title: Transcriptional and epigenetic landscape of the mouse intestine during aging identifies key molecular drivers of aging -associated dysfunctions and diseases [scRNA-seq].

first: Seyed Mohammd Mahdi

last: Rasa

summary: Aging is a complex multifactorial process leading to the loss of tissue/organ functionality and to an increase in disease risk. Aging-related intestinal dysfunctions include loss of barrier integrity, altered stress responses, nutrient malabsorption, and cancer formation. Many molecular mechanisms related to dysfunction and diseases are well-known (e.g. in cancer), however how aging impact on them before the occurrence of dysfunctions and diseases is poorly understood.  In this study, we applied a multi-layered omics-approach to characterize the transcriptional and the epigenetic landscape of mouse intestinal epithelium during aging. We found gender and cell-type specific transcriptional and epigenetic alterations on key pathways and genes linked to intestinal dysfunctions, stem cell aging, organismal lifespan and cancer. Moreover, we identified a switch in the composition of the old intestinal stem cell subpopulations, represented by a drift towards a more secretory lineage committed (and less stem) state accompanied by functional epigenetic alterations.

overall_design: Transcriptional and epigenetic landscape of the mouse intestine during aging.

first: Anna

last: Krepelova

first: Seyed

first: Olena

last: Husak

first: Omid

last: Omrani

first: Dovydas

last: Sirvinskas

first: Suneetha

last: Nunna

first: Lisa

last: Adam

first: Sandra

last: Käppel

first: George

last: Garside

first: Farzaneh

last: Pourmasoumi

first: Ying-Pei

last: Huang

first: Hajo

last: Kries

first: Karl

last: Rudolph

first: Francesco

last: Neri


title: olfactory bulb from control mouse and a mouse with developmentally-induced olfactory bulb degeneration

status: Public on Sep 04 2023

city: Jerusalem

first: Tamar

last: Licht

address: Hadassah ein karem

department: Medical Neurobiology

country: Israel

institute: Hebrew University

type: Expression profiling by high throughput sequencing

summary: The olfactory bulb (OB) is a critical component of mammalian olfactory neuroanatomy. Beyond being the first and sole relay station for olfactory information to the rest of the brain, it also contains elaborate stereotypical circuitry that is considered essential for olfaction. Indeed, substantial lesions of the OB in rodents lead to anosmia. Here, we examined the circuitry that underlies olfaction in a mouse model with severe developmental degeneration of the OB. These mice could perform odor-guided tasks and even responded normally to innate olfactory cues. Despite the near total loss of the OB, piriform cortex in these mice responded to odors normally and its neural activity sufficed to decode odor identity. We found that sensory neurons expressthe full repertoire of olfactory receptors and their axons project primarily to the rudiments of the OB, but also ectopically, to olfactory cortical regions. Within the OB, the number of principal neurons was greatly reduced and the morphology of their dendrites was abnormal, extending over large regions within the OB. Glomerular organization was totally lost in the severe cases of OB degeneration and altered in the more conserved OBs, and the transcriptional profile of the glomerular layer was highly inflammatory. This study shows that olfactory functionality can be preserved despite reduced and aberrant circuitry that is missing many of the elements that are believed to be essential for olfaction, and may explain reported retention of olfaction in humans with degenerated OBs

overall_design: olfactory bulb from control mouse and a mouse with degenerated (28%) of the olfactory bulb

first: Dan

last: Rokni

first: Idit

last: Shiff


title: aristaless-like homeobox-3 is wound induced in muscle and stem cells and is required for planarian head regeneration

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

country: USA

institute: Oregon Health and Science University

summary:
To investigate the role of alx-3 in activating wound-induced transciptional programs during anterior regneneraiton, control(RNAi) and alx-3(RNAi) planarians were amputated below the pharynx and were allowed to regenerate for 0.5 hours post-amputation (HPA), 6HPA, 24HPA, 48HPA and 72HPA. Intact animals were are also included.Tissue from tail fragments and intact animals was collected at each time point for RNA extraction and cDNA synthesis.
Gene expression profiling analysis was performed using data obtained from RNA-seq of planarian tissues at 5 timepoints after regeneraiton and in uninjured animals .

first: Tanner

last: Scidmore


title: Transcriptome analysis of TSC1 and TSC2 using Nanopore long-read sequencer

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

country: Japan

institute: Kanazawa Medical University Hospital

summary: Tuberous sclerosis complex (TSC) is a relatively common autosomal dominant disorder characterized by multiple dysplastic organ lesions and neuropsychiatric symptoms, caused by loss-of-function mutation of either TSC1 or TSC2. Target-capture full-length double-stranded cDNA sequencing using long-read sequencer Nanopore (Nanopore Long-read Target Sequencing) revealed that the various kinds of the TSC1 and TSC2 full-length transcripts and the novel intron retention transcripts of TSC2 in TSC patient. Our results indicate that the Nanopore Long-read Target Sequencing is useful for the detection of mutations and confers information on the full-length alternative splicing transcripts for the genetic diagnosis.

overall_design: Total RNA extracted from the peripheral blood mononuclear cells (PBMCs) of two controls and TSC patient were used for the full-length double-stranded cDNA synthesis with SMARTer method. Then the full-length double-stranded cDNA generated by SMARTer method was captured using TSC1 and TSC2 probe and then the captured double-stranded cDNA was ligated adapter for Nanopore long-read sequencing using the ligation sequencing kit. The libraries were sequenced on Nanopore MinION long-read sequencer.

first: Yo

last: Niida


title: Total skin transcriptome modification induced by IL-17A blockade

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

summary: We studied psoriasis skin transcriptome modification induced by systemic IL-17A blockade with microarray analyses of total skin as part of a randomized placebo-controlled clinical trial (ClinicalTrial.gov identifier: NCT03131570)

overall_design: Whole tissue samples of (1) 33 psoriasis skin lesions before IL-17A blockade, (2) 28 psoriasis skin lesions after IL-17A blockade, and (3) 8 normal skin (including GSE78097 data) were obtained via skin biopsy and subjected to microarray analysis.

first: James

middle: G

last: Krueger

first: Jaehwan

last: Kim


title: Global gene expression of post-senescent telomerase negative ter1Δ strain of Ustilago maydis

city: Puebla

first: Patricia

last: Sanchez-Alonso

state: Puebla

address: Av. San Claudio y 24 Sur, Col. San Manuel

department: Centro de Investigaciones en Ciencias Microbiologicas

country: Mexico

institute: Instituto de Ciencias, Benemerita Universidad Autonoma de Puebla

summary: The dimorphic fungus Ustilago maydis transits from unicellular sporidia to multicellular mycelium and accomplish its life cycle in planta with teliospore formation. Mutations in either of telomerase core subunits, trt1 or ter1 cause deficiencies or inability to produce galls and teliospores when crossed to a wild-type strain. Here, the global transcriptome analysis of two ter1Δ survivor strains of U. maydis is reported. It revealed the deregulation of many telomerase-deleted response (TDR) genes previously reported in other telomerase-negative fungi, as the DDR and stress response genes, cell cycle, subtelomeric and some telomere proximal genes. Interestingly, other differentially expressed genes (DEGs) found in those ter1Δ survivors were pathogenic lifestyle factors, plant-pathogen crosstalk, iron uptake, meiosis, and melanin synthesis. The studied survivors were phenotypically comparable, yet they exhibited DEGs between them. Our global results suggest the teliospore formation in U. maydis controlled by key genes of pathogenic lifestyle and meiosis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for haploid U. maydis strain 518 and its KD derivatives (ter1::hph)

first: Juan

middle: A

last: Sanpedro-Luna

first: Leticia

last: Vega-Alvarado

first: Candelario

last: Vázquez-Cruz

first: Maria

middle: P

last: Sánchez-Alonso


title: Transcriptional and epigenetic landscape of the mouse intestine during aging identifies key molecular drivers of aging -associated dysfunctions and diseases [Total RNA-seq - crypts]

status: Public on Sep 05 2023

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

first: Anna

last: Krepelova

first: Mahdi

first: Olena

last: Husak

first: Omid

last: Omrani

first: Dovydas

last: Sirvinskas

first: Suneetha

last: Nunna

first: Lisa

last: Adam

first: Sandra

last: Käppel

first: George

last: Garside

first: Farzaneh

last: Pourmasoumi

first: Ying-Pei

last: Huang

first: Hajo

last: Kries

first: Karl

middle: L

last: Rudolph


title: In vitro grown organoids treated with IFNγ mimicking in vivo intestinal crypts cells aging

summary: Aging-related intestinal dysfunctions include loss of barrier integrity, altered stress responses, nutrient malabsorption, and cancer formation. Influence of aging on intestinal stem cell (ISC) and their niches can explain underlying causes for perturbation in ISC function during aging. However, molecular mechanisms for such decrease in functionality of ISCs during aging remain largely undetermined. Using different transcriptome-wide approaches including single-cell RNA-seq from intestinal crypt cells and immune cells of lamina propria, we characterized age-specific transcriptional programs in the intestinal epithelium. We found that aged ISCs strongly upregulate antigen presenting pathway genes and over-express secretory lineage marker genes leading to a compromised homeostasis of the intestinal epithelium. Mechanistically, increase of interferon gamma (IFNgamma) release by cytotoxic CD4 T cells and innate lymphoid type 2 cells (ILC2) in lamina propria of aged intestine lead to induction of Stat1 in ISCs that trigger MHC class II expression and prime them towards a secretory fate. Altogether these findings, clarify the cross talk between immune cells and ISC in aged intestine and identified the IFNgamma-Stat1-MHCII axis as the key gene network driving intestinal inflammaging phenotype and loss of tissue homeostasis. Our data provide basic and complementary knowledge for the development of therapeutic intervention for aging-related intestinal dysfunction and diseases.

