title: Extracellular molecular response of bovine oviductal organoids to thermal stress.

status: Public on Oct 27 2023

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: The mammalian oviduct is a complex, fibromuscular organ known for its role in orchestrating a series of timely and dynamic changes to suitably support early embryogenesis. Establishing successful reproductive outcomes are largely determined through effective and cohesive communication systems between the transient embryo and the maternal environment. Climate change-induced, Heat stress (HS), is one of the largest single stressors compromising reproductive function. Systemic changes in the redox status of the maternal environment, adversely affect fertilization and early embryonic development, negative causation of HS. Oviductal organoids represent a 3-dimensional, biomimetic model to study the physiological impact of HS on the physiology of the oviduct and the subsequent developing embryo. In this study, we aimed to generate a robust bovine oviductal organoid culture system to decrypt the oviducts' differential response to HS in terms of secreted EV-miRNome, to elucidate the impact of thermal stress on oviductal physiology with subsequent potential impacts on early embryo development.

overall_design: The proposed research utilized the bovine species as a large animal model to study EV-mediated response of oviductal organoids to thermal stress. Bovine reproductive tissues, readily obtained from a local slaughterhouse were utilized to establish a BOEC organoids for the production of extracellular vesicles to study the physiology of the oviduct under HS and the potential embryo-maternal signals shuttled through the oviduct microenvironment. Oviductal organoids cultured under normal (37 °C) or heat stress (42 °C) conditions and EVs were isolated from the culture media for RNA isolation and small-RNA sequencing.

first: Nico

middle: G

last: Menjivar

first: Riley

middle: E

last: Thompson

first: Melinda

last: Meyers

first: Fiona

last: Hollinshead

first: Dawit

last: Tesfaye


title: Genome-wide methylation profiles of post-mortem tissue samples (human)

status: Public on Oct 22 2023

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: USP28-regulated mitochondrial homeostasis mechanism that involves the PPARα-Mfn2 axis in diabetic hearts [ChIP-seq]

status: Public on Oct 15 2023

city: Wuhan

first: Saiyang

last: Xie

address: Jiefang Road 238

country: China

institute: Wuhan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The majority of diabetics are susceptible to cardiac dysfunction and heart failure, while conventional drug therapy cannot correct diabetic cardiomyopathy (DCM) progression. Herein, we assessed the potential role and therapeutic value of ubiquitin-specific protease 28 (USP28) on the metabolic vulnerability of DCM. PPARα-/- in the db/db background mice were constructed to check the mechanism of USP28 in vivo. Inducible cardiac-specific deletion of Mfn2 in the db/db background mice was utilized to evaluate USP28-mediated cardioprotection. chromatin immunoprecipitation (ChIP) assays revealed that PPARα promote mitofusin 2 (Mfn2) transcription, thereby impeding mitochondrial morphofunctional defects.

overall_design: The interaction of PPARα and Mfn2 promoter was verified by chromatin immunoprecipitation (ChIP) assay in hiPSC-CMs

first: Qizhu

last: Tang


title: Transcriptomic analysis of differentially expressed genes in the Winnie mouse model of chronic colitis

status: Public on Oct 08 2023

city: Werribee

first: Ramya

middle: Sindhoora

last: Ephraim

state: VIC

address: 235 Hoppers Ln

country: Australia

institute: Victoria University

type: Expression profiling by high throughput sequencing

summary: The Winnie mouse, carrying a missense mutation in the Muc2 gene, is a model for chronic colitis closely resembling the pathological changes of human IBD. Herein, transcriptomic analyses of the differentially expressed genes in the distal colon of Winnie mice with mild colitis and Winnie-Prolapse mice with severe colitis are compared to control C57BL/6 mice. Gene ontology analysis and KEGG pathway analysis demonstrated the upregulation of genes in immune and inflammation-related pathways, metabolic pathways, cancer-related pathways, and neurological processes. Further research into these pathways and individual genes may lead to the identification of new targets for the treatment of IBD. The overexpression of oncogenes, in particular, may serve as an indicator of inflammation progressing to cancer.

overall_design: To investigate different pathways involved in the up and down-regulated genes from Winnies (spontaneous IBD model), highly inflamed Winnie-Prolapse mouse models, closely resembling human IBD, to discover novel therapeutics as well as give insights into the paths of inflammation that might lead to cancer.

first: Sarah

last: Fraser

first: Jeannie

last: Devereaux

first: Lauren

last: Sahakian

first: Rhian

last: Stavely

first: Majid

last: Davidson

first: Jack

last: Feehan

first: Kulmira

last: Nurgali

first: Vasso

last: Apostolopoulos


title: GRAMD2+ alveolar type I cell plasticity facilitates cell state transitions in organoid culture

status: Public on Oct 04 2023

city: Glendale

first: Crystal

last: Marconett

state: CA

address: 1856 Kirkby Rd

department: Translational Genomics

country: USA

institute: Keck School of Medicine

summary: Alveolar epithelial regeneration is critical for normal lung function and becomes dysregulated in disease. While alveolar type 2 (AT2) and club cells are known distal lung epithelial progenitors, determining if alveolar epithelial type 1 (AT1) cells also contribute to alveolar regeneration has been hampered by lack of highly specific mouse models labeling AT1 cells.  To address this, the Gramd2CreERT2 transgenic strain was generated and crossed to ROSAmTmG mice. Extensive cellular characterization, including distal lung immunofluorescence and cytospin staining, confirmed that GRAMD2+ AT1 cells are highly enriched for green fluoresecent protein (GFP).  Interestingly, Gramd2CreERT2 GFP+ cells were able to form colonies in organoid co-culture with Mlg fibroblasts. Temporal scRNAseq revealed that Gramd2+ AT1 cells transition through numerous intermediate lung epithelial cell states including basal, secretory and AT2 cell in organoids while acquiring proliferative capacity.  Our results indicate that Gramd2+ AT1 cells are highly plastic suggesting they may contribute to alveolar regeneration.

overall_design: Primary isolation of FACS sorted GFP+ cells were defined as day 0. On days 8, 13, and 20 of 3D culture, to obtain single cells, colonies were dissociated with dispase (#354235, BD Gibco) and TrypLE express (#12604013, Gibco). Biotinylated EpCAM Ab (#130-096-419, Miltenyi Biotec, San Diego, California), anti-biotin microbeads (#130-900-485, Miltenyi Biotec,) and MS columns (#130-042-201, Miltenyi Biotec) were used to enrich for epithelial cells. For each time point, cells were counted, and viability was measured using an automated cell counter (Countess 3, Thermo Fisher Scientific). Single cell suspensions were processed using Chromium Single Cell 3’ Reagent Kits v3.1 (10x Genomics, PN-1000128, PN-1000127 and PN-1000213). Briefly, cells resuspended in the reaction mix were loaded into the Chromium Single Cell Chip G, together with the 10x Barcoded Gel Beads and partitioning oil. The Chip G was placed into the 10x Chromium controller for cell partitioning, targeting a final number of 10,000 cells per sample. After partitioning, the GEMs (Gel Bead-In EMulsions) were transferred to the C1000 Touch Thermal Cycler for the first phase of reverse transcription followed by library preparation following the manufacturer’s instructions. Libraries were deep sequenced using the Illumina NovaSeq platform.

first: Shen

last: Hua

first: Chen

last: Weimou

first: Liu

last: Yixin

first: Castaldi

last: Alessandra

first: Castillo

last: Jonathan

first: Horie

last: Masafumi

first: Floody

last: Per

first: Sundar

last: Shivah

first: Li

last: Changgong

first: Minoo

last: Parviz

first: Ji

last: Yanbin

first: Marconett

last: Crystal N

first: Zhou

last: Beiyun

first: Borok

last: Zea


title: USP28 Serves as A Key Suppressor of Mitochondrial Morphofunctional Defects and Cardiac Dysfunction in the Diabetic Heart [RNA-seq]

first: Saiyang

last: Xie

summary: The majority of diabetics are susceptible to cardiac dysfunction and heart failure, while conventional drug therapy cannot correct diabetic cardiomyopathy (DCM) progression. Herein, we assessed the potential role and therapeutic value of ubiquitin-specific protease 28 (USP28) on the metabolic vulnerability of DCM. cardiac USP28 deficient diabetic mice showed cardiac dysfunction, lipid accumulation, and mitochondrial disarrangement, compared to their controls. Conversely, USP28 overexpression improved systolic and diastolic dysfunction and ameliorated cardiac hypertrophy and fibrosis in the diabetic heart. Mechanistically, USP28 directly interacted with peroxisome proliferator-activated receptor α (PPARα), deubiquitinating and stabilizing PPARα (Lys152) to promote mitofusin 2 (Mfn2) transcription, thereby impeding mitochondrial morphofunctional defects.

overall_design: To evaluate function of USP28 overexpression in diabetic heart failure and cardiac remodeling, recombinant adeno-associated virus serotype 9 carrying USP28 under cTnT promoter (rAAV9-cTnT-USP28) was injected into db/db mice to evaluate the effects of USP28 overexpression on DCM.

first: Qizhu

last: Tang


title: Genome-wide methylation profiles of post-mortem tissue samples (human) 1

first: Hwan Young

last: Lee

summary: In this study, 60 post-mortem tissue samples comprising three tissue types (blood, brain, and heart) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).

overall_design: DNA methylation profiling of sixty post-mortem tissue samples was conducted using the Infinium MethylationEPIC Beadchip array.

first: Jeong Min


title: ADAR1 utilizes independent mechanisms to suppress MDA5 and PKR activation by cellular double-stranded RNA

status: Public on Oct 03 2023

city: Stanford

first: Shibin

last: Hu

address: 240 pasteur drive, 4300

department: Genetics

institute: Stanford University

summary: The antiviral defense in vertebrates requires the innate immune system to sense foreign “non-self” nucleic acids while avoiding “self” nucleic acids, which is accomplished by an intricate system. Cellular double-stranded RNAs (dsRNAs) are edited by the RNA editing enzyme ADAR1 to prevent their dsRNA structure pattern from being recognized as viral dsRNA. Lack of RNA editing by ADAR1 enables activation of MDA5, a cytosolic dsRNA sensor, by cellular dsRNA. Additional RNA editing- independent functions of ADAR1 have been proposed, but the specific mechanism remains elusive. Here we demonstrate that RNA binding by ADAR1, independent of its editing activity, restricts the activation of PKR, another cytosolic dsRNA sensor, by cellular dsRNA. Mechanistically, the loss of ADAR1 editing caused MDA5 activation to induce interferon signaling, while a lack of ADAR1 protein or its dsRNA binding ability led to PKR activation, with subsequent stress granule formation and proliferation arrest. Based on these findings we rescued the Adar1−/− mice from embryonic lethality to adulthood by deleting both MDA5 and PKR, in contrast to the limited rescue of Adar1−/− mice by removing MDA5 or PKR alone. Our findings reveal a multifaceted contribution of ADAR1 in regulating the immunogenicity of “self” dsRNAs. Furthermore, ADAR1 is an immuno-oncology target for drug development, and the separation of ADAR1’s RNA editing and binding functions provides mechanistic insights for such developments.

