivity resulting in transient neonatal diabetes and glucose dyshomeostasis in adults

status: Public on Sep 26 2023

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

summary: A strong association of the gain-of-function mutation in the TALK-1 K+ channel (p.L114P) with maturity-onset diabetes of the young (MODY) was recently reported in two distinct families. TALK-1 is a key regulator of β-cell electrical activity and glucose-stimulated insulin secretion (GSIS). KCNK16, the gene that encodes TALK-1, is the most abundant and β-cell–restricted K+ channel transcript and KCNK16 locus is strongly associated to type-2 diabetes. To investigate the impact of TALK-1-L114P on glucose homeostasis and confirm its association with MODY, a mouse model containing the TALK-1-L114P mutation was generated. Heterozygous and homozygous TALK-1-L114P mice exhibit increased neonatal lethality in the C57BL/6J and the CD-1(ICR) genetic background, respectively. Lethality is likely a result of severe hyperglycemia observed in the homozygous TALK-1-L114P neonates due to lack of GSIS and can be reduced with insulin treatment. TALK-1-L114P drastically increases whole-cell β-cell K+ currents resulting in blunted glucose-stimulated Ca2+ entry and a complete loss of glucose-induced Ca2+ oscillations. Thus, adult TALK-1-L114P mice have reduced GSIS and plasma insulin levels, which significantly impairs glucose homeostasis. Taken together, this study shows that the MODY-associated TALK-1-L114P mutation disrupts glucose homeostasis in adult mice resembling a MODY phenotype and causes neonatal lethality by altering islet hormone secretion during development. These data strongly suggest that TALK-1 is an islet-restricted target for the treatment for diabetes

overall_design: Total of 8 samples were analyzed, 4 were wild type (WT) and 4 were Kcnk16 L114P (L/P) mutation samples. RNA was extracted from each of these samples for bulk RNA-Sequencing analysis

first: Arya

last: Nakhe

first: Prasanna

last: Dadi

first: Jinsun

last: Kim

first: Jean-Philippe

last: Cartailler

first: Leesa

last: Sampson

first: Mark

last: Magnuson

first: David

last: Jacobson