overall_design: Single cell RNA sequencing on organoids cultured from isolated crypts of small intestine with control group and treated with IFNγ.

first: Jing

last: Lu

first: Seyed

middle: M

first: Francesco

last: Neri


title: Transcriptional and epigenetic landscape of the mouse intestine during aging identifies key molecular drivers of aging -associated dysfunctions and diseases. [Total RNA-seq - Lgr5]

first: Seyed Mohammd Mahdi


title: Digging into the transcriptomic profile of mesenchymal stem cells diagnosed with 21 trisomy

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

summary: The molecular mechanism involved in Down's syndrome (DS) is more complex than previously thought. This study provides a comprehensive overview of DS through the whole transcriptomic profile obteined by NGS of MSCs  isolated from CV derived from women carrying foetuses with diagnosed DS in comparison to their euploid counterparts (CV), revealing the existence of a wide range of molecular signatures involved in the regulation of cell cycle, proliferation and phenotype.

overall_design: Total RNA was obtained from Mesenchymal stem cells (MSCs) isolated from chorionic Villi (CV) and chorionic Villi with down's syndrome (DS-CV). CV was used as controls.

first: Salvatore

last: Vaiasicca


title: A Hub Gene Signature as a Therapeutic Target and Biomarker for Sepsis and Geriatric Sepsis-Induced ARDS Concomitant with COVID-19 Infection

status: Public on Sep 01 2023

city: guangzhou

first: anning

last: chen

address: 195 West Dongfeng Road

country: China

institute: Guangzhou Medical University Cancer Hospital

summary: Background: COVID-19 and sepsis represent formidable public health challenges, characterized by incompletely elucidated molecular mechanisms. Elucidating the interplay between COVID-19 and sepsis, particularly in geriatric patients suffering from sepsis-induced acute respiratory distress syndrome (ARDS), is of paramount importance for identifying potential therapeutic interventions to mitigate hospitalization and mortality risks.We employed bioinformatics and systems biology approaches to identify hub genes, shared pathways, molecular biomarkers, and candidate therapeutics for managing COVID-19, sepsis, and sepsis-induced ARDS. We corroborated these hub genes utilizing murine sepsis-ARDS models and blood samples derived from geriatric patients afflicted by sepsis-induced ARDS.Results: Our investigation revealed 189 differentially expressed genes (DEGs) shared among COVID-19 and sepsis datasets. We constructed a protein-protein interaction network, unearthing pivotal hub genes and modules. Notably, nine hub genes displayed significant alterations and correlations with critical inflammatory mediators of pulmonary injury in murine septic lungs. Simultaneously, 12 displayed significant changes and correlations with a neutrophil-recruiting chemokine in geriatric patients with sepsis-induced ARDS. Of these, six hub genes (CD247, CD2, CD40LG, KLRB1, LCN2, RETN) showed significant alterations across COVID-19, sepsis, and geriatric sepsis-induced ARDS. Our single-cell RNA sequencing analysis of hub genes across 3 diverse immune cell types furnished insights into disease pathogenesis. Functional analysis underscored the interconnection between sepsis/sepsis-ARDS and COVID-19, enabling us to pinpoint potential therapeutic targets, transcription factor-gene interactions, DEG-microRNA co-regulatory networks, and prospective drug and chemical compound interactions involving hub genes.Our investigation offers potential therapeutic targets/biomarkers, sheds light on the immune response in geriatric patients with sepsis-induced ARDS, emphasizes the association between sepsis/sepsis-ARDS and COVID-19, and proposes novel avenues for targeted therapies.

overall_design: On the first and seventh days of admission, we obtained blood samples from three patients with sepsis-ARDS, as well as PBMC single-cell sequencing.

first: Guojun

last: Qian

first: Hongwei

last: Fang

first: Anning

last: Chen

first: Zhun

last: Sun

first: Meiying

first: Mengyuan

last: Luo

first: Erdeng

last: Cheng

first: Shengyi

last: Zhang

first: Xiaokai

last: Wang

first: Hao


title: Gene expression profile at the single cell level of leukocytes in the livers of untreated and beta-glucan treated mice

city: Philadelphia

first: Max

last: Wattenberg

state: PENNSYLVANIA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We used scRNAseq to analyze gene changes that occur in liver leukocytes following treatment with a beta-glucan.

overall_design: Female C57BL/6J mice were treated without (Ctrl) or with β-glucan (BG, odetiglucan/Imprime PGG) on Day 0. On Day 2, mice were euthanized, and the CD45+ cells isolated from the livers for scRNAseq.

first: Stacy

middle: K

last: Thomas

first: Gregory

last: Beatty


title: Single-cell genomics segregate different transcriptomic impacts of anti-IL-17A blockade on type 17 T-cells and regulatory immune cells in psoriasis skin

first: JAEHWAN

last: KIM

summary: Durable psoriasis improvement has been reported in a subset of psoriasis patients after treatment withdrawal of biologics blocking IL-23/Type 17 T-cell (T17) autoimmune axis. However, it is not well understood if systemic blockade of the IL-23/T17 axis promotes immune tolerance in psoriasis skin. The purpose of the study was to find translational evidence that systemic IL-17A blockade promotes regulatory transcriptome modification in human psoriasis skin immune cell subsets. We analyzed human psoriasis lesional skin 6 mm punch biopsy tissues before and after systemic IL-17A blockade using the muti-genomics approach integrating immune cell-enriched scRNA-seq (n = 18), microarray (n = 61), and immunohistochemistry (n = 61) with repository normal control skin immune cell-enriched scRNA-seq (n = 10) and microarray (n = 8) data. For the T17 axis transcriptome, systemic IL-17A blockade depleted 100% of IL17A + T-cells and 95% of IL17F + T-cells in psoriasis skin. The expression of IL23A in DC subsets was also downregulated by IL-17A blockade. The expression of IL-17-driven inflammatory mediators (IL36G, S100A8, DEFB4A, and DEFB4B) in suprabasal keratinocytes was correlated with psoriasis severity and was downregulated by IL-17A blockade. For the regulatory DC transcriptome, the proportion of regulatory semimature DCs expressing regulatory DC markers of BDCA-3 (THBD) and DCIR (CLEC4A) was increased in posttreatment psoriasis lesional skin compared to pretreatment psoriasis lesional skin. In addition, IL-17A blockade induced higher expression of CD1C and CD14, which are markers of CD1c+ CD14+ dendritic cell (DC) subset that suppresses antigen-specific T-cell responses, in posttreatment regulatory semimature DCs compared to pretreatment regulatory semimature DCs. In conclusion, systemic IL-17A inhibition not only blocks the entire IL-23/T17 cell axis but also promotes regulatory gene expression in regulatory DCs in human psoriasis skin.

overall_design:
23 adult psoriasis patients received anti-IL-17A monoclonal antibody (secukinumab) injections for more than 12 weeks in the phase II clinical trial (ClinicalTrial.gov identifier: NCT03131570). Patients received the anti-IL-17A monoclonal antibody at a dose of 300 mg with injections administered once weekly at baseline and at weeks 1, 2, 3, and 4 and then every 4 weeks.

For this study, psoriasis skin biopsy samples obtained from the clinical trial were further analyzed by immune cell-enriched scRNA-seq (n = 18; GSE183047), microarray (n = 61; GSE226244), and immunohistochemistry (n = 61) together with our repository normal control skin immune cell-enriched scRNA-seq data (n = 10) (16) and microarray data (n = 8). To minimize the batch effects, all the molecular experiments from the initial sample processing to cDNA library construction were performed by the same investigators under the same protocol.

Lesional biopsy specimens were harvested with a 6 mm punch biopsy from areas with representative psoriasis lesions. Psoriasis lesional skin biopsy samples before anti-IL-17A monoclonal antibody injections (pretreatment) and psoriasis lesional skin biopsy samples after 12 weeks of anti-IL-17 monoclonal antibody injections (posttreatment) were compared for this study.