overall_design: In order to study the effect of ADAR1 deficiency in human cells, HEK293T or U937 cells were transfected or infected with Cas9 and sgRNAs to make ADAR1 knockout (ADAR1KO) or ADAR1 editing deficient (ADAR1E912A) single clones. In HEK293T, wild type (WT), ADAR1KO, and ADAR1E912A cells were harvest and subjected to stranded, paired-end RNAseq. In U937, WT or ADAR1KO cells were treated with or without 50nM phorbol myristate acetate for three days to induce the differentiation of U937 cells to macrophages. After that, the cells were subjected to stranded, paired-end RNAseq. In order to identify the factors accounting for IFN-induced cell growth arrest in the absence of ADAR1, U937 ADAR1KO cells were infected with human CRISPR gRNA library followed by IFN treatment for 14 days. The genomic DNA was then purified for gRNA sequencing.  der to identify PKR-enriched endogenous RNAs, flag-PKR was overexpressed in WT and ADAR1 KO HEK293T cells . Then,  flag-PKR native RNA IP was performed to enrich RNAs. Flag-PKR-enriched RNAs were sequenced.

first: Hu

last: Shibin


title: RNA catabolism restricts ERV expression and functionalization [KD RNA-Seq]

status: Public on Oct 01 2023

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Endogenous retroviruses (ERVs) are remnants of ancient parasitic viral integrations and comprise a sizable portion of the genome in most organisms. Deregulated expression of ERVs in human is associated with a plethora of disease conditions, such as cancer and neurodegeneration. Epigenetic mechanisms silence most ERVs by generating a local repressive environment (heterochromatin) to prevent their expression. However, the mechanisms controlling the fate of ERVs residing in euchromatic regions of the genome (e.g. MERVL elements) are not well understood. Here, by integrating multidimensional epigenetic and genomic analyses, we demonstrate that silencing of euchromatic MERVL elements is achieved via transcription-coupled RNA degradation. Disrupting RNA catabolism promotes RNAPII elongation from MERVL promoters, increases MERVL expression and exonization, creating novel chimeric gene isoforms, and directing embryonic stem (ES) cells toward a terminal undifferentiated state.  Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards cell identity and potency, restricts MERVL functionalization and suppresses gene birth.

overall_design: Total RNA-Seq of mESCs undergoing siRNA-mediated KD of Exosc3, Ints11, Rbm7, Cpsf2 and Zcchc8. Three separate KD experiments were performed, each with respective siCtrl samples (see "experiment" column for metadata detail).

first: D

last: Torre

first: Y

last: Fstkchyan

first: I

last: Marazzi


title: Transcriptome analysis of familial dysautonomia reveals tissue-specific gene expression disruption in the peripheral nervous system

status: Public on Sep 28 2023

city: Boston

first: Susan

last: Slaugenhaupt

state: Massachusetts

address: 185 Cambridge Street, CPZN-5254

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Familial Dysautonomia (FD) is a rare recessive neurodevelopmental disease caused by a splice site mutation in the Elongator acetyltransferase complex subunit 1 (ELP1) leading to tissue-specific skipping of exon 20 and reduction of the ELP1 protein, distinctly in the central nervous system (CNS) and peripheral nervous system (PNS).  Here we performed a transcriptome-wide study to dissect the molecular mechanisms underlying FD in specific neuronal tissues from the FD phenotypic mouse which expresses human ELP1, including the dorsal root ganglion (DRG), trigeminal ganglion (TG), medulla (MED), cortex, and spinal cord (SC). We focused our analyses on differentially expressed genes (DEGs) representing the most dominant transcriptomic alterations; and on genes in co-expression modules that are highly correlated with full-length ELP1 expression (ELP1 dose-responsive genes). We identified higher number of DEGs (342) in the PNS (DRG, TG) as compared to the CNS (MED, SC, Cortex) (143). ELP1 dose-responsive genes are only found in DRG, TG, and MED, not in Cortex or SC, tissues. Gene Ontology analyses of both DEGs and ELP1-dose-responsive genes highlight the regulation of neurotransmitters. The transcriptome-wide signals were highly convergent between PNS tissues (DRG and TG) but not among CNS tissues. Those convergent genes were enriched for known protein-protein interactions and cell type-specific markers defining myelinated neurons and peptidergic nociceptors. Our findings support the involvement of specific neuronal subtypes underlying the PNS phenotypes in FD. Our study comprehensively investigates transcriptome-wide alterations in FD neuronal tissues and identifies the functional dysregulations in the peripheral nervous system contributing to disease.

overall_design: 3-month old FD and Control mice were dissected for cortex, dorsal root ganglion, medulla, spinal cord and trigeminal ganglion neurons and paired-end mRNA-seq was performed.  124 Libraries were generated.

first: Ricardo

last: Harripaul

first: Elisabetta

last: Morini

first: Dadi

last: Gao

last: Slaugenahaupt


title: Mutant GNAS drives a pyloric metaplasia with tumor suppressive glycans in intraductal papillary mucinous neoplasia

status: Public on Oct 02 2023

city: Nashville

first: Kathleen

last: DelGiorno

state: TN

address: 465 21st Ave S

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Intraductal papillary mucinous neoplasms (IPMNs) are cystic lesions and bona fide precursors of pancreatic ductal adenocarcinoma (PDAC), one of the deadliest solid tumors. Although ?90% of IPMNs are detected before PDAC forms, markers distinguishing benign from malignant disease are lacking, resulting in an abundance of unnecessary, invasive surgeries. Recent studies show that pancreatic precancer assumes a pyloric phenotype. To identify the regulators of this plasticity, cell lines, organoids, tumors from mouse models of IPMNs, and patient samples underwent multiplex immunostaining, RNA sequencing, glycosylation profiling, and computational analysis. These data revealed that GNASR201C drives an indolent phenotype in IPMNs by amplifying a differentiated, pyloric phenotype through SPDEF/CREB3L1, which is characterized by distinct glycans. Acting as a glycan rheostat, GNASR201C elevates LacdiNAcs at the expense of pro-tumorigenic acidic Lewis epitopes, inhibiting cancer cell invasion and disease progression. LacdiNAcs and 3?-sulfo-LeA/C are mutually exclusive and may serve as markers to risk stratify IPMN patients for surgery.

overall_design: Cell lines or organoids with doxycyline-inducible human GNASR201C expression were grown with or without doxycycline. Cell lines were also treated with siRNA targeting Kras, Gnas, both in combination, or control.

first: Marcus

middle: C

last: Tan

first: Katherine

last: Ankenbauer

first: Sabrina

middle: M

last: Torbit

first: Sergey

last: Ivanov


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA and circRNA in lean and obese individuals

status: Public on Sep 13 2023

city: Changzhou

first: Shuai

last: Chen

state: Jiangsu

address: 68 Gehu Rd, Wujin District

institute: The Affiliated Changzhou NO.2 People’s Hospital of Nanjing Medical University

summary: Fat accumulation is the main manifestation of obesity. Obesity forms the largest fat pool because white adipocytes primarily store energy, whereas larger adipocytes may encounter hypoxia and mechanical stress and have higher levels of inflammatory cytokines and lipolysis release. In this study, we performed high-throughput sequencing to analyze the differentially expressed circRNAs in visceral adipose tissue between lean and obese individuals, and searched for the important mechanisms involved in the regulation of adipogenesis

overall_design: Visceral adipose tissue from four lean individuals and four obese individuals was sequenced to search for differentially expressed RNA.

first: S

first: P

last: Song

first: L

last: Tang


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiC_LpreB_Steadystate]

status: Public on Nov 20 2023

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

summary: A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific assembly of chromatin that supercedes these constraints is required to configure the genome to support the gene expression changes that guide faithful lineage progression. Using loss-of-function approaches in B cell precursors in vivo we show that IKAROS assembles interactions between sites often separated by megabase distances to configure a significant fraction of the genome in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries and assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains.In vitro deletion provides temporal resolution to changes in chromatin modifications, loops, and compartmental localization. Gain-of-function experiments in epithelial cells confirm IKAROS’ ability to reconfigure chromatin architecture at multiple scales.  While the compaction of the Igk locus required for genome editing represents a function of IKAROS unique to the lymphoid system, the more general function of this lineage-defining DNA binding protein to preconfigure the genome to support lineage specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.

overall_design: We performed in situ Hi-C in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the genome organization in early B cell development.

first: Yeguang

last: Hu

first: Daniela

last: Salgado Figueroa

first: Zhihong

last: Zhang

first: Margaret

last: Vaselits

first: Sourya

last: Bhattacharyya

middle: R

last: Clark

first: Mariko

last: Kashiwagi

first: Bruce

middle: A

last: Morgan

first: Ferhat

last: Ay


title: Impact of Age and Sex on neuroinflammation due to SARS-CoV2 infection in a murine model.

status: Public on Sep 06 2023

city: Minneapolis

first: Ling

last: Li

state: MN

address: Mcguire Translational Research Facility, 4-419

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

summary:
Objectives: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes the worldwide COVID-19 pandemic. While SARS-CoV-2 can infect people of all ages and both sexes, senior populations are at greatest risk of severe disease and worse outcomes, and sexual dimorphism has been reported in COVID-19. COVID-19 causes damage to multiple organ systems, including the brain. Neurological symptoms are widely observed in patients with Covid-19, with many survivors suffering from persistent neurological impairment, potentially accelerating Alzheimer’s disease (AD). This study aims to investigate the mechanisms underlying the impact of age, and sex on neuroinflammation due to SARS-CoV-2 infection using mouse models.
Methods: Wild-type C57BL/6 mice were subjected to intranasal inoculation of SARS-CoV-2 lineage B.1.351, followed by daily body weight monitoring. At 7 dpi, viral burden and inflammatory cytokine/chemokine responses in the lung and brain were determined by quantitative RT-PCR, followed by immunohistochemical and transcriptomic analyses.
Results: Older age, male sex, showed increased lung viral loads and severity of SARS-CoV-2 infection in mice. No viral RNA was detected in the brains of infected mice; however, IL-6 and CCL2 mRNA increased significantly, particularly in brains of old and APOE4 mice. Unbiased brain RNA-seq/transcriptomic analysis showed that SARS-CoV-2 infection caused significant changes in gene expression profiles, and pathway analysis identified innate immunity and defense response to virus and other organisms as the major molecular networks affected in the brain by SARS-CoV-2 infection.
Conclusions: Our findings demonstrate that age, and sex, modify the progression and outcome of SARS-CoV-2 infection. SARS-CoV-2 infection triggers neuroinflammatory responses despite the lack of detectable virus in the brain. Changes in molecular networks of innate immunity and defense response to microorganisms underlie the impact of SARS-CoV-2 infection in the brain. These findings in mice mimic epidemiological and clinical observations in humans with Covid-19.

overall_design: We performed bulk mRNA-seq to examine the transcriptomic changes associated with SARS-CoV-2 infection in wild-type mice. RNA-Seq data was collected from 12 mice (6 males & 6 female)  at 10 months of age at 7 days post-infection. Sequencing was performed using Illumina NovaSeq 6000 platform, generating 20 million reads per sample on a 150-bp paired-end run.

first: Venkatramana

middle: D

last: Krishna

first: Allison

last: Chang

first: Holly

last: Korthas

first: Susanna

last: Var

first: Walter

last: Low

first: Maxim

last: Cheeran


title: Single cell RNA-sequencing studies to examine the heterogeneity of infarct macrophages

status: Public on Nov 03 2023

city: Bronx

first: Silvia

last: Hernandez

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

summary: Cardiac macrophages exhibit remarkable heterogeneity that is accentuated after myocardial infarction. In order to characterize the transcriptional profile of cardiac macrophage subpopulations after infarction we performed scRNA-seq in FACS-sorted macrophages from normal and infarcted CSF1R-EGFP (macrophage reporter) mouse hearts. CSF1R-EGFP 12-16 week-old mice were subjected to permanent coronary occlusion, and 7 days after surgery macrophage suspensions were harvested from infarcted and control mice. Non-neutrophils (Ly6G-) were gated to identify EGFP+ macrophages, which were sorted with the FACSAria Sorter (BD Biosciences). Subsequently, scRNA-seq was performed.

overall_design: Cardiac Macrophages from CSF1R-EGFP mice were isolated by Fluorescence-activated cell sorting (FACS) based on the presence of EGFP signal after exclusion of Ly6G+ cells. Previous to cell isolation surgery was preformed for the infarct groups (n=3). Seven days after surgery, hearts were harvested for baseline (n=1, 3 control hearts pooled) and infarcted (n=3) mice. Before digestion, the non-infarcted region (remote zone) was excised from the heart and excluded from the digestion. Samples were analyzed using scRNA-seq.

first: Bijun

last: Chen

first: Ruoshui

first: Anis

last: Hanna

first: Yang

last: Liu

first: Richard

last: Ma

first: Deyou

last: Zheng

first: Nikolaos

last: Frangogiannis


title: NRF2 is a spatiotemporal metabolic hub driving the polyfunctionality of Th2 cells in allergic asthma

status: Public on Aug 25 2023

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

institute: Incheon National University

summary: Polyfunctional Th2 cells play a crucial role in triggering diverse pathogenic responses in allergic diseases by producing multiple cytokines. However, the precise mechanism underlying their polyfunctionality remains elusive. In this study, we elucidate the pivotal role of Nrf2 in polyfunctional Th2 cells during allergic asthma. We found that an increase in reactive oxygen species (ROS) in immune cells infiltrating the lungs is necessary for the development of eosinophilic asthma. Deletion of the ROS sensor Nrf2 specifically in T cells, but not in dendritic cells, significantly abolished eosinophilia and polyfunctional Th2 cells in the airway. Mechanistically, Nrf2 intrinsic to T cells is essential for inducing optimal oxidative phosphorylation and glycolysis capacity, thereby driving Th2 cell polyfunctionality, partially by inducing PPARγ, independently of IL-33. Treatment with an Nrf2 inhibitor leads to a substantial decrease in polyfunctional Th2 cells and subsequent eosinophilia in mice, and a reduction in the production of Th2 cytokines from peripheral blood mononuclear cells (PBMCs) in asthmatic patients. These findings highlight the critical role of Nrf2 as a spatial and temporal metabolic hub that is essential for polyfunctional Th2 cells, suggesting potential therapeutic implications for allergic diseases.

overall_design: We employed murine models of allergic asthma to study the role of Nrf2 in helper T cell immunity and allergic disorders. We disrupted the Nrf2 activity with a small molecule inhibitor or a conditional deletion of Nfe2l2 in T cells (CD4∆Nrf2). Single cell RNA-seq was performed to screen for potential target pathways of Nrf2.

first: Garam

last: Choi

first: Hye-Yeon

last: Ju

first: Jahyun

last: Bok

first: Jungseo

first: Jae

middle: W

last: Shin

first: Hansol

last: Oh

first: Yeojin

last: Jeon

first: Jiyeon

last: Kim

first: Daehong

first: Heesu

last: Moon

first: Jeong-Eun

last: Lee

first: Young-Sam

last: Keum

first: You-Me

first: Hye

middle: Y

first: Sung

middle: H

last: Park

first: Yeonseok

last: Chung


title: RNA catabolism restricts ERV expression and functionalization

first: Robert

last: Sebra

type: Methylation profiling by high throughput sequencing


title: High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults (single-cell BCR)

status: Public on Aug 20 2023

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Seasonal influenza contributes to a substantial disease burden annually, resulting in approximately 10 million hospital visits and 50 thousand deaths in a typical year in the US. 90% of the annual mortality from influenza occurs in people over the age of 65. While influenza vaccination is the best protection against the virus, it is less effective for the elderly. This may be due to differences in the quantity or type of B cells induced by vaccination in older individuals. To investigate this possibility, we leveraged recent development in single-cell technology that allows for simultaneous measurement of both gene expression profile and the B cell receptor (BCR) at single-cell resolution. Pre- and post-vaccination peripheral blood B cells were sorted from three young and three older adults who responded to the inactivated influenza vaccine and were profiled using single-cell RNAseq with paired BCR sequencing. At pre-vaccination, we observed a higher somatic hypermutation frequency and a higher abundance of activated B cells in older adults than in young adults. Following vaccination, young adults mounted a more clonal response than older adults. The response involved a mix of plasmablasts, activated B cells, and resting memory B cells in both age groups. The response in young adults was dominated by expansion in plasmablasts, while the response in older adults also involved activated B cells. We observed a consistent change in gene expression in plasmablasts after vaccination between age groups but not in the activated B cells. These quantitative and qualitative differences in the B cell response may provide insights into the age-related change of influenza vaccination response.

overall_design: To understand the age-group difference in B cells underlying a successful vaccination response, we selected three young (20- to 30-years-old) and three older (60- to 100-years-old) subjects who responded to seasonal influenza vaccine with at least 4 fold increase of HAI titer for at least one vaccine strain from a cohort recruited at Yale University over the five vaccination seasons between 2010 and 2014.

first: Tony

last: Melillo

first: Mamie

last: Wang

first: Steven

last: Kleinstein

first: Albert

last: Shaw


title: Epigenomic analysis of Formalin-Fixed Paraffin-Embedded samples by CUT&Tag

status: Public on Sep 08 2023

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: For more than a century, Formalin Fixed Paraffin Embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our single-tube CUTAC protocol are sufficient to produce high-resolution maps of paused RNA Polymerase II (RNAPII) at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumor specimens and identify regulatory element markers with high confidence and precision. Our simple workflow is suitable for automation, making possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We used FFPE-CUTAC, a modification of the CUT&Tag chromatin profiling strategy, whereby antibody-targeted controlled integration of DNA sequencing adapters at sites of paused RNA Polymerase II or between nucleosomes flanking open chromatin sites produces libraries for paired-end sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) sections.

Grant information: T32CA009515 - Ronald M. Paranal - National Cancer Institute

first: Kami

last: Ahmad

first: Ronald

last: Paranal

first: Derek

last: Janssens

first: Zachary

last: Russell

first: Frank

last: Szulzewsky

first: Sita

last: Kugel

first: Eric

last: Holland


title: High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults (single-cell Gene Expression)


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

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

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

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

first: Hiroko

last: Nobuta


title: High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults

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

relation:
SuperSeries of: GSE175522
SuperSeries of: GSE175523

overall_design: Refer to individual Series


title: The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer

status: Public on Aug 10 2023

city: Pamplona

first: Silvestre

last: Vicent

address: Avenida Pío XII 55

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

summary: RNA profiling of mut KRAS lung cancer cells (A549) where PITPNC1 is depleted using two specific shRNAs

overall_design: Comparison of GFPsh-transduced A549 cells compared to PITPNC1sh-expressing cells. 3 replicates per condition were used


summary: RNA profiling of FOSL1- and KRAS-regulated transcriptomes in human lung cancer cells harboring KRAS mutation

overall_design: H358 cell line was transduced with tet-inducible lentiviral plasmids expressing a control shRNA (GFPsh) or a specific shRNA to FOSL1 or KRAS

first: Vicent

last: Silve


title: LAMC2-regulated transcriptome

summary: RNA profiling of pancreatic cancer cells (HPAFII) where LAMC2 is depleted using a specific shRNA

overall_design: Comparison of GFPsh-transduced HPAFII cells compared to LAMC2sh-expressing cells. 3 replicates per condition were used

first: Silve


title: Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification [DAb-seq]

status: Public on Aug 07 2023

city: San Francisco

first: Catherine

last: Smith

state: California

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

summary: Mixed phenotype acute leukemia (MPAL) also known as acute leukemia of ambiguous lineage (ALAL), is characterized by leukemic blasts with both lymphoid and myeloid cell surface markers.   Here, we use SC multiomic profiling on newly diagnosed MPAL samples to characterize the immunophenotypic, genetic, and transcriptional landscapes of MPAL. This profiling allows us to definitively contradict the paradigm of MPAL as a disease on a continuum with myeloid and lymphoid lineage acute leukemias, and instead identifies MPAL as a distinct, stem-like disease that, unlike other leukemias, cannot be defined by genetics alone. We further describe a stem cell gene expression signature for MPAL that can predict patient survival. These results broaden our understanding of MPAL biology and suggest a path toward novel risk stratification for MPAL. Importantly, these findings have potential to direct treatment and, hopefully, ultimately improve the prognosis of this disease.

overall_design: Samples from 14 adult patients with de novo MPAL were analyzed for single cell DNA, RNA, protein.