Harvested skin samples were bisected immediately after the skin biopsy. Half of the two bisected skin tissue was incubated in a culture medium for single-cell RNA sequencing (scRNA-seq) experiments. Another half of the bisected skin tissue was snap-frozen and embedded in the Optimal Cutting Temperature (OCT) compound (Ted Pella, Redding, CA) for microarray and immunohistochemistry experiments.

first: Jaehwan

last: Kim

first: James

last: Krueger


title: Gene expression

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

overall_design: Refer to individual Series


title: Distinct defects in early innate and late adaptive immune responses typify impaired fracture healing in diet-induced obesity

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Bone fractures, the most common musculoskeletal injuries, heal through three main phases: inflammatory, repair, and remodeling. Around 10% of fracture patients suffer from impaired healing that requires surgical intervention, a huge burden on the healthcare system. The rate of impaired healing increases with metabolic diseases such as obesity-associated hyperglycemia/type 2 diabetes (T2D), an increasing concern given the growing incidence of obesity/T2D. Immune cells play pivotal roles in fracture healing, and obesity/T2D is associated with defective immune-cell functions. However, there is a gap in knowledge regarding the stoichiometry of immune cells that populate the callus and how that population changes during different phases of healing. Here, we used complementary global and single-cell techniques to characterize the repertoire of immune cells in the fracture callus and to identify populations specifically enriched in the fracture callus relative to the unfractured bone or bone marrow. Our analyses identified two clear waves of immune-cell infiltration into the callus: the first wave occurs during the early inflammatory phase of fracture healing, while the second takes place during the late repair/early remodeling phase. Innate immune cells were activated during the early inflammatory phase, but in later phases they returned to homeostatic numbers and activation levels. Of the innate immune cells, distinct subsets of activated dendritic cells were particularly enriched in the inflammatory healing hematoma. In contrast to innate cells, lymphocytes, including B and T cells, were enriched and activated in the callus primarily during the late repair phase. The Diet-Induced Obesity (DIO) mouse, an established model of obesity-associated hyperglycemia and insulin resistance, suffers from multiple healing defects. Our data demonstrate that DIO mice exhibit dysregulated innate immune responses during the inflammatory phase, and defects in all lymphocyte compartments during the late repair phase. Taken together, our data characterize, for the first time, immune populations that are enriched/activated in the callus during two distinct phases of fracture healing and identify defects in the healing-associated immune response in DIO mice, which will facilitate future development of immunomodulatory therapeutics for impaired fracture healing.

overall_design: Adult (20-week-old), lean and diet-induced obese (DIO) mice underwent open tibial fracture osteotomy in the right hindlimb. The fracture callus was harvested on days 3, 5, 7, 10, 14, or 21 post-fracture. The harvested tissue was snap-frozen in liquid nitrogen, RNA was extracted using TRIzol, and RNA-seq was performed.

first: Deepak

last: Khajuria

first: Irene

last: Reider

first: Fadia

last: Kamal

first: Christopher

middle: C

last: Norbury

first: Reyad

last: Elbarbary


title: A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia  (bulk ATAC-seq data from ganglioid cultures)

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Glial cells have been proposed as an endogenous source of progenitors for the treatment of neural deficits. However, the cellular and molecular mechanisms underpinning the neurogenic potential of certain populations of adult glial cells, are not known. Using single cell transcriptomic profiling, we show here that enteric glial cells represent a cell state attained by autonomic neural crest cells as they transition during development along a linear default differentiation trajectory that allows them to retain neurogenic potential while acquiring a gene expression profile associated with their role in neuronal support and immunomodulation. Key neurogenic loci in early enteric nervous system progenitors remain in open chromatin configuration in mature enteric glia, thus facilitating neuronal differentiation under appropriate conditions. Molecular profiling and gene targeting of enteric glial cells in a novel cell culture system of enteric neurogenesis and a gut injury model, demonstrated that neuronal differentiation of glia is driven by transcriptional programs employed in vivo by early progenitors. Our work provides mechanistic insight into the dynamic regulatory landscape underpinning the development of intestinal neural circuits and generates a platform for advancing glial cells as therapeutic agents for the treatment of neural deficits.

overall_design: We performed bulk ATAC-seq of the tdT+ descendants of enteric glial cells from DIV4 ganglioids.

first: Anna

last: Laddach

first: Song

middle: H

last: Chng

first: Reena

last: Lasrado

first: Fränze

last: Progatzky

first: Michael

last: Shapiro

first: Alek

last: Erickson

first: Marisol

last: Sampedro-Castaneda

first: Artem

last: Artemov

first: Ana

last: Bon-Frauches

first: Eleni-Maria

last: Amaniti

first: Jens

last: Kleinjung

first: Stefan

last: Boeing

first: Sila

last: Ultanir

first: Igor

last: Adameyko


title: Myeloid cell deficiency of the inflammatory transcript factor STAT4 protects long-term synaptic plasticity from the effects of a high-fat, high-cholesterol diet

city: Valhalla

first: Patric

last: Stanton

state: New York

address: 15 Dana Road Basic Sciences Bldg Room 217

department: Cell Biology & Anatomy

institute: New York Medical College

summary: Neuroinflammation is associated with neurodegenerative diseases, including Alzheimer’s and Parkinson’s. The cytokine interleukin-12 activates signal transducer and activator of transcription 4 (Stat4), consumption of a high-fat, high-cholesterol diet (HFD-C) and Stat4 activity are associated with inflammation, atherosclerosis, and a diabetic metabolic phenotype. In studies of in vitro hippocampal slices from control Stat4fl/flLdlr-/- mice fed a HFD-C diabetogenic diet, we found that Schaffer collateral-CA1 synapses exhibited larger reductions in activity-dependent, long-term potentiation (LTP) of synaptic transmission, compared to mice fed a standard diet. Glucose tolerance and insulin sensitivity shifts produced by HFD-C diet were reduced in Stat4ΔLysMLdlr-/- mice compared to Stat4fl/flLdlr-/- controls. Stat4ΔLysMLdlr-/- mice, which lack Stat4 under control of the LysMCre promoter, were resistant to HFD-C induced impairments in LTP. In contrast, Schaffer collateral-CA1 synapses in Stat4ΔLysMLdlr-/- mice fed the HFD-C diet showed larger LTP than control Stat4fl/flLdlr-/- mice. Expression of a number of neuroinflammatory and synaptic plasticity genes was reduced by HFD-C diet in control mice, and less affected by HFD-C diet in Stat4ΔLysMLdlr-/- mice. Suppression of Stat4 activation has potential for protecting against effects of western diet on cognition, type 2 diabetes, and reduce risk of Alzheimer’s disease and other neurodegenerative disorders associated with neuroinflammation.

overall_design: We collected the gene expression profile in a Host Response Panel, a custom Code Set which profiled 785 genes in mouse across 50+ pathways. Tissue was extracted and analyzed from the hippocampus of the following groups of animals at 24 weeks old: Stat4ΔLysMLdlr-/- mice on normal chow diet, Stat4ΔLysMLdlr-/-  on HFD-C diet for 16 weeks, Stat4fl/flLdlr-/- mice on normal chow diet, and Stat4fl/flLdlr-/- mice on HFD-C diet for 16 weeks.

first: Melinee

last: D'silva

first: Robin

last: Bai

first: William

last: Keeter

first: Elena

middle: V

last: Galkina

first: Jerry

last: Nadler


title: Bulk RNA seq of WT and TSC2KO mouse mesenchymal vascular progenitors

city: Denver

first: Susan

last: Majka

email: majkas@njhealth.org, susanmajka@mac.com

state: co

address: 1400 Jackson St, Goodman Bldg K810a

department: Medicine

institute: NJH

summary: To elucidate potential cell-based mechanisms by which deregulation of mTOR signaling in MVPC drives microvessel rarefaction and afore mentioned loss of tissue structure, we isolated eGFP positive MVPC lines by flow sorting  and analyzed their transcriptomic signatures. Unbiased transcriptomic comparison was used to define mechanisms underlying the decreased stemness and angiogenic ability in Tsc2KD mTOR activated versus WT MVPC. Additionally, we identified a Tsc2KD line that exhibited pS6 expression similar to WT levels suggesting cell intrinsic adaptive regulation of mTOR. Bulk RNA seq was performed in triplicate using primary WT, Tsc2KD mTOR regulated and Tsc2KD mTOR activated (mTOR+) lines. Following normalization, hierarchical clustering analyses were presented as a heatmap depicting significant differences in gene expression between WT and Tsc2KD lines. Tsc2 KD was confirmed in bulk RNA sequencing analysis of the MVPC lines

overall_design: mRNA (Qiagen kit/column) Poly A selected total RNA Lib/Bulk RNA seq; NOVA seq 6000 Paired End 150 cycle 2x150; 80 million PE reads; Nugen library kit/prep; 100ng mRNA (polyA selected) in 50uL or less (water or TE)


title: A comparative study of cellular heterogeneity and gene expression at single-cell resolution in air-liquid interface culture models of the human airway epithelium

city: New York

first: Alec

last: Pankow

address: 1 Gustave L. Levy Place, Anbg 17 17-70

institute: Icahn School of Medicine at Mount Sinai

summary: The airway epithelium is composed of diverse cell types with specialized functions that mediate homeostasis and protect against respiratory pathogens. Human airway epithelial cultures at air-liquid interface (HAE) are a physiologically relevant in vitro model of this heterogeneous tissue, enabling numerous studies of airway disease. HAE cultures are classically derived from primary epithelial cells, the relatively limited passage capacity of which can limit experimental methods and study designs. BCi-NS1.1, a previously described and widely used basal cell line engineered to express hTERT, exhibits extended passage lifespan while retaining capacity for differentiation to HAE. However, gene expression and innate immune function in HAE derived from BCi-NS1.1 versus primary cells have not been fully characterized. Here, combining single cell RNA-Seq (scRNA-Seq), immunohistochemistry, and functional experimentation, we confirm at high resolution that BCi-NS1.1 and primary HAE are largely similar in morphology, cell type composition, and overall transcriptional patterns. While we observed cell-type specific expression differences of several interferon stimulated genes in BCi-NS1.1 HAE cultures, we did not observe significant differences in susceptibility to infection with influenza A virus and Staphylococcus aureus. Taken together, our results further support the BCi-NS1.1 cell line as a valuable tool for the study of airway infectious disease.