first: Cheryl

last: Peretz

first: Vanessa

last: Kennedy

first: Anushka

last: Walia

first: Cyrille

last: Delley

first: Andrew

last: Koh

first: Elaine

last: Tran

first: Iain

last: Clark

first: Corey

last: Hayford

first: Chris

last: Amato

first: Kristina

last: Fontanez

first: Ritu

last: Roy

first: Aaron

last: Logan

first: Alexander

last: Perl

first: Adam

last: Abate

last: Olshen


title: Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [lncRNA-seq]

status: Public on Aug 03 2023

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: The hereditary information encoded in DNA sequence is intrinsically susceptible to alterations, being continually threatened by a variety of genotoxic perturbations. To safeguard the stability of the genome, eukaryotic cells have evolved a set of sophisticated surveillance system that controls several aspects of the cellular response, including the detection of DNA lesions, a temporary cell cycle arrest, regulation of transcription, and the repair of the damaged DNA. However, it is still poorly understood how the DNA damage checkpoints and stalled RNAPII molecules convert a very limited amount of molecular-level information (even a single DNA lesion) in the context of an otherwise genome into regulation that halts and resumes the cell-cycle engine in a coordinated way. In this study, we reveal a map of extensive lncRNA transcription during DDR by using synchronized cells, leading to the unexpected identification of a poorly characterized mammalian lncRNA-ZFAS1. We describe that ZFAS1 functions as a key player of cellular response to DNA damage in both human and rodent cells by fine tuning RNAPII kinetics, suggesting a lncRNA-dependent transcriptional regulatory axis that maintains genomic stability upon DNA damage in mammalian cells.

overall_design: To illustrate the transcriptome map for both mRNAs and lncRNAs during DNA damage response, we synchronized human fibroblasts MRC5_VA at G1/S block and UV irradiated prior to release from the arrested cell cycle phase. We then performed gene expression profiling analysis using data obtained from RNA-seq of 14 samples, including undisturbed (6 samples) and UV-irradiated (8 samples) cell lines at the indicated time intervals after release from G1/S block.

first: Jiena

last: Liu

first: Tingting

last: Zhu

first: Zhaoya

last: Han

first: Qing

last: Lu


title: Drug repurposing unveils new combinatorial treatments to treat mutant KRAS lung cancer

first: Silvestre

last: Vicent

summary: We report data on a drug combination with synergistic antitumor effect in KRAS-driven lung cancer. We used RNAseq to characterize the transcriptional changes elicited by each drug in a mutant KRAS lung cancer cell lines (H1792)

overall_design: H1792 cell line treated with Trametinib (MEKi) or Lestaurtinib (multikinase FLT3i) for 16 hours

first: Silve

first: Marta

last: Román


title: Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation

status: Public on Aug 15 2023

first: Jiehui

last: Chen

address: 320 Longwood Ave

institute: Boston Children’s Hospital

summary: The blueprint of lineage segregation of early mouse embryo is established during gastrulation in which progenitors of various cell fates are regionalized and patterned in specific embryo locations. Despite the central importance of this period of mammalian development, we currently lack a comprehensive understanding of the underlying developmental trajectories and molecular processes, principally because research efforts either employed in vitro systems, focused on small numbers of genes, or limited the number of developmental stages or cell types that were studied. Here, we study the regulatory landscape of gastrulation by combining single-cell RNA-seq (A total of ~35,000 single cells isolated at E6.5, E6.75, E7.0, E7.25, E7.5) and geographical position sequencing (Geo-seq) technique, and we report a de novo identification of spatial signatures and a method to enable retrospective locating of single cells to their origins. Our work provides insights into the exit from pluripotency and priming for differentiation, and the emergence of regulatory networks associated with cell fate decisions. Finally, we reconstruct the spatio-temporal roadmap of gastrula mouse embryo in single-cell resolution. This result uncovers the cell migration trajectories and molecular processes associated with lineage segregation.

overall_design:
By using spatial transcriptome of Geo-seq , we carried out transcriptome profiling on embryo locations at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatio-temporal transcriptome map from the pre-gastrulation to late-gastrulation embryos. Combining single-cell RNA-seq data generated using 10x Genomics Chromium system, we visualized the spatio-temporal map in a 3D embryonic model.

Definitions:
region AP: region of 1st section of epiblast
region EAP: region of 1st section of endoderm
region Aregion of anterior epiblast/ectoderm
region EP: region of posterior endoderm
region P: region of posterior epiblast/ectoderm
region EA: region of anterior endoderm
region M: region of mesoderm
region L: region of left lateral epiblast/ectoderm
region R: region of right lateral epiblast/ectoderm
region L1: region of left anterior lateral epiblast/ectoderm
region L2: region of left posterior lateral epiblast/ectoderm
region MA: region of anterior mesoderm
region MP: region of posterior mesoderm
region R1: region of right anterior lateral epiblast/ectoderm
region R2: region of right posterior lateral epiblast/ectoderm
region Epi: region of epiblast
region VE: region of visceral endoderm
region MAR: region of anterior right lateral mesoderm
region MPL: region of posterior left lateral mesoderm
region MPR: region of posterior right lateral mesoderm
region MAL: region of anterior left lateral mesoderm

first: Ran

first: Xianfa

last: Yang

first: Guizhong

last: Cui

first: Naihe

last: Jing


title: Transcriptional profiling of the developing murine intestine

status: Public on Sep 11 2023

city: Los Angeles

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

summary: To identify transcriptional changes during the development of the small intestine, we performed scRNAseq using MULTI-seq on 86,845 cells collected from embryos at E13.5-E18.5. We additionally identified transcriptional changes along the proximal-distal axis of the small intestine by isolating RNA from 2.5mm fragments of the tissue that had been cut along this axis. Mice were collected from Pdgfra-H2BGFP mice to enrich for mesenchymal populations.

overall_design: Single-cell RNA sequencing was performed using MULTI-seq on mouse embryonic intestinal tissues from Pdgfra-H2BGFP mice across five developmental time points with pooled replicates (E13.5, 4 replicates; E14.5, 3 replicates; E15.5, 2 replicates; E16.5, 2 replicates; and E18.5, 2 replicates). The intestines were divided into 2.5mm-length pieces along its proximal-distal axis (E13.5, 3 segments; E14.5, 5 segments; E15.5, 10 segments; E16.5, 15 segments; E18.5, 20 segments). We enriched for rare cell populations (PdgfraHigh, or Epcam+, or CD31+ or CD45+).

first: Tyler

last: Huycke

first: Hikaru

last: Miyazaki

first: Christopher

middle: S

last: McGinnis

first: Dedeepya

last: Vaka

first: Ophir

last: Klein

first: Zev

middle: J

last: Gartner


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [ZFAS1-mRNA-seq]

first: Yuming

last: Wang

overall_design: To study the effect of ZFAS1 lncRNA on mature RNA synthesis upon DNA damage, we knocked down ZFAS1 in MRC5_VA cells by using lentiviral shRNA plasmids targeting two distinct regions of ZFAS1. Cells were UV irradiated and recovered for the indicated time intervals (3 h and 24 h), total RNA was extracted from the three cell lines (empty vector, ZFAS1-sh1, and ZFAS1-sh2). We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 samples.

first: Jiena

last: Liu

first: Tingting

first: Zhaoya


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [ZFAS1 ChIRP-seq]

overall_design: To illustrate the genome wide binding capacity of ZFAS1, ChIRP (chromatin isolation by RNA purification) was performed using biotinylated probes against ZFAS1. Independent even and odd probe pools were used to ensure ZFAS1 specific retrieval. High-throughput sequencing libraries were constructed from ChIRPed DNA according to ChIP-seq protocol.

last: Zhu

last: Han

first: Qing


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for phosphorylated isoforms of RNA polymerase II (RNAPII-Ser5P and RNAPII-Ser2P) in the WT and ZFAS1-depleted cells with or without UV-C irradiation.

last: Lu


title: Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification [PIP-seq]

first: Catherine

last: Smith

first: Cheryl

last: Peretz

first: Vanessa

last: Kennedy

first: Anushka

last: Walia

first: Cyrille

last: Delley

first: Andrew

last: Koh

first: Elaine

last: Tran

first: Iain

last: Clark

first: Corey

last: Hayford

first: Chris

last: Amato

first: Kristina

last: Fontanez

first: Ritu

last: Roy

first: Aaron

last: Logan

first: Alexander

last: Perl

first: Adam

last: Abate

last: Olshen


title: Insight into integrated control of pituitary function revealed through analysis of Musashi target mRNAs

status: Public on Jul 31 2023

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

department: Neuroscience

institute: UAMS

summary: The anterior pituitary is comprised of distinct cell types that each secrete specific hormones to control a variety of biological processes including growth, metabolism, reproduction and stress responses.  The anterior pituitary shows a remarkable level of cell type plasticity that allows shifts in hormone producing populations to meet organismal demands.  Pituitary cell plasticity is tightly regulated and both deficiency in cell plasticity and excessive cell plasticity are associated with common pituitary pathologies.  The molecular mechanisms underlying this plasticity are not well characterized but recent work has implicated the stem cell determinants and sequence-specific mRNA binding proteins of the Musashi family as regulators of adult pituitary hormone production.  In this study we have sought to identify the full range of Musashi target mRNAs in the adult mouse pituitary.  Using Musashi RNA immunoprecipitation we identify a cohort of 1192 mRNAs that show specific Musashi binding.  These include mRNAs restricted to discrete hormone-producing cell lineages as well as mRNAs associated with stem and progenitor cells.  The processes influenced by the proteins encoded by the Musashi-associated mRNAs include cellular homeostasis, protein trafficking and secretion, unfolded protein response, endocrine processes and female pregnancy.  Functional analysis of validated mRNA regulatory 3' untranslated regions (3’ UTRs) reveals UTR-specific positive or negative control by the Musashi proteins within the same cellular context.  Together, our findings indicate a broad role for Musashi proteins in the control of pituitary function.