overall_design: scRNA-Seq of BCi-NS1.1 HAE (3 replicates) and primary normal human bronchial epithelium (NHBE) HAE (3 replicates).

first: Rachel

last: Prescott

first: Maren

last: de Vries

first: Meike

last: Dittmann

first: Brad

last: Rosenberg


title: Hypoxia primes human ISCs for interleukin-dependent rescue of stem cell activity

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

institute: Altis Biosystems

summary: Background & Aims: Hypoxia in the intestinal epithelium can be caused by acute ischemic events or conditions like Inflammatory Bowel Disease (IBD) where immune cell infiltration produces ‘inflammatory hypoxia’, a chronic condition that starves the mucosa of oxygen. Epithelial regeneration after ischemia and IBD suggests intestinal stem cells (ISCs) are highly tolerant to acute and chronic hypoxia; however, the impact of acute and chronic hypoxia on human ISC (hISC) properties have not been reported. Here we present a new microphysiological system (MPS) to investigate how hypoxia affects hISCs isolated from healthy human tissues. We then test the hypothesis that some inflammation-associated interleukins protect hISCs during prolonged hypoxia.   Methods: hISCs were exposed to <1.0% oxygen in the MPS for 6-, 24-, 48- & 72hrs. Viability, HIF1a response, transcriptomics, cell cycle dynamics, and hISC response to cytokines were evaluated.   Results: The novel MPS enables precise, real-time control and monitoring of oxygen levels at the cell surface. Under hypoxia, hISCs maintain viability until 72hrs and exhibit peak HIF1a at 24hrs. hISCs lose stem cell activity at 24hrs that recovers at 48hrs of hypoxia. Hypoxia increases the proportion of hISCs in G1 and regulates hISC capacity to respond to multiple inflammatory signals. Hypoxia induces hISCs to upregulate many interleukin receptors and hISCs demonstrate hypoxia-dependent cell cycle regulation and increased organoid forming efficiency when treated with specific interleukins  Conclusions: Hypoxia primes hISCs to respond differently to interleukins than hISCs in normoxia through a transcriptional response. hISCs slow cell cycle progression and increase hISC activity when treated with hypoxia and specific interleukins. These findings have important implications for epithelial regeneration in the gut during inflammatory events.

overall_design: Bulk RNA sequencing libraries from jejunal hISC-derived epithelial monolayers were prepared from normoxic and hypoxic samples that were exposed to different durations of acute hypoxia (6, 24, and 48 hours) in technical triplicates

first: Kristina

middle: R

last: Rivera

first: R

first: Joseph

last: Burclaff

first: Michael

last: Czerwinski

first: Jintong

last: Liu

first: Jessica

last: Trueblood

first: Caroline

last: Hinesley

first: Keith

last: Breau

first: Shlok

last: Joshi

first: Vladimir

last: Pozdin

first: Ming

last: Yao

first: Amanda

last: Ziegler

first: Anthony

middle: T

last: Blikslager

last: Daniele

first: Scott

last: Magness


title: Cortistatin deficiency reveals a dysfunctional brain endothelium with impaired gene pathways, exacerbated immune activation, and disrupted barrier integrity

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

summary:
Background: Brain activity governing cognition and behaviour depends on the fine-tuned microenvironment provided by a tightly controlled blood-brain barrier (BBB). Brain endothelium dysfunction is a hallmark of BBB breakdown in most neurodegenerative/neuroinflammatory disorders. Therefore, the identification of new endogenous molecules involved in endothelial cell disruption is essential to better understand BBB dynamics. Cortistatin is a neuroimmune mediator with anti-inflammatory and neuroprotective properties that exerts beneficial effects on the peripheral endothelium. However, its role in the healthy and injured brain endothelium remains to be evaluated. Herein, this study aimed to investigate the potential function of endogenous and therapeutic cortistatin in regulating brain endothelium dysfunction in a neuroinflammatory/neurodegenerative environment.

Methods: Wild-type and cortistatin-deficient murine brain endothelium and human cells were used for an in vitro barrier model, where a simulated ischemia-like environment was mimicked. Endothelial permeability, junction integrity, and immune response in the presence and absence of cortistatin were evaluated using different size tracers, immunofluorescence labelling, qPCR, and ELISA. Cortistatin molecular mechanisms underlying brain endothelium dynamics were assessed by RNA-sequencing analysis. Cortistatin role in BBB leakage was evaluated in adult mice injected with LPS.

Results: The endogenous lack of cortistatin predisposes endothelium weakening with increased permeability, tight-junctions breakdown, and dysregulated immune activity. We demonstrated that both damaged and uninjured brain endothelial cells isolated from cortistatin-deficient mice, present a dysregulated and/or deactivated genetic programming. These pathways, related to basic physiology but also crucial for the repair after damage (e.g., extracellular matrix remodelling, angiogenesis, response to oxygen, signalling, and metabolites transport), are dysfunctional and make brain endothelial barrier lacking cortistatin non-responsive to any further injury. Treatment with cortistatin reversed in vitro hyperpermeability, tight-junctions disruption, inflammatory response, and reduced in vivo BBB leakage.

Conclusions: The neuropeptide cortistatin has a key role in the physiology of the cerebral microvasculature and its presence is crucial to develop a canonical balanced response to damage. The reparative effects of cortistatin in the brain endothelium were accompanied by the modulation of the immune function and the rescue of barrier integrity. Cortistatin-based therapies could emerge as a novel pleiotropic strategy to ameliorate neuroinflammatory/neurodegenerative disorders with disrupted BBB.

overall_design: Transcriptome profiling (RNA-seq) of multiple mice samples under the following conditions: endothelial cell cultures from ischemic stroke mice model (MCAO), CST KO and WT, subjected to NM and OGD environments

first: Julia

last: Castillo-González

first: José

last: Ruiz

first: Ignacio

last: Serrano-Martínez

first: Irene

last: Forte-Lago

first: Ana

last: Ubago-Rodriguez

first: Marta

last: Caro

first: Jesús

last: Pérez-Gómez

first: Alejandro

last: Benítez-Troncoso

first: Eduardo

last: Andrés-León

first: Macarena

last: Sánchez-Navarro

first: Raúl

last: Luque

first: Elena

last: González-Rey


title: Single cell ATAC-seq of neural crest derivatives in mouse embryos

city: Vienna

first: Artem

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

summary: Neural crest cells are multipotent embryonic progenitors that give rise to a large number of cell types in a vertebrate embryo, thus, sometimes being considered as a 4th germ layer. Neural crest cells originate within the dorsal neural tube at the time of its closure, delaminate and migrate to multiple destinations. The paths of fate selection and differentiation in the neural crest cells are not fully understood. The analysis of open chromatin regions at single cell level will help to clarify the genetic programs behind the development of a vagal neural crest stream.

overall_design: Mouse embryos were collected at embryonic day E9.5. Transgenic embryos contained Wnt1-Cre/R26Tomato construct (therefore, Tomato-positive cells had expressed Wnt at some point in their lineage and are expected to be the derivatives of Neural crest cells). After the dissociation of a certain anatomical part of the embryo, Tomato-positive cells (neural crest derivatives) were FACS-sorted and profiled with single-cell ATAC-seq.

first: Alek

last: Erickson

first: Igor

last: Adameyko


title: Efficient genetic editing of human intestinal organoids using ribonucleoprotein-based CRISPR

status: Public on Aug 31 2023

city: Cambridge

first: Elisa

last: Moutin

address: Robinson Way

department: CRUK Cambridge Institute

institute: University of Cambridge

summary: Organoids are currently one of the most widely used ex vivo models in epithelial biology. Combined with genetic editing strategies, organoids offer a promise of rapid and efficient investigation of gene function in many models of human disease.  However, to date, the editing efficiency of organoids with the use of non-viral electroporation methods has been only up to 30%, with implications for the subsequent need for selection including turnaround time and exhaustion or adaptation of the organoid population. Here, we describe an efficient method of intestinal organoid editing using a Ribonucleoprotein CRISPR-based approach. Editing efficiencies of up to 98% in target genes were robustly achieved across different anatomical gut locations and developmental timepoints from multiple patient samples with no observed off-target editing. The method allowed us to study the effect of the loss of the tumour suppressor gene, PTEN, in normal human intestinal cells.  Analysis of PTEN deficient organoids defined phenotypes that likely relate to its tumour suppressive function in vivo, such as a proliferative advantage and increased organoid budding. Transcriptional profiling revealed differential expression of genes in pathways commonly known to be associated with PTEN loss including mTORC1 activation.

overall_design: We generated PTEN KO human intestinal organoids using CRISPR and  performed RNA-seq to identify the trasncriptional effect of the loss of a colorectal cancer tumour suppressor gene and functionally validate the KO.


title: Global mapping of the macrophage-HIV-1 transcriptome reveals that productive infection induces remodeling of the host cell DNA and chromatin [miRNA-seq]

city: Montreal

first: Eric

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

country: Canada

institute: IRCM

type: Non-coding RNA profiling by high throughput sequencing

summary: This data corresponds to the microRNA expression profiles for the exact same samples from GSE180273.

overall_design: Human monocytes from healthy donors were differentiated in MØ by adherence for 3 days in the presence of RPMI-1640 culture medium supplemented with M-CSF (25 ng/mL) and 10% human AB serum. Cells were maintained in culture medium in absence of M-CSF for an additional 3 days, treated with Accutase™ (Stem Cell Technologies) for 60 to 90 min, and detached with a soft cell scraper (Sarstedt). Cells were plated at 2.5 x 10exp5 cells/mL for 24 (cell-culture coated dishes) or 72 h (Ultra-Low attachment dishes). MØ were infected with replication-competent NL/Bal-HSA (see A. Deshiere et al., Scientific Reports 2017) with multiplicities of infection (MOI) ranging from 0.004 to 2.5. HSApos and HSAneg MØ were isolated using biotinylated anti-HSA (clone M1/69; eBiosciences) and anti-Biotin Magnetic Beads (Miltenyi) in a MS separation column (Miltenyi). Purified MØ populations (HSAneg and HSApos) were resuspended and frozen in QIAzol lysis buffer. Total RNA was isolated from sorted cell populations using the miRNeasy Kit from QIAGEN (Valencia, CA).

first: Robert

last: Lodge

first: Alexandre

last: Deshiere

first: Michel

last: Tremblay


title: Sleeping Beauty transposon mutagenesis identified genes involved in colorectal cancer development in the inflammatory microenvironment.