overall_design: RIP-seq

first: Jewel

last: Banik

first: Alicja

last: Urbaniak

first: Ana

last: Silva Moriera

first: Katherine

last: Bronson

first: Sophia

last: Tomlinson

first: Alex

last: Lagrasse

first: Linda

middle: L

last: Hardy

first: Allen

last: Gies

first: Stephanie

last: Byrum

first: Ania

last: Wilczynska

first: Angela

last: Odle

first: Gwen

middle: V

last: Childs

first: Angus


title: Identification of FOSL1 targets in cholangiocarcinoma

status: Public on Jul 22 2023

first: Silvestre

last: Vicent


title: FOSL1 target genes in cholangiocarcinoma (CCA) cells

summary: We report the characterization of FOSL1-bound transcriptional targets in CCA cells. Target genes include different RNA species involving protein coding genes, lncRNA, miRNA and others

overall_design: Examination of FOSL1-bound regions in CCA cells overexpressing a Flag-tagged FOSL1 overexpressing lentivector

first: Silve


title: Analysis of skeletal muscle gene expression upon mouse hindlimb unloading and reloading

status: Public on Jul 16 2023

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: To investigate the molecular mechanisms governing the transition of skeletal muscle from atrophy to compensatory regeneration and hypertrophy, we employed a mouse model involving hindlimb unloading and subsequent reloading, conducting a comprehensive analysis of global gene expression using RNA-sequencing (RNA-seq). Gastrocnemius muscle samples were obtained from three groups: control mice, mice subjected to 10 days of hindlimb unloading-induced muscle atrophy, and mice reintroduced to normal cage activity for 1 day following the unloading period (reloading).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse gastrocnemius muscle from model of hindlimb unloading/reloading assessing transitions from atrophy to compensatory regeneration and hypertrophy. Control mice were kept in conventional cages throughout the entire protocol. Experiment was performed in replicates (Control n = 4, Unloading n = 2, Reloading n = 3). Paired-end DNA libraries were prepared using Illumina TrueSeq and sequenced on Illumina HiSeq2000 (.

first: Jorge

last: Correia

first: Vicente

last: Martinez-Redondo

first: Paulo

last: Jannig

first: Serge

last: Ducommun

first: Stine

last: Præstholm

first: Kyle

last: Dumont

first: Daniel

last: Edsgärd

first: Olof

last: Emanuelsson

last: Ruas


title: Intra-tumoural Microbiota Remodels the Tumour Immune

status: Public on Jul 07 2023

city: chengdu

first: hong

last: wu

address: 55 renmin south road

institute: sichuan cancer hospital

summary: Esophageal squamous cell carcinoma (ESCC) accounts for ~90% of all cases of esophageal cancer and the sixth most common cause of cancer related death worldwide. 1, 2 It remains a globally challenging disease and mostly diagnosed cases requires a multidisciplinary approach with extensive treatments including surgery, chemoradiotherapy and/or chemotherapy.  ESCC has a relatively high tumor mutational burden,3 suggesting that it could benefit from PD-1 blockade.  Recently, three phase III clinical trials reported that PD-1 blockade significantly improved progression-free survival (PFS) and overall survival (OS) when combined with chemotherapy as first-line therapy in advanced/metastatic ESCC.4, 5 Moreover, in 2021 ASCO annual meeting,  two phase II clinical trials reported that neoadjuvant chemo-immunotherapy (NACI) induced an obvious improvement of the pathologic complete response (pCR) for resectable ESCC (35.  3% and 42.5%, respectively).  Several phase III trials on this topic are ongoing (NCT04807673, NCT04848753, NCT04280822) (https://clinicaltrial s.gov/ct2/show/NCT04807673), indicating that neoadjuvant NACI would become promising treatment for locally advanced ESCC.  Nevertheless, not all ESCC patients could respond to NACI. Patients who responded well or poorly to neoadjuvant immunotherapy were treated with surgery. We collected samples from these patients and conducted single-cell sequencing to analyze the tumor immune microenvironment of patients with different therapeutic effects, compare the differences in immune cell composition in the immune microenvironment, and explore more effective neoadjuvant therapy methods.

overall_design:
Patients who received 2 cycles of neoadjuvant immunotherapy were assessed by imaging, followed by surgical removal of the tumor. Tumor samples from patients with good and bad efficacy were collected, digested into single cells, and analyzed by single-cell sequencing.
3 human Esophageal Squamous Cell Carcinoma tissue samples; ESCC2-NACI NR; ESCC1-NACI R; ESCC3-NACI R.

[UPDATE] 10-26-2023: ESCC2 samples were corrected from responder to non-responder; ESCC3 and ESCC1 samples were corrected from non-responder to responder.

first: Hong

last: Wu

first: Chuan

last: Xu


title: Renal transcriptome of the desert adapted Jaculus jaculus during water restriction and rehydration

status: Public on Jul 04 2023

city: Bristol

first: Benjamin

middle: Thomas

last: Gillard

address: Dorothy Hodgkin Building

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

summary: Jaculus jaculus were split into three experimental groups: control (water access ad libitum), dehydrated (11 days water restriction), and rehydrated (7 days water restriction followed by 3 days water ad libitum). Kidney samples were extracted and sequenced to investigate changes in gene expression during osmotic challenge in a desert adapted model.

overall_design: Whole Jaculus jaculus left kidney samples from control (n=4), dehydrated (n=4), rehydrated (n=5) groups

middle: T

first: Nabil

last: Amor

first: Fernando

last: Alvira-Iraizoz

first: Audrys

last: Pauza

first: Colin

last: Campbell

first: Michael

middle: P

last: Greenwood

first: Abdulaziz

middle: N

last: Alagaili

first: David

last: Murphy


title: PD-L1 Enhanced by cis-Urocanic Acid on Langerhans Cells Inhibits Vg4+ gdT17 Cells in Psoriatic Skin Inflammation

status: Public on Jun 30 2023

city: Taipei City

first: Yeh Fong

last: Tan

state: Taipei

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of BioMedical Sciences

country: Taiwan

institute: Academia Sinica

summary:
To establish the role of PD-L1 expression on Langerhans cells and its influence on psoriatic skin inflammation, we isolated Langerhans cells from harvested ears of wild type mice treated with Vaseline or Imiquimod.
We then determined the gene expression profile of isolated Langerhans cells from the different groups at a single time point using data from RNA-seq. The experiment was performed in duplicate.

overall_design: Transcriptomic analysis of RNA-seq data of isolated Langerhans cells from ears of wild type mice treated with Vaseline (negative control) or Imiquimod (test).

first: Yeh

middle: F

first: Chen-Yun

last: Yeh

first: Yungling

last: Lee


title: Effect of ionizing radiation exposure on zebrafish embryo development by single-cell RNA profiling

status: Public on Jul 05 2023

city: 경상남도 양산시

first: Eun Jung

last: Kwon

state: 경상남도

address: Pusan National University, Yangsan,, Republic of Korea

institute: Pusan National University

summary: Ionizing radiation (IR) affects brain development in vertebrates at early developmental stages, but its effects of IR on other developing tissues have not yet been clarified. To investigate the IR effects on the developing organs, single-cell RNA sequencing was conducted using zebrafish embryos at 24hpf.

overall_design: Thirty 24hpf zebrafish embryos were pooled as a control group(wild type) and IR-exposed group for single-cell RNA sequencing.

first: Eunjung

first: Hansong

first: Chang-kyu

last: Oh

first: Yunhak

last: Kim


title: Uncovering the epigenomic determinants of kidney vascular development [scRNA-seq]

status: Public on Jul 06 2023

city: Charlottesville

first: Jason

middle: Paul

last: Smith

state: VA

address: 409 Lane Rd

institute: University of Virginia

summary: Renin cells are essential for survival. They control the morphogenesis of the kidney arterioles, and the composition and volume of our extracellular fluid, arterial blood pressure, tissue perfusion, and oxygen delivery. Renin cells and associated arteriolar cells descend from FoxD1+ progenitor cells. The chromatin states and transcription factors that determine the differentiation of these cells into those that compose the kidney vasculature are unknown. To answer these questions, we isolated progenitors and their descendants at different embryonic and postnatal stages, and using integrated scRNA-seq and scATAC-seq established the developmental trajectory that leads to the mosaic of cells that compose the kidney arterioles. We constructed a single-cell atlas of chromatin accessibility and gene expression profiles-including the critical transcription factors that determine the identity and fate of the mosaic of cells that occur during kidney vascular development. Furthermore, we identified the factors that determine the elusive, myo-endocrine adult renin-secreting juxtaglomerular cell.

overall_design: FoxD1+ cells, demarcating the renin lineage, were isolated at embryonic (E) day 12, E18, post-natal (P) day 5, and P30 and subjected to independent scRNA-seq and scRNA-seq to uncover the epigenomic determinants of kidney vascular development.

first: Alexandre

middle: G

last: Martini

first: Silvia

last: Medrano

first: Nathan

middle: C

last: Sheffield

first: Maria

last: Sequeira-Lopez

first: R

last: Gomez


title: Sugt1 loss skeletal muscle stem cells impairs muscle regeneration and causes premature muscle aging

city: Hong Kong

first: Gexin

last: Liu

state: Sha Tin

address: 503, Li Ka Shing Medical Science Building, PWH, Yin Cheng Street

country: Hong Kong

institute: Chinese University of Hong Kong

summary: Sugt1 RNA-seq in ASC cells from young and old mice are performed

overall_design: RNA-seq

first: Huating

last: Wang

first: Zhiming

last: He


title: Gene expression profile of grafts in 6-week-old and 12-week-old recipients 24 h after receiving similar donor kidneys

status: Public on Jun 20 2023

city: Chongqing

first: Chengjun

last: Yu

address: No.136, Zhongshan 2nd Road, Yuzhong District, Chongqing City, China

institute: Children’s Hospital of Chongqing Medical University

summary: To investigate the effect of youthful systemic milieu on acute kidney injury in a rat kidney transplantation model based on young (6-week-old) and adult (12-week-old) recipients receiving similar donor kidneys (12-week-old)

overall_design: 12-week SD rat donor kidneys were heterotopically transplanted into 6-week Wistar rats (young recipients, Y group, shown in initial data as "IM") and 12-week Wistar rats (adult recipients, A group, shown in initial data as "M").

first: Shengde

last: Wu

first: Yi

last: Hua

first: Guanghui

last: Wei


title: FOSL1 transcriptome in cholangiocarcinoma (CCA) cells

first: Silvestre

last: Vicent

summary: A cholangiocarcinoma cell line was used to inhibit FOSL1 and study dowsntream effectors in vitro

overall_design: EGI-1 cells expressing a TET-inducible control shRNA (GFPsh) or shRNAs against FOSL1 were treatd with doxycycline for 4 days and seeded for 24 h to harvest RNA for RNA-seq analysis.