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

summary: To identify genes and molecular pathways involved in colorectal cancer (CRC) that developed in an inflammatory microenvironment, we performed Sleeping Beauty (SB) transposon mutagenesis screening in Dextran Sodium Sulfate treated-mice. We have shown that cell cycle-related genes and TGFb pathway-related genes are frequently mutated in inflammation-related tumors. We have demonstrated that TNFa can promote dedifferentiation of colonic epithelial cells via epigenomic reprogramming, and activate both Cdkn2a-p53 signaling and CycD-Cdk4/6, creating advantageous conditions for selecting cells carrying mutations in the Cdkn2a-p53 pathway genes.  We have also showed that Cdk4/6 inhibitors are effective against colorectal tumors in an inflammatory microenvironment using the SB mouse model, presenting a potential new therapeutic strategy. Thus, SB screening is not only powerful in identifying genes involved in cancers that develop in specific microenvironments, but also helpful in validating the efficacy of drugs.

overall_design: wt colonic organoids were treated with TNFa (40 ng/ml) for 3 wks.

first: Kana

last: Shimomura

first: Haruna

last: Takeda


title: Loss of RANK signaling leads to stem cell activation in post pregnancy mammary glands

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

summary: The purpose of this study was to elucidate the molecular changes of the mammary epithelium induced by luminal cell specific RANK deletion. We have characterized the phenotypic consequences of RANK deletion in the luminal lineage of the mammary epithelium, and uncovered that Rank KO luminal cells have reduced long term renewal following sucessive pregnancies. Lineage tracing analysis has demonstrated that during pregnancy 2, Rank deleted luminal cells are repleace by a wt luminal cell population, derived from the basal epithelium. We therefore decided to perform RNA seq in resting mammary glands from virgin and parous (following pregnancy one) females, cells were FACS sorted based on the traditional markers CD24 and CD49f and in the case of luminal cells GFP (recombined cells). We have isolated luminal cells to identify the molecular pathways involved in reduced long term renewal oberved in the parous context; basal cells were isolated to adress the putative mechanims regulated the bipotency observed during second pregnancy

overall_design: Animal were treated with doxicyclin (1mg/ml in the drinking water) between 3 and 8 weeks of age to induce cre recombination

first: Ana

middle: S

last: Rocha

last: Graña-Castro

first: Eva

last: Suárez


title: Expression data from K562 hemin differentiation

city: Murcia

first: Lola

last: Rodríguez Ruiz

address: C/Campus universitario, 5

institute: University of Murcia

summary: We used microarrays to detail the global programme of gene expression underlying erythroid differentiation using K562 cell line.

overall_design: K562 were collected at 0 and 24 h hemin treatment fro RNA extraction and hybridization on Affymetrix microarrays.

last: Rodríguez-Ruiz

first: Juan

last: Lozano-Gil

first: Diana

last: García-Moreno

middle: B

last: Pérezz-Oliva

first: Victoriano

last: Mulero


title: Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [bulk RNA-Seq]

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

summary:
To investigate the effect of Grin2a (a schizophrenia risk gene) and Grin2b (an autism spectrum disorder risk gene) loss of function on brain transcriptome.
We performed unbiased transcriptomic profiling (bulk RNAseq analysis) in 5 brain regions and at four postnatal ages in Grin2a and Grin2b mutant mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 2, 4, 12 and 20 weeks of age in Grin2a and Grin2b mutant mice.  rna.

first: Zohreh

last: Farsi


title: Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice [snRNA-seq]

summary: To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age.

overall_design: SnRNAseq analysis of prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST) and Thalamus (TH) at 12 weeks, as well as PFC and HP at 4 weeks in Grin2a mutant mice.

first: Farsi

last: Zohreh

first: Nicolella

last: Ally


title: Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice


title: RNA Seq off visceral adipose tissue from human Cushing patients and Controls

status: Public on Aug 30 2023

city: Ulm

first: Ulrich

last: Stifel

address: Helmholtzstrasse 8/1

department: CME

institute: Universität Ulm

summary: Visceral adipose tissue from human patients with Cushing was sequnced to identify novel markers of disease progression and other changes related to the disease in adipose tissue.

overall_design: RNA Seq from visceral adipose tissue of patients with Cushing´s diesease  (n=12) and matched control patients (n=5)


title: The obesity-linked human lncRNA AATBC regulates adipocyte plasticity by stimulating mitochondrial dynamics and respiration

status: Public on Aug 29 2023

city: Munich

first: Stefan

last: Kotschi

address: Max-Lebsche-Platz 30

department: Institute for Cardiovascular Prevention

institute: Klinikum der Universitaet Muenchen

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

overall_design: Refer to individual Series


title: Gene expression analysis of primary human vascular wall-derived stem cells (VW-MSCs) and dermal fibroblasts

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: gene expression profiles of primary human VW-MSCs and fibroblasts were comparatively analyzed

overall_design: both cell-types were compared

last: Klein


title: The obesity-linked human lncRNA AATBC regulates adipocyte plasticity by stimulating mitochondrial dynamics and respiration [II]

summary: Adipocytes are critical regulators of metabolism and energy balance. While white adipocyte dysfunction is a hallmark of obesity-associated disorders, the activation of thermogenic brown and beige adipocytes is linked to improved cardiometabolic health. As adipocytes dynamically adapt to environmental cues by functionally switching between white and thermogenic phenotypes, a molecular understanding of this adipocyte plasticity could help improving energy balance and weight loss. Here, we show that the long non-coding RNA (lncRNA) Apoptosis associated transcript in bladder cancer (AATBC) is a human-specific regulator of adipocyte plasticity. Searching for new human lncRNAs implicated in adipocyte biology we compared transcriptional profiles of human adipose tissues and cultured adipocytes and discovered that AATBC was enriched in thermogenic conditions. Using primary human adipocytes and immortalized human adipocytes we found that gain-of-function of AATBC enhanced the thermogenic phenotype whereas loss-of-function diminished this effect. The AATBC-mediated increase in mitochondrial respiration was linked to a more fragmented mitochondrial network and vice versa. While we found that AATBC is predominantly located in the nucleus, its effect on global transcription was only marginal. As AATBC is specific to humans, we expressed AATBC in adipose tissue of mice to study its systemic impact, which led to lower plasma leptin levels. Interestingly, this association was also present in human subjects, as AATBC in adipose tissue was inversely correlated with plasma leptin levels, body mass index and other measures of metabolic health. In conclusion, AATBC is a novel obesity-linked regulator of adipocyte plasticity and mitochondrial function in humans.

overall_design: Human supraclavicular brown (FDG-PET positive) and white adipose tissue of 5 metabolically healthy donors

first: Kotschi

last: Stefan

first: Giroud

last: Maude

first: Bartelt

last: Alexander


title: The obesity-linked human lncRNA AATBC regulates adipocyte plasticity by stimulating mitochondrial dynamics and respiration [1]

overall_design: hMADS cells treated with either scramble and siRNA AATBC for knockdown experiments or AV_GFP and AV_AATBC respectively for overexpression of the lncRNA AATBC

first: Maude

last: Giroud

first: Alexander

last: Bartelt


title: DNA methylome analysis of primary human vascular wall-derived stem cells (VW-MSCs) and dermal fibroblasts

type: Methylation profiling by genome tiling array

summary: DNA-methylation profiles of primary human VW-MSCs and fibroblasts were comparatively analyzed.