first: Silve

first: Adrian

last: Vallejo


title: An EZH2-NF-kB Regulatory Axis Drives Expression of Pro-Oncogenic Genetic Signatures in TNBC

status: Public on Jul 10 2023

city: Boston

first: Jeremy

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: EZH2 has been studied most extensively in the context of PRC2-dependent gene repression. Paradoxically, accumulating evidence indicates non-canonical functions for EZH2 in cancer contexts including promoting gene expression in triple negative breast cancer (TNBC) cells through interactions with the transcription factor NF-kB.  We define a genomic profile of EZH2 and NF-kB factor RelA, RelB, and NFKB2/p52 co-localization and positive regulation of a subset of NF-kB targets and genes associated with oncogenic functions in TNBC, which is enriched in patient datasets.  We demonstrate interaction between EZH2 and RelA requiring the recently identified EZH2 transactivation domain (TAD), which mediates EZH2 recruitment to and activation of certain NF-kB-dependent genes, and supports downstream stemness phenotypes in TNBC cells. Interestingly, EZH2-NF-kB positive regulation of genes and stemness does not require PRC2. This study provides new insight into pro-oncogenic regulatory functions for EZH2 in breast cancer through PRC2-independent, and NF-kB-dependent regulatory mechanisms.

overall_design: We performed ChIP-seq for EZH2, RelA, RelB, and NFKB2 alongside input control in MDA-MB-231 and SUM149 breast cancer cells in biological triplicate. We also performed RNA-seq in MDA-MB-231 breast cancer cells following control, EZH2, RelA, or RelB knockdown via siRNA in biological duplicate, and RNA-seq in SUM149 cells following control or EZH2 knockdown via siRNA in biological duplicate

middle: M

first: Gabrielle

last: Dardis

first: Albert

last: Baldwin


title: Virological characterization of the 2022 outbreak-causing monkeypox virus using human keratinocytes and colon organoids

status: Public on Jun 06 2023

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

summary: The outbreak-causing monkeypox virus of 2022 (2022 MPXV) is classified as a clade IIb strain and phylogenetically distinct from prior endemic MPXV strains (clades I or IIa), suggesting that its virological properties may also differ. Here, we used human keratinocytes and induced pluripotent stem cell-derived colon organoids to examine the efficiency of viral growth in these cells and the MPXV infection-mediated host responses. MPXV replication was much more productive in keratinocytes than in colon organoids. We observed that MPXV infections, regardless of strain, caused cellular dysfunction and mitochondrial damage in keratinocytes. Notably, a significant increase in the expression of hypoxia-related genes was observed specifically in 2022 MPXV-infected keratinocytes. Our comparison of virological features between 2022 MPXV and prior endemic MPXV strains revealed signaling pathways potentially involved with the cellular damages caused by MPXV infections and highlights host vulnerabilities that could be utilized as protective therapeutic strategies against human mpox in the future.

overall_design: The MPXV-infected colon organoids and keratinocytes were collected, and then total RNA was collected and RNA-seq was performed.


title: Bulk RNA-seq of Human Platelets Before and After Flu Vaccination

status: Public on May 31 2023

city: New Haven

first: Hailong

last: Meng

address: 300 George Str

institute: Yale University

summary: The goal of this study was to examine differential gene expression in human platelets, focusing on it's relationship to flu vaccine response and how it may vary with age.

overall_design: A total of 82 subjects were sequenced. Samples were taken prior to flu vaccination, then again at two, seven or 28 days post-vaccination.

first: Anthony

last: Melillo

first: Anna

last: Konstorum

first: Steven

last: Kleinstein

last: Shaw


title: ER reprogramming promotes a select pro-metastatic secretome in high FOXA1-expressing ER-positive endocrine-resistant and metastatic breast cancer [RNA-seq]

status: Public on May 21 2023

city: Houston

first: Xiaoyong

last: Fu

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, to date, key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) highly enriched in ER+ endocrine-resistant (EndoR) cells. We identified Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, strongly predicts poor outcomes of ER+ BC and is elevated in ER+ metastases vs. primary tumors, irrespective to the ESR1 mutations. Parental (P) ER+ BC cells and their endocrine-resistant (EndoR) derivatives, and ER+ BC cells expressing doxycycline (Dox)-inducible ectopic FOXA1 were used in this study. Differential gene expression analysis was performed in EndoR vs. P cells and P cells +Dox vs. -Dox. We found that the FOXA1-CGS was highly enriched in the altered transcriptomes of two ER+ BC cell models (ZR75-1 and T47D) expressing ectopic H-FOXA1. The enriched hallmark gene sets, shared by the H-FOXA1 cell models, include “inflammatory response”, “complement”, and “interferon gamma response” for the H-FOXA1-induced, and “estrogen response early” and “estrogen response late” for the H-FOXA1-repressed genes. These findings point to the common transcriptional profile exhibiting an immune- over estrogen-responsive signature induced by H-FOXA1. In addition, we found that both the tamoxifen-resistant (TamR) and estrogen deprivation-resistant (EDR) derivatives of the 600MPE P cells were enriched for the H-FOXA1-induced CGS and FOXA1/ER-activated Secretome14. Our findings uncover H-FOXA1-induced ER reprogramming driving EndoR and metastasis, possibly via a H-FOXA1/ER-dependent secretome that warrants further studies to clarify its involvement in disease progression of ER+ metastatic BC.

overall_design: RNA-seq of ER+ breast cancer cell models and derivatives with resistance to endocrine therapy, and ER+ breast cancer cells with Dox-inducible ectopic FOXA1 overexpression using Illumina NextSeq500 (single-end) and Illumina NovaSeq6000 (paired-end) system, respectively.

first: Rinath

last: Jeselsohn

first: Carmine

last: De Angelis

first: Agostina

last: Nardone

first: Myles

last: Brown

first: Rachel

last: Schiff


title: Single-cell RNA sequencing defines disease-specific differences between chronic nodular prurigo and atopic dermatitis

status: Public on May 24 2023

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: Chronic nodular prurigo (CNPG) is a chronic inflammatory skin disease that is maintained by a chronic itch-scratch cycle likely rooted in neuro-immunological dysregulation. This condition may be associated with atopy in some patients, and there are now promising therapeutic results from blocking type-2 cytokines such as IL-4, IL-13 and IL-31. Nevertheless, underlying pathomechanisms as well as the molecular relationship with atopy remain ill-defined.
Methods: We profiled skin lesions from patients with CNPG in comparison to atopic dermatitis (AD) and healthy control (HC) individuals using single-cell RNA sequencing combined with T-cell receptor sequencing.
Results: We found type-2 immune skewing in both CNPG and AD, as evidenced by CD4+ helper T cells expressing IL13. However, only AD harbored an additional, oligoclonally expanded CD8A+ IL9R+ IL13+ cytotoxic T cell population, and immune activation pathways were highly upregulated in AD, but less so in CNPG. Conversely, CNPG showed signatures of extracellular matrix organization, collagen synthesis, and fibrosis, including a unique population of CXCL14- IL24+ secretory-papillary fibroblasts. Besides known itch mediators such as IL31 and oncostatin M (OSM), we also detected increased levels of neuromedin B (NMB) in fibroblasts of CNPG lesions compared to AD and HC, with NMB receptors detectable on some nerve endings.
Conclusion:  These data show that CNPG does not harbor the strong disease-specific immune activation pathways that are typically found in AD, but is rather characterized by upregulated stromal remodeling mechanisms that might directly impact itch fibers.

overall_design:
Comparison of skin cells obtained from PN, AD and HC donors.
Raw data is not provided due to patient privacy concerns.
Healthy Control samples 112 – HC1, 115 – HC2, 116 – HC3 and 121 – HC4 used in this manuscript are already publicly available via Gene Expression Omnibus GSE173205.

first: Frank

last: Assen

first: Tamara

last: Arnoldner

first: Wolfgang

last: Bauer

first: Marco

middle: A

last: Medjimorec

first: Lisa

middle: E

first: Katharina

last: Rindler

first: Gregor

last: Holzer

first: Philipp

last: Weber

last: Weninger

first: Christian

last: Freystätter

first: Tamar

last: Kinaciyan

first: Matthias

last: Farlik

first: Constanze

last: Jonak

first: Johannes

last: Griss

first: Christine

last: Bangert

first: Patrick

last: Brunner


title: ER reprogramming promotes a select pro-metastatic secretome in high FOXA1-expressing ER-positive endocrine-resistant and metastatic breast cancer [ChIP-seq]

first: Xiaoyong

last: Fu

summary: Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, to date, key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) and an ER-dependent secretome highly enriched in ER+ endocrine-resistant (EndoR) cells. ER+ BC MCF7-parental (P) cells treated with estrogen deprivation or estrogen, and with doxycycline (Dox)-inducible FOXA1 overexpression were used in this study. We found that a majority of the lost or retained ER binding induced by H-FOXA1 overlapped with the ER binding sites in P cells induced by estrogen vs. tamoxifen treatment. The lost ER binding sites were also significantly enriched for the ER binding under E2 vs. ED, which corresponds to 11% of the total E2-stimulated ER binding, suggesting that H-FOXA1 induces a loss of selective E2-stimulated ER binding sites. In addition, we found that the proportion of H-FOXA1-induced ER-loss regions were significantly enriched for the unique ER binding sites in P vs. tamoxifen-resistant (TamR) cells, yet no enrichment of the ER-gain regions was observed in the unique ER binding in TamR vs. P cells. Our findings uncover H-FOXA1-induced ER reprogramming driving EndoR and metastasis, possibly via a H-FOXA1/ER-dependent secretome that warrants further studies to clarify its involvement in disease progression of ER+ metastatic breast cancer.

overall_design: Examination of ER-chromatin binding in MCF7-P cells upon ectopic FOXA1 overexpression and in MCF7-P cells upon estrogen-deprivation vs. estrogen treatment.

first: Rinath

last: Jeselsohn

first: Carmine

last: De Angelis

first: Agostina

last: Nardone

first: Myles

last: Brown

first: Rachel

last: Schiff


title: ER reprogramming promotes a select pro-metastatic secretome in high FOXA1-expressing ER-positive endocrine-resistant and metastatic breast cancer

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

overall_design: Refer to individual Series


title: Effect of degradation of IGFRIL/PTBP1 in HepG2 cells

status: Public on May 13 2023

city: Beijing

first: Chengzhi

last: Gao

address: Taiping Road

department: Genetics & Integrative Omics

institute: Beijing Institute of Radiation Medicine

summary: To investigate the effect of IGFRIL/PTBP1 in HCC, we established HepG2 cell lines in which IGFRIL/PTBP1 mRNA has been degraded using siRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells and its knockdown derivatives(si-IGFRIL and si-PTBP1).