overall_design: both cell-types were compared with regard to their specific DANN methylation profiles


title: Transcriptome Analysis of the Mesenteric Adipose and Liver Reveals Novel Mechanisms by Which Prenatal Alcohol Exposure Contributes to Worse Stroke Outcome

city: Bryan

first: Rajesh

last: Miranda

state: Texas

address: 8441 Riverside Pkwy

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University School of Medicine

summary: Prenatal alcohol exposure (PAE) is linked to elevated risk for systemic adult-onset diseases like hypertension, impaired glucose and immune regulation, and in animal models, to impaired recovery from acute onset diseases like cerebrovascular ischemic stroke. Recent evidence suggests that the gastrointestinal system rapidly becomes dysbiotic following cerebrovascular stroke, resulting in systemic inflammation. We hypothesized that a history of PAE would modify the systemic effects of stroke, and transduce exposure-dependent transcriptomic changes in downstream sentinel tissues of the enteric portal circulation that have previously been linked to biobehavioral outcomes in rodent PAE models.  Pregnant Sprague Dawley rats were exposed to repeated episodes of vaporized ethanol or room air from gestational day 8 to 19. At 5 months, progeny from each treatment condition were subjected to unilateral endothelin-1 induced occlusion of the middle cerebral artery and outcomes evaluated after 2 days while other progeny stayed stroke-naïve. Stroke induced disabilities were assessed by behavioral assays (adhesive removal, Vibrissae evoked fore-limb placement, circling) and infarct size. The mesenteric adipose tissue and liver transcriptomes were assessed by sequencing, from age-matched stroke-exposed and stroke-naïve offspring. In stroke-naïve animals, pathway analysis identified rRNA processing as downregulated and citric acid cycle as upregulated in mesenteric adipose. Weighted gene correlation network analysis (WGCNA) identified, in the liver of stoke-naïve animals, a moderate but significant correlation between PAE status and necroptosis, a proinflammatory form of programmed cell death (Pearson’s r=0.554, p<0.05). Two days after a stroke, PAE rats exhibited worse neurological scores compared to controls (p<0.05).  WGCNA after stroke identified an adipose gene network associated with B cell differentiation and NF-kappa B signaling as moderately correlated with post-stroke neurological function (Pearson's r=0.52, p=0.05). Post-stroke WGCNA also identified a liver proinflammatory gene network strongly correlated with post-stroke neurological function (Pearson's r=-0.63, p<0.01). PAE persistently alters the transcriptome of afferent tissue targets of enteric circulation in adult rat offspring. Moreover, PAE-linked enteric inflammation is correlated to worse outcomes following cerebrovascular ischemic stroke in adulthood. Enteric disturbances may mediate adverse brain health outcomes due to PAE in adulthood.

overall_design: There were a total of 60 samples; 4 Control Female stroke-naïve, 3 Control Male stroke-naïve, 4 PAE Female stroke-naïve, 4 PAE Male stroke-naïve, 4 Control Female stroke, 3 Control Male stroke, 4 PAE Female stroke, 4 PAE Male stroke. Done for mesenteric adipose and for liver.

first: Marisa

last: Pinson

first: Shameena

last: Bake

first: Farida

last: Sohrabji


title: Functional characterization of a single nucleotide polymorphism associated with Alzheimer’s Disease in a hiPSC-based neuron model.

status: Public on Aug 28 2023

city: North Chicago

first: Ameya

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

summary: Neurodegenerative diseases encompass a group of debilitating conditions resulting from progressive nerve cell death. Of these, Alzheimer’s disease (AD) occurs most frequently, but is currently incurable and has limited treatment success. Late onset AD, the most common form, is highly heritable but is caused by a combination of non-genetic risk factors and many low-effect genetic variants whose disease-causing mechanisms remain unclear. By mining the FinnGen study database of phenome-wide association studies, we identified a rare variant, rs148726219, enriched in the Finnish population that is associated with AD risk and dementia, and appears to have arisen on a common haplotype with older AD-associated variants such as rs429358. The rs148726219 variant lies in an overlapping intron of the (FosB proto-oncogene) FOSB and (ERCC excision repair 1) ERCC1 genes. To understand the impact of this SNP on disease phenotypes, we performed CRISPR/Cas9 editing in a human induced pluripotent stem cell (hiPSC) line to generate isogenic clones harboring heterozygous and homozygous alleles of rs148726219. hiPSC clones differentiated into induced excitatory neurons (iNs) did not exhibit detectable molecular or morphological variation in differentiation potential compared to isogenic controls. However, global transcriptome analysis showed differential regulation of nearby genes and upregulation of several biological pathways related to neuronal function, particularly synaptogenesis and calcium signaling, specifically in mature iNs harboring rs148726219 homozygous and heterozygous alleles. Functional differences in iN circuit maturation as measured by calcium imaging were observed across genotypes. Edited mature iNs also displayed downregulation of unfolded protein response and cell death pathways. This study implicates a phenotypic impact of rs148726219 in the context of mature neurons, consistent with its identification in late onset AD, and underscores a hiPSC-based experimental model to functionalize GWAS-identified variants.

overall_design: The BIONi010-C-13 line (donor biosample SAMEA103988285) with doxycycline (DOX)-inducible neurogenin 2 (NGN2) transgene was obtained and is available from the European Bank for Induced pluripotent Stem Cells (EBiSC, www.ebisc.org). CRISPR/Cas9-mediated SNP editing of BIONi010-C-13 was completed by the Genomic Engineering & iPSC Center (GEIC) at Washington University School of Medicine. To generate clones Heterozygous for rs148726219, the parental BIONi010-C-13 line was transfected with HiFi Cas9 v3 (IDT), gRNA with sequence GAGCTGTGGGTGGCTAGGGC, and ~60 bp single-stranded DNA oligos as homology arms flanking the PAM site (left HA: cccgggctctttctacccttaacactctggaaagcctgtgaaatgaaattattccacctcT; right HA: ctagccacccacagctctcctggtgctggtggcatcccccaaaacccactcccttcctac). An episomal vector expressing GFP was used for selection of transfected cells by FACS-based single-cell sorting. Clones were expanded and genotypes confirmed by next generation sequencing (NGS). The wild-type clone was generated in the same CRISPR experiment but was untargeted. To generate homozygous clones, heterozygous clones were re-targeted a second time. Directed differentiation of hiPSCs to excitatory iNs was performed as previously described, with modifications. RNA was isolated from hiPSC-derived induced neurons (iNs) at days 0, 2, 6, 13, and 23 using the AllPrep DNA/RNA mini kit (Qiagen). Samples were extracted manually according to the manufacturer’s instructions or on a QIAcube using the AllPrep DNA/RNA mini kit protocol (Qiagen). For each timepoint, RNA from 4 technical replicates (4 independent wells of cells cultured simultaneously) were used per line. RNA library preparation from total RNA was conducted following the manufacturer’s protocol for the Kapa mRNA HyperPrep Kit (Roche). Briefly, 250 ng of total RNA was enriched for mRNA using magnetic oligo-dT beads. The remaining RNA was then fragmented by magnesium under elevated temperature. After fragmentation, RNA was depleted of rRNA and globin mRNA using the QIAseq FastSelect RNA Removal Kit (Qiagen). The depleted RNA then underwent first strand synthesis using reverse transcriptase and random primers. Combined second strand synthesis and A-tailing incorporated dUTP into the second cDNA strand for stranded RNA sequencing and added dAMP to the 3’ ends for adapter ligation. The cDNA fragments were then ligated to sequencing adaptors (IDT xGEN Dual Index UMI adapters) and was enriched using 16 cycles of PCR. Final libraries were assessed using the Agilent Tapestation and Qubit (ThermoFisher) assay methods then sequenced on an Illumina HiSeq 4000 sequencer using 2 x 75bp read length. Raw fastq reads were subjected to quality control using FastQC (v0.11.7) and quality profiling, filtering for low quality and short reads, adapter trimming and mismatch correction using fastp (v0.20.1) [18]. RNA reads were aligned to the hg38 build of the reference human genome, with transcript annotations from GENCODE, using the STAR aligner. Gene expression was quantified using RSEM (RNA-Sequencing by Expectation Maximization) [19]. The expected count matrix from RSEM was filtered for low expression using a counts-per-million threshold of 1 in at least 40 samples (number of samples in the smallest group of comparison) and further filtered for genes annotated as pseudogenes or pseudo-autosomal regions.

first: Lindsay

last: Stolzenburg

first: Sahar

last: Esmaeeli

first: Erin

last: Murphy

first: Taekyung

last: Kwon

first: Christina

last: Preiss

first: Lamiaa

last: Bahnassawy

first: Joshua

middle: D

last: Stender

first: Justine

last: Manos

first: Peter

last: Reinhardt

first: Fedik

last: Rahimov

first: Jeffrey

middle: F

last: Waring

first: Cyril

middle: Y

last: Ramathal


title: TET2 lesions enhance the aggressiveness of CEBPA-mutant AML by rebalancing GATA2 expression [WGBS]

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

type: Methylation profiling by high throughput sequencing

summary: The myeloid transcription factor CEBPA is recurrently biallelically mutated (i.e., double mutated; CEBPADM) in acute myeloid leukemia (AML) with a combination of hypermorphic N-terminal mutations (CEBPANT), promoting expression of the leukemia-associated p30 isoform, and amorphic C-terminal mutations. CEBPADM AML features recurrent co-occurring mutations including GATA2 lesions, however insights into mechanisms governing this co-mutational spectrum are incomplete.   By combining transcriptomic and epigenomic analyses of CEBPA-TET2 co-mutated patients with models thereof, we identify GATA2 as a conserved target of the CEBPA-TET2 mutational axis, providing a rationale for the mutational spectra in CEBPADM AML. Mechanistically, we suggest that elevated CEBPA levels, driven by CEBPANT, mediate recruitment of TET2 to the Gata2 distal hematopoietic enhancer thereby increasing Gata2 expression. Conversely, CEBPADM AML gains a competitive advantage through TET2 loss, by decreasing Gata2 promoter demethylation thereby rebalancing GATA2 levels. Of clinical relevance, demethylating treatment of Cebpa-Tet2 co-mutated AML restores Gata2 levels and prolongs disease latency.

overall_design: WGBS of Cebpa-/p30 and Cebpa-/p30Tet2-/- AML blasts: Live donor-derived non-lymphoid and non-erythroid bone marrow cells (DAPI-CD45.2+CD3-B220-Ter119-) FACS-sorted. Two or three biological replicates per genotype were sequenced.

first: Anna

last: Wilhelmson

first: Anne

last: Wenzel


title: Germline piRNAs counteract endogenous retrovirus invasion from somatic cells

status: Public on Aug 25 2023

city: CLERMONT-FERRAND

first: Emilie

last: BRASSET

address: 28 place Henri dunant

country: France

institute: CNRS 6293 INSERM U1103 Université Clermont Auvergne

summary: In metazoan gonads, transposable elements (TEs) mobilization is limited by PIWI-interacting RNAs (piRNAs). These small RNAs originate from specific source loci, the piRNA clusters. piRNAs are known to silence TEs in the cells where they are produced. Endogenous retroviruses (ERVs), a subclass of TEs, pose a particular threat because they are capable of transiting from cell to cell. In this study, we reveal that piRNAs produced locally in germ cells counteract invasion by ERVs arriving from adjacent somatic cells. We reactivated the Drosophila ERVZAMin somatic gonadal cells by deleting, using CRISPR-Cas9 genome editing, its single copy in the somaticflamencopiRNA cluster, while keeping the piRNA pathway fully functional. Upon reactivation,ZAMinvaded the oocytes, resulting in transposition and severe fertility defects. We show that onceZAM-piRNAs are produced in germ cells they counter the invasion. Our study sheds new light on the mechanisms of recognition and regulation of invasive genetic elements, which is essential for the maintenance of genome integrity.

overall_design: RNA sequencing

first: Marianne

last: Yoth

first: Nathalie

last: Guegen

first: Silke

last: Jensen

last: Brasset


title: TET2 lesions enhance the aggressiveness of CEBPA-mutant AML by rebalancing GATA2 expression [RNA-Seq]

overall_design: RNA-seq of Cebpa-/p30 and Cebpa-/p30Tet2-/- AML blasts: Live donor-derived non-lymphoid and non-erythroid bone marrow cells (DAPI-CD45.2+CD3-B220-Ter119-) FACS-sorted. Three biological replicates per genotype were sequenced.


title: Genetic and dietary modulators of inflammation in the gastro-intestinal tract of BXD genetic reference population

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

summary: Transcriptome data measured by microarray in colon of  the BXD mouse genetic diversity model under a standard chow or a high fat diet at a fastd state.

overall_design: At 29 weeks of age, mice of 52 BXD strains including parental C57BL/6J and DBA/2J strains were fasted overday and then were sacrificed. Phenotyping were performed and multi-organ were flash-frozen and bio-banked for future use, the assoiacted datasets are mentioned in the paper. In this study, proximal colon samples were collected and immediately frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Johan

last: Auwerx

first: Alexis

last: Bachmann

last: Rapin

first: Maroun

last: Sleiman

first: Jean-David

last: Morel


title: Comparision of primay murine airway basal cells and ESC-derived basal cells

status: Public on Aug 24 2023

city: Boston

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: The goal of this experiment is to study the transcriptomic similarity and differences between ESC-derived cultured basal cells and their primary counterparts in the same culture condition.

overall_design: We analyzed mouse mouse iBC culture from the directed differentiation protocol outlined in Ma et al., 2023. iBC cultures are previously sorted on Nkx2-1mCherry+/NGFR+ gate and cultured for 9 days in Basal Cell Medium. Meanwhile, we harvested airway basal cells from syngeneic adult mouse trachea and cultured them in the same BCM media. Both samples are outgrowth from NGFR+ FACS purified samples.

first: Liang

last: Ma

first: Pushpinder

last: Bawa

first: Darrell

last: Kotton


title: Murine ESC-derived basal cell (iBC) 5th generation secondary transplantation

summary: The goal of this experiment was to compare the transcriptome of iBC-derived lineages to endogenous tracheal epithelial cells after transplantation after serial secodnary transplantation.

overall_design: Tracheas from two iBC 5th generation secondary transplantation were harvested 7 months post-transplantation. Tracheas were digested with a pronase-based method (Plasschaert et al., 2018), beforE FACS to separate GFP+ donor-derived cells and GFP- endogenous cells.


title: TET2 lesions enhance the aggressiveness of CEBPA-mutant AML by rebalancing GATA2 expression

last: Porse


title: murine ESC-derived basal cell (iBC) transplantation (40&56 days post-transplantation)

summary: The goal of this experiment was to compare the transcriptome of iBC-derived lineages to endogenous tracheal epithelial cells after transplantation.

overall_design: Tracheas from two iBC transplantation recipients are analyzed (40 days and 56 days post-transplantation, respectively), along with the trachea of a control mouse (sample genetic background, sex, without injury or transplantation)

first: Bibek

last: Thapa

first: Jonathan

last: Lindstrom-Vautrin

first: Carlos

last: Villacorta-Martin


title: murine primary basal cell (BC) recipient (69 days post-transplantation) and ESC-derived basal cell (iBC) recipient (192 days post-transplantation)

summary: The goal of the experiment is to: 1) compare transcriptome of primary BC-derived lineages to endogenous tracheal epithelial cells after transplantation; 2) compare the transcriptome of iBC-derived lineages to their endogenous counterparts, and study them together with a previous dataset of iBC recipient 40&56 days post-transplantation to study any temporal changes

overall_design: Tracheas from one primary BC recipient (69 days post-transplantation) and one iBC recipient (192 days post-transplantation) were analyzed.

last: Sawa


title: in vitro murine iBC culture

summary: The goal of this experiment is to study mouse pluripotent stem cell-derived airway basal cell (iBC) culture at a single cell resolution.

overall_design: We analyzed mouse P6 D129 mouse iBC culture from the directed differentiation protocol outlined in Ma et al., 2022. iBC cultures are previously sorted on Nkx2-1mCherry+/NGFR+ gate at P5 and cultured for 9 days in Basal Cell Medium before sample collection and sequencing analysis.


title: Human primary basal cell (BC) or iPSC-derived basal cell (iBC) recipients (6 weeks post-transplantation)

summary: The goal of this experiment is to study the transcriptome of

overall_design: Six tracheas from human donor cell recipients (two primary BC recipients, two KOLF2 iBC recipients, two BU3-NGPT iBC recipients) were analyzed 6 weeks post transplantation.

first: Jake

last: Le Suer

first: Taylor

last: Matte

first: Finn

last: Hawkins


title: BC and iBC

overall_design: Refer to individual Series


title: Alveolar type II epithelial cell FASN maintains lipid homeostasis in experimental COPD

status: Public on Aug 22 2023

city: New York

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Alveolar epithelial type II cells (AEC2) strictly regulate lipid metabolism to maintain surfactant synthesis. A loss in AEC2 cell function and surfactant production are implicated in the pathogenesis of the smoking related lung disease, chronic obstructive pulmonary disease (COPD). It is unclear if smoking alters lipid synthesis in AEC2 cells and if altering lipid metabolism in AEC2 cells contributes to COPD development. In this study, high throughput lipidomic analysis revealed increased lipid biosynthesis in AEC2 cells isolated from mice chronically exposed to cigarette smoke (CS). Mice with a targeted deletion of the de novo lipogenesis enzyme, fatty acid synthase (FASN) in AEC2 cells (FasniAEC2) exposed to CS exhibited higher bronchoalveolar lavage fluid (BALF) neutrophils, higher BALF protein, more severe air-space enlargement and were more susceptible to age-induced emphysema. FasniAEC2 mice exposed to CS had lower levels of key surfactant phospholipids but higher levels of BALF ether phospholipids, sphingomyelins and polyunsaturated fatty acid containing-phospholipids, as well as increased BALF surface tension.  FasniAEC2 mice exposed to CS also had higher markers of ferroptosis in the lung. These data suggest that AEC2 cell FASN modulates the response of the lung to smoke by regulating the composition of the surfactant phospholipidome.

overall_design: The lung tissue from FASN gene specifically deleted in AEC2 cells mice (n=3) and the control mice (n=3)

first: Suzanne

last: Cloonan

first: Lichao

last: Fan

first: Adrian

last: Tan


title: Dynamic regulation of pancreatic β cell function and gene expression by the SND1 coregulator in vitro

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

summary: The pancreatic β cell synthesizes, packages, and secretes insulin in response to glucose-stimulation to maintain blood glucose homeostasis. Under diabetic conditions, a subset of β cells fail and lose expression of key transcription factors (TFs) required for insulin secretion. Among these TFs is Pancreatic and duodenal homeobox 1 (Pdx1), which recruits a unique subset of transcriptional coregulators to modulate its activity. Here we describe a novel interacting partner of Pdx1, the Staphylococcal Nuclease and Tudor domain-containing protein (Snd1), which has been shown to facilitate protein-protein interactions and transcriptional control through diverse mechanisms in a variety of tissues. Pdx1:Snd1 interactions were confirmed in rodent β cell lines, mouse islets and human islets. Utilizing CRISPR-Cas9 gene editing technology, we deleted Snd1 from the mouse β cell lines, which revealed numerous differentially expressed genes linked to insulin secretion and cell proliferation, including limited expression of Glp1r. We observed Snd1 deficient β cell lines had reduced cell expansion rates, Glp1r protein levels and limited cAMP accumulation under stimulatory conditions, and further show that acute ablation of Snd1 impaired insulin secretion in rodent and human β cell lines. Lastly, we discovered that PDX1:SND1 interactions were profoundly reduced in human β cells from donors with type 2 diabetes (T2D). These observations suggest the Pdx1:Snd1 complex formation is critical for controlling a subset of genes important for β cell function and is targeted in diabetes pathogenesis

overall_design: CRISPR/Cas9 was utilized to knockout Snd1 from mouse insulinoma MIN6 cell lines (Snd1 KO). RNA purified from 3 Control and 3 Snd1 KO cell lines was sequenced


title: Staurois parvus adult frog tissue

status: Public on Aug 21 2023

city: Northampton

first: Lisa

last: Mangiamele

address: Clark Science Center, 44 College Ln

department: Dept of Biological Sciences

institute: Smith College

summary: To identify unique expression patterns in spinal cord, leg muscle, and brain of Staurois parvus frogs, with the goal of creating a resource for future studies to understand the evolution of an elaborate hind limb signaling behavior called "foot flagging" in this species.