first: Pengbo

last: Cao


title: Transcriptional Profile of ZIKV Infection in HTR8 cells and U251 cells

status: Public on Jun 07 2023

city: Shenzhen

first: Qiqi

last: Chen

state: Guangdong Province

address: Guangming District, Shenzhen City, Guangdong Province

department: School of Public Health (Shenzhen)

institute: Sun Yat-sen University

summary: To identify the various host factors involved in ZIKV infection, we compared the transcriptional profile for ZIKV-infected human first-trimester placenta trophoblast cell (HTR8) and glioblastoma astrocytoma (U251-MG). Our results demonstrated that the common IFN, inflammatory cytokine, and chemokine production were activated upon ZIKV infection of these two cell types while serval DEGs were enriched in distinct biological processes related to the characteristics of cell types. Our findings identified multiple host factors associated with ZIKV pathogenesis and potential treatment of congenital zika syndrome (CZS)

overall_design: We identified the differentially expressed genes through transcriptome analyses between mock-infected and ZIKV-infected HTR8 cells and U251 cells, the ZIKV-infected group and the mock-infected group had three samples.

first: Nina

last: Li

first: Shike

last: Zeng


title: Uncovering the epigenomic determinants of kidney vascular development [scATAC-seq]

first: Jason

last: Smith

first: Alexandre

last: Martini

first: Silvia

last: Medrano

first: Nathan

last: Sheffield

first: Maria

last: Sequeira-Lopez

first: R

last: Gomez


title: Adrenergic signaling stimulates body-wide stem cell activation for limb regeneration (4N RNA-Seq)

city: Cambridge

first: Jessica

last: Whited

address: 7 Divintiy Street, Sherman Fairchild - Whited Lab

institute: Harvard University

summary: In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify which cells drive systemic-activation response in the limbs distant to the amputation.

overall_design: We dissociated homeostatic or systemically-activated limbs at 14 days post-amputation, and sorted them by their DNA content using FACS. We then performed single-cell RNA sequencing of the dividing, 4C population using 10X genomics.

first: Steven

last: Blair


title: Adrenergic signaling stimulates body-wide stem cell activation for limb regeneration (ATAC-Seq)

summary: In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify whether the proliferating cells of the systemically-activated limbs are epigenetically different from those of homeostatic limbs. identify which cells drive systemic-activation response in the limbs distant to the amputation.

overall_design: We dissociated homeostatic or systemically-activated limbs at 14 days post-amputation, and sorted them by their DNA content using FACS. We then performed bulk ATAC sequencing of the dividing, 4C population.


title: Adrenergic signaling stimulates body-wide stem cell activation for limb regeneration (2N RNA-Seq)

summary: In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify how the cells surrounding the systemically activated cells respond to an amputation.

overall_design: We dissociated homeostatic or systemically-activated limbs at 14 days post-amputation, and sorted them by their DNA content using FACS. We then performed single-cell RNA sequencing of the dividing, 2C population using 10X genomics.


title: Effect of depletion of IGFRIL in HepG2 cells

summary: To demonstrate that IGFRIL is the cognate RNA of PTBP1, we established HepG2 cell lines in which IGFRIL gene has been depleted.

overall_design: Comparative analysis of CLIP-seq data for HepG2 cells and its IGFRIL-depleted derivatives.


title: Plasma cell infiltrate populating the muscle tissue of patients with inclusion body myositis feature distinct BCR repertoire properties

status: Public on Apr 25 2023

first: Hailong

last: Meng

summary: Inclusion body myositis (IBM) is an autoimmune and degenerative disorder of skeletal muscle. The B cell infiltrates in IBM muscle tissue are predominantly fully differentiated antibody-secreting plasma cells, with scarce naïve or memory B cells. The role of this infiltrate in the disease pathology is not well understood. To better define the humoral response in IBM, we used adaptive immune receptor repertoire sequencing to generate large B cell receptor (BCR) repertoire libraries from IBM muscle biopsies and compared them to those generated from dermatomyositis (DM), polymyositis (PM), and circulating CD27+ memory B cells, derived from healthy controls and antibody secreting cells (ASC) collected following vaccination. The repertoire properties of the IBM infiltrate included: expanded clones that equaled or exceeded the highly clonal vaccine-associated ASC repertoire; reduced somatic mutation selection pressure in the complementary determining regions and framework regions; and enriched usage of class switched IgG and IgA isotypes, with a minor population of IgM expressing cells. These IBM IgM-expressing population revealed unique features, including an elevated somatic mutation frequency and distinct CDR3 physicochemical properties., These findings demonstrate that the IBM muscle BCR repertoire is highly distinct from DM and PM and circulating antigen-experienced subsets, suggesting that it may form through selection by a disease-specific set of antigens.

overall_design:
Bulk BCR was performed on muscle specimens that were colected from three PM (polymyositis), three DM (dermatomyositis) and four IBM (inclusion body myositis) patients. The analysis also included bulk BCR data from peripheral blood collected from six healthy donors used in previous studies, as well as single-cell repertoires from three ASC subsets from previous studies.
This series includes re-analyzed data from:SRX8984266, SRX8984267, SRX8984268, SRX10918775, SRX1816135, SRX1816143, SRX1816152, SRX2018047, SRX2018081, SRX2018050, SRX2018060, SRX3791988, SRX3791985, SRX3791983
Re-analyzed data are included in the tar archive available at the foot of this record.

first: Ruoyi

last: Jiang

first: Roy

last: Bhaskar

first: Qian

last: Wu

first: Subhasis

last: Mohanty

first: Richard

last: Nowak

first: Albert

last: Shaw

last: Kleinstein

first: Kevin

last: O'Connor


title: ChIP-seq for Histone variants and Histone modifictaions

status: Public on May 09 2023

first: Bhagyshree

middle: Babasaheb

last: Jamge

address: Dr. Bohr Gasse -3

institute: Gregor Mendel Institute


title: Uncovering the epigenomic determinants of kidney vascular development

first: Jason

last: Smith


title: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone H2A variants and histone modifications in WT Col-0 seedlings.

summary:
How histone intrinsic sequence variation or regulatory modifications regulate nucleosome interactions with transcription remain unclear. To clarify this question, we examined how histone variants and histone modifications assemble in the Arabidopsis thaliana genome, identifying a limited number of chromatin states that divide euchromatin and heterochromatin in biologically significant subdomains. We showed that histone variants were as significant as histone modifications to determine the composition of chromatin states. The loss of function of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) prevented the exchange between the histone variants H2A.Z and H2A.W over transposons resulting in their enrichment in chromatin states found only on proteins coding genes in the wild type. Hence, the dynamics of histone H2A variants exchange impacted the definition and distribution of chromatin states. We propose that dynamics of histone variants control the organization of histone modifications into chromatin states to achieve landmarks that signify the ability for transcription.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone H2A variants and histone modifications in seedlings .

overall_design: Each set has its own Input and H3


title: Single Cell RNA / Single Nucleus RNA Sequencing Data of Human Pancreaitc Islet

status: Public on Apr 07 2023

city: Duarte

first: Randy

middle: B

last: Kang

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Endocrinology

institute: City of Hope Beckman Research Center

summary: To investigate novel markers for snRNA seq and graft in-vivo snRNA seq.

overall_design: scRNA and integrate with snRNA, extract the DEG in each cluster, create reference and projection

first: Geming

last: Lu

first: Adolfo

last: Garcia-Ocana


title: High througuput sequencing of skeletal muscle-specific Site-1 Protease knockout mouse gastrocnemius and soleus

status: Public on Apr 01 2023

city: Saint Louis

first: Rita

last: Brookheart

state: MO

address: 660 S. Euclid Ave

institute: Washington University School of Medicine

summary: The processes by which mitochondria respond to cellular energy demands brought on by physiologic and pathophysiologic stimuli are essential to cellular adaptation and organismal survival. Disrupted mitochondrial function is implicated in several human disease states, underscoring the need to elucidate the molecular mechanisms that control mitochondrial function and metabolism. We previously described a patient with a gain-of-function mutation in Site-1 Protease (S1P) who exhibited idiopathic hyperCKemia, myoedema, and altered muscle mitochondrial morphology. To date, S1P has been heavily characterized in liver and bone, with very little known about its potential function in skeletal muscle. In our current study, we generated a skeletal muscle-specific S1P knockout mouse line (S1PsmKO) to examine the role of S1P in skeletal muscle. S1PsmKO mice were overtly normal in their appearance and health. However, examination of 12-week-old S1PsmKO mice showed increased gastrocnemius muscle mass and aged S1PsmKO mice exhibited increased muscle mass in both gastrocnemius and soleus relative to age-matched controls. Moreover, isolated muscle from S1PsmKO exhibited increased maximal mitochondrial respiration relative to floxed littermates (controls). RNA-Seq analysis showed increased transcript numbers of the mitochondrial-resident gene, Mss51 in S1PsmKO gastrocnemius relative to control mice. Mss51 is a member of the TGF-β/MSTN pathway, which controls mitochondrial metabolism. Similar to S1PsmKO muscle, S1P-depleted C2C12 cells also had increased maximal respiration, which was reversed by exogenous MSS51 expression. These data identify S1P as a regulator of muscle mass and mitochondrial metabolism, and implicate S1P as a novel modulator of TGF-β signaling. Method: Male mice were maintained on standard chow diet until 12 weeks of age.

overall_design: Examination of gastrocnemius and soleus from Site-1 Protease floxed (control) and Site-1 Protease floxed HSACre+ (skeletal muscle-specific Site-1 Protease knockout) mice on standard chow diet, fasted for 4 h prior to organ harvesting. n=4/group


title: Hepatic gene expression profiles during fed–fasted–refed state in mice

status: Public on Feb 24 2023

city: shanghai

first: NANA

last: JI

address: Dongan road 130

institute: Fudan university


title: Dissecting cell-type specific pathophysiological changes in human type-2 diabetic pancreatic islets using single-cell transcriptomic data

status: Public on Mar 30 2023

city: Farmington

first: Efthymios

last: Motakis

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

summary: Pancreatic islet (dys)function is central to glucose homeostasis and type 2 diabetes (patho)physiology. Human islets consist of multiple endocrine (alpha, beta, delta, gamma), endothelial, and resident/inflitrating immune cells whose coordinated functions modulate glucose mobilization or disposal. Single cell transcriptome profiling (scRNA-seq) studies have been applied to dissect human islet cellular heterogeneity, identify islet cell (sub)populations, and define their molecular repertoire. However, precise understanding of cell type-specific alterations in type 2 diabetic vs. non-diabetic individuals is lacking, due in part to the limited number of individuals or single cell transcriptomes per individual profiled for comparison. Here, we create a comprehensive single cell transcriptome atlas of 245,878 human islet cells from 48 individuals spanning non-diabetic (ND), pre-diabetic (PD), and type 2 diabetic (T2D) states and matched for sex, age, and ancestry and define marker gene sets that are robustly expressed across disease states for each of the 14 cell types identified. We observe significant decreases in the number of beta cells sampled from T2D vs. ND or PD donors. Two of eight putative beta cell subpopulations, with ‘high functioning’ and ‘senescent’ cell gene signatures, increase and decrease in T2D donor islets, respectively. Importantly, we identify 511 differentially expressed genes in beta cells from T2D vs. ND donors. This includes monogenic and type 2 diabetes effector genes, such as HNF1A, DGKB, ST6GAL1, and FXYD2, for which genetic and environmental effects on their expression is concordant.  Human beta cell and islet knockdown of selected newly-identified down-regulated genes impairs beta cell viability or function. Together, this study provides new and robust, cell type-resolved insights on the cellular and molecular changes in healthy vs. diabetic human islets and represents a valuable resource to the islet biology and type 2 diabetes communities.

overall_design:
Pancreatic islets from 17 type 2 diabetic (T2D), 17 non-diabetic (ND) and 14 prediabetic (PD) cadaveric organ donors were dissociated to single cell suspension and captured/profiled using 10x Genomics single-cell RNA-seq platform
ND: Islet29, Islet34, Islet37, Islet38, Islet42, Islet45, Islet47, Islet54, Islet57, Islet59, Islet61, Islet68, Islet73, Islet80, Islet104, Islet107, Islet123
PD: Islet40, Islet50, Islet53, Islet55, Islet56, Islet58, Islet62, Islet63, Islet70, Islet85, Islet89, Islet101, Islet118, Islet127
T2D:  Islet28, Islet30, Islet31, Islet32, Islet33, Islet39, Islet41, Islet44, Islet48, Islet52, Islet60, Islet71, Islet84, Islet91, Islet126, Islet119, Islet128

first: Siddhi

last: Nargund

first: Romy

last: Kursawe

first: Nathan

last: Lawlor

first: Sai

last: Krishnan

first: Vijay

last: Selvam

first: Michael

last: Stitzel


title: Exposure to elevated Temperature affects the Expression of Piwi-interacting RNAs and Associated Transcripts in Mouse Testes [small RNA-seq]

status: Public on Jan 31 2023

city: guangzhou

first: wenbin

last: Chen

address: Industrial Avenue Central

department: zhujiang hospital

institute: Southern medical university

summary: Exposure to heat waves could result in adverse effects on human health, especially in male testicles. Piwi-interacting RNA (piRNA) is a novel type of small non-coding RNA, which can notably impact mRNA turnover and preserve germline maintenance in germline cells. In this study, a mouse testicular heat stress model was constructed and the testes were removed for piRNA-sequencing. Bioinformatics analysis was used to discover the differential expressed piRNAs, piRNA clusters, and enriched pathways.

overall_design: Twelve C57BL/6 mice were randomly divided into two groups:control groups and heat stress groups. The scrota of the control groups were put into a 36 °C water bath for 15 minutes, and the testicular heat stress groups utilized a 43 °C water bath instead for the same time. Small RNA sequencing was performed in the testicular tissues of control and testicular heat stress groups after 24 hours.

first: Wenbin

first: Zhang

last: Zhao

first: Shengren

last: Cen

first: Xiangming

last: Mao


title: Hepatic gene expression profiles during fed–fasted–refed state in mice [mRNA-seq]

summary: Regulation of nutrient status during fasting and refeeding plays an important role in  maintaining metabolic homeostasis in the liver. Thus, we investigated the impact of the  physiological fed–fasted–refed cycle on hepatic gene expression in nutrient-sensitive  mice. We performed transcriptomic analysis of liver samples in fed, fasted and refed  groups of mice. Through mRNA-sequencing (RNA-Seq) and miRNA-Seq, we  compared fasted and fed states (fasted versus fed cohort) as well as refed and fasted  states (refed versus fasted cohort) to detect dynamic alterations of hepatic mRNA–  miRNA expression during the fed–fasted–refed cycle

overall_design: The animal procedures were approved by the Animal Experiment Ethics Committees  of Shanghai Jiao Tong University School of Medicine. Wild-type male C57BL/6J mice  aged 8 weeks were purchased from Shanghai Laboratory Animal Company (SLAC,  Shanghai, China). All mice were housed at 21±1°C with a humidity of 55±10% and 12-  h light/12-h dark cycle in a specific-pathogen-free facility. After 2 weeks of  acclimatization, mice were divided into three groups. The fasted group was fed a regular  diet with subsequent fasting for 24 h. The refed group underwent 24 h fasting and was  refed a fixed-calorie meal for 2 h. Mice were anesthetized with sodium pentobarbital  (Nembutal, 80 mg/kg, i.p.) and killed during the fasted and refed states. Liver tissues  were harvested and snap-frozen in liquid nitrogen for further analysis.  RNA-Seq

first: Yan

first: Min

last: Zhang

first: Nana

last: Ji

first: Liping

last: Xiang

first: Bing

last: Zhou


title: Haptoglobin Gene Expression and Anthracycline-related Cardiomyopathy in Childhood Cancer Survivors

city: Birmingham

first: Smita

last: Bhatia

state: AL

address: 1600 7th Avenue South Lowder 500

institute: University of Alabama at Birmingham

summary: In this study RNA-Seq was performed in anthracycline- exposed childhood cancer survivors who had cardiomyopathy (cases) matched to those without cardiomyopathy (controls) to understand the pathogenesis of anthrcaycline-related cardiomyopathy

overall_design: Peripheral whole blood transcriptome assessed by RNA-Seq on Illumina HiSeq in 40 cases and 64 matched controls


title: Crnic Institute Human Trisome Project: PolyA RNA-seq from whole blood

status: Public on Mar 20 2023

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

summary: Analysis of steady-state mRNA levels in whole blood of euploid controls and subjects with trisomy 21. This dataset is part of the Human Trisome Project run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of trisomy 21 (T21) subjects (n=304) to euploid controls (n=96)

first: Angela

last: Rachubinski

first: Keith

last: Smith

first: Kelly

last: Sullivan

first: Joaquin

last: Espinosa


title: Chamber selective enhancers identified in vivo by AAV-MPRA

city: Jamaica Plain

first: Xiaoran

state: MA

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

summary: Measurement the activity of candidate CSEs in aCMs and vCMs.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: AAV library was delivered to P0 pups. Atria and ventricles were harvested at P7 for MPRA library construction.

first: Yangpo

last: Cao

first: Brynn

last: Akerberg

first: William

last: Pu


title: BLM deficiency affects cytotoxicity of temozolomide and olaparib against human glioma cells and induces cellular senescence or polyploidy

status: Public on May 17 2023

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: BLM deficient cells responded differently to the temozolomide and olaparib treatment in comparison to the wild type cells. The double treatment evoked cell cycle arrest, cellular senescence or polyploidy in BLM KO LN229 and LN18 cells, respectively.

overall_design: BLM knock-out and wild type LN18 and LN229 cell lines were used to the experiments.

first: Kamil

last: Wojnicki

first: Agnieszka

last: Kaczmarczyk

first: Bozena

last: Kaminska


title: Molecular Logic of Synaptic Diversity Between Drosophila Tonic and Phasic Motoneurons

status: Public on Feb 08 2023

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Although neuronal subtypes often display unique synaptic organization and function, the underlying transcriptional differences necessary to establish these features is poorly understood. To identify molecular pathways that establish synaptic diversity, single neuron PatchSeq RNA profiling was performed on Drosophila tonic and phasic glutamatergic motoneurons. Tonic motoneurons form weaker facilitating synapses onto single muscles, while phasic motoneurons form stronger depressing synapses onto multiple muscles. Super-resolution microscopy and in vivo imaging demonstrated synaptic active zones in phasic motoneurons are more compact and display enhanced Ca2+ influx compared to their tonic counterparts. Genetic analysis identified unique synaptic properties that mapped onto gene expression differences in several cellular pathways, including distinct signaling ligands, post-translational modifications and intracellular Ca2+ buffers. These findings provide insights into how unique transcriptomes can drive functional and morphological differences between two closely related neuronal subgroups.

overall_design: PatchSeq RNA profiling of 105 1B motor neurons, 101 1S motor neurons, 17 M1 muscle cells and 26 M4 muscle cells.

first: Suresh

middle: K

last: Jetti

first: Andrés

last: Crane

first: Yulia

last: Akbergenova

first: Nicole

last: Aponte-Santiago

first: Karen

last: Cunningham

first: J

last: Littleton


title: Transposase-accessible chromatin with high-throughput sequencing for purified neonatal aCMs and vCMs

last: Zhang

summary: Examination of chamber selective chromatin accessibility and investigate if chromatin accessibility regulates CSEs.

overall_design: Neonatal atrial and ventricular cardiomyocytes were isolated and purified for ATAC-seq to identify the chamber selective chromatin accessibility regions.


title: Generate 3D genome database for atrial and ventricles and using chamber selective chromatin loops link a subset of CSEs to target genes

summary: Measurement the contribution of 3D genome structure to chamber specific transcriptional programs and CSE activity.

overall_design: P0 aCMs and vCMs were isolated and purified for H3K27ac HiChIP.


title: Dense, systematic mutagenesis to identify the features required for CSEs

summary: Investigate the sequence features required for CSE activity and selectivity.

overall_design: Candidate region was synthesized as 80 190 nt oligonucleotides tiled in 5 nt steps. Each wild type 190 nt oligonucleotide was mirrored by a matching mutant in which the central 5 nt were deleted. The activity of mutant and mirrored wt oligos was compared to identify the import sequence.


title: Next-generation sequencing facilitates quantitative analysis of atrial and ventricular cardiomyocytes transcriptomes

summary: To investigate the chamber selective transcriptional programs, we performed RNA-seq on purified cardiomyocytes. Totally we have 5 replicates for atrial cardiomyocytes and 5 replicates for ventricular cardiomyocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for atrial cardiomyocytes and ventricular cardiomyocytes.


title: Transcriptional response to collateral RNA cleavage by LbuCas13a

status: Public on Jan 19 2023

city: Leiden

first: Niels

last: Geijsen

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: LUMC

summary: LbuCas13a exhibits widespread collateral RNA cleavage in human cells after activation by a specific target RNA. We wanted to explore the cells response to this collateral RNA cleavage. Therefore we performed RNA-seq at 16 hours after RNP transduction. From prior experiments we know that at this timepoint RNA integrity has largely recovered and cells are entering apoptosis.

overall_design: dEGFP expressing HAP1 cells were transduced with either an empty transduction, LbuCas13a protein, LbuCas13a protein and a non-targeting crRNA or LbuCas13a protein an a dEGFP targeting crRNA. RNA was harvested 16 hours after transduction and gene expression profiles compared using RNA-seq.

first: Jorik

last: Bot

first: Zhihan

last: Zhao

first: Darnell

last: Kammeron

first: Peng

last: Shang