overall_design: We dissected whole brain (n=2), spinal cord (n=4), and hind leg thigh muscle (n=5) from adult male Staurois parvus frogs raised in captivity at the Vienna Zoo. We placed fresh tissue in RNAlater until further processing.

first: Mika

last: Holtz

first: Riccardo

last: Racicot

first: Adam

last: Stuckert


title: RNAseq analysis of Plasmodium falciparum extracellular vesicles

status: Public on Aug 23 2023

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

summary: Plasmodium falciparum secretes extracellular vesicles that contain RNA. The biological benefit of this secretion to the secreting parasite is not known. Here, we sequenced the RNA content of extracellular vesicles and compared with that of the secreting whole parasites. The data suggests that extracellular vesicles might be part of a post-transcriptional regulatory mechanism that shapes intracellular RNA levels in the parasite.

overall_design: To investigate the biological benefit of extracellular vesicles to the asexual blood stages of Plasmodium falciparum, we isolated the RNA content of extracellular vesicles obtained from six parasite isolates (at 4-hourly intervals) and compared with that of the whole parasite.

first: Kioko

last: Mwikali


title: Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

city: Beijing

first: Yunke

last: Zhu

address: Zhongguancun South Street

institute: Chinese Academy of Agricultural Sciences

summary:
Background
The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome level assembled lycophyte genomes, has hindered our understanding of evolution and environmental adaption of lycophytes.
Findings
We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and the I. taiwanensis revealed conserved and different genomic features between diploid and polyploid lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provides insights into environmental adaption of lycophytes.
Conclusions
The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic research and the environmental studies of not only I. sinensis but also other lycophytes.


summary:
Background
The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome level assembled lycophyte genomes, has hindered our understanding of evolution and environmental adaption of lycophytes.
Findings
We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and the diploid I. taiwanensis revealed of genomic features and polyploid of lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provides insights into environmental adaption of lycophytes.
Conclusions
The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic research and the conservation of not only I. sinensis but also other lycophytes.

overall_design: Iso-seq of Isoetes sinensis

first: Jinteng

last: Cui

first: Zhe

last: Liang


overall_design: HiSeq/MiSeq of Isoetes sinensis


overall_design: RNA-seq of Isoetes sinensis


title: Resident regulatory T cells reflect the immune history of individual lymph nodes

city: Würzburg

first: Milas

last: Ugur

state: Bayern

address: Versbacherstr. 9

department: Institute of Systems Immunology

institute: Universität Würzburg

summary: Regulatory T cells (Treg) are present in lymphoid and non-lymphoid tissues where they restrict immune activation, prevent autoimmunity and regulate inflammation. Treg in non-lymphoid tissues are typically resident, while those in lymph nodes (LNs) are considered to recirculate. However, Treg in LNs are not a homogenous population and circulation kinetics of different Treg subsets are poorly characterized. Furthermore, whether Treg can acquire memory T cell properties and persist for extended periods after their activation in LNs is unclear. Here, we used in situ labeling with a stabilized photoconvertible protein to uncover turnover rates of Treg in LNs in vivo. We found that while the majority of Treg in LNs recirculate, 10-20% are memory-like resident cells that remain in their respective LNs for weeks to months. Single cell RNA sequencing revealed that LN-resident cells are a functionally and ontogenetically heterogeneous population and share the same core residency gene signature with conventional CD4+ and CD8+ T cells. Resident cells in LNs did not actively proliferate and did not require continuous TCR signaling for their residency. Yet, resident and circulating Treg had distinct TCR repertoires, and each LN contained exclusive clonal subpopulations of resident Treg. Our results demonstrate that, similar to conventional T cells, Treg can form resident memory-like populations in LNs after adaptive immune responses. Specific and local suppression of immune responses by resident Treg in draining LNs might provide new therapeutic opportunities for the treatment of local chronic inflammatory conditions.

overall_design: Mesenteric lymph node of Vav-H2B-Dendra2 mice were photoconverted and 7 days later D-Red+ and D-Red- cells among CD19-CD8-CD4+CD62Llo cells were sorted and analyzed by scRNAseq

first: Oliver

last: Pabst

first: Lydia

last: Kopplin


title: A Human Post-Implantation Embryoid Model Derived Ex Utero Solely from Genetically Unmodified Naïve PSCs (scRNA-Seq II)

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

institute: Weizmann Institute of Science

summary: Our ability to study early human post-implantation development remains highly limited due to the ethical and technical challenges associated with intrauterine development of the human embryo after implantation. Despite the great progress made on human blastoids or gastruloids, such elegant models do not constitute an integrated synthetic stem cell-derived embryoid models (SEMs) that includes all the key extra-embryonic tissues of the early pre-gastrulating implanted human conceptus (e.g. hypoblast, yolk-sac, trophoblasts, amnion and extraembryonic mesoderm), and thus, do not recapitulate post-implantation epiblast development within the context of these extra-embryonic compartments. Mouse naïve pluripotent stem cells (PSCs) have recently been shown to give rise to embryonic and extra-embryonic stem cells capable of self-assembling into post-gastrulation mouse SEMs, while bypassing the blastocyst-like stage, and eventually initiating organogenesis ex utero. Here, we implement critical adaptations to extend these finding in humans, using only genetically unmodified human naïve PSCs, circumventing the need for ectopic expression of lineage promoting transgenes. Such integrated human SEMs recapitulate all known compartments of early post-implantation stage human embryos, including epiblast, hypoblast, extra-embryonic mesoderm, and trophoblast surrounding the latter layers. The organized human SEMs recapitulate key hallmarks of post-implantation stage embryogenesis up to 13-14 days post-fertilization (dpf, Carnegie stage 6a), such as bilaminar disk formation, epiblast lumenogenesis, amniogenesis, anterior-posterior symmetry breaking, PGC specification, primary and secondary yolk sac formation, and extra-embryonic mesoderm expansion that defines a chorionic cavity and a connective stalk. This new platform constitutes a tractable stem cell-based model for experimentally interrogating previously inaccessible windows of human early peri- and post-implantation development.

overall_design: 10X single-cell RNA-seq measured on two human naïve stem-cell populations that were maintained in either RCL medium (RPMI based medium supplemented with CHIR99021 and LIF and B27 WITHOUT Insulin) to induce PrE/ExEM cells, or in BAP(J) medium, to induce TE lineage.

first: Bernardo

last: Oldak

first: Emilie

last: Wildschutz

first: Vladyslav

last: Bondarenko

first: Jacob

last: Hanna


title: A Human Post-Implantation Embryoid Model Derived Ex Utero Solely from Genetically Unmodified Naïve PSCs (Multiome ATAC-Seq)

status: Public on Aug 16 2023

overall_design: Four stem cell culture samples (two Naïve and two primed) were sequenced using 10X Multiome

first: Tom

last: Shani


title: A naturally de novo-evolved gene contributes to rice grain shape difference between indica and japonica

status: Public on Aug 20 2023

city: Yangzhou

first: Rujia

last: Chen

address: Wenhui

institute: Yangzhou unversity

summary:
To investigate the role of OsGSE9 in grain shape, we generate its overexpressing lines, and knockout lines by CRISPR/Cas9 system.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the panicles of the WT and OsGSE9 transgenic lines

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the panicles of WT and OsGSE9-overexpressing/knockout lines.

first: Zefeng

last: Yang


title: mRNA sequencing of ADH4 overexpression in HBV-associated hepatoma cell line HepG2.2.15

status: Public on Aug 19 2023

city: Chongqing

first: Ping

last: Yan

address: No. 1 Youyi Road, Yuzhong District

department: Department of Hepatobiliary Surgery

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Liver cancer is the sixth most common cancer globally and the third leading cause of cancer-related death. Alcohol dehydrogenase families (ADHs), which predominantly exist in the livers of humans and animals, serve as essential enzymes in the metabolism of short-chain alcohols and ω-oxidation of certain fatty acids, playing crucial roles in numerous physiological processes. A cluster of genes consisting of seven alcohol dehydrogenase-encoding genes (ADH1A, ADH1B, ADH1C, ADH4, ADH5, ADH6 and ADH7) is situated on chromosome 4q and encodes ADHs. Loss of Chromosome 4q is a frequent occurrence in liver cancer, leading to the loss of an entire cluster of seven genes. As a result, there is typically a decrease in the expression of ADHs (ADH1A, ADH1B, ADH1C, ADH4 and ADH6) in liver cancer. Amongst these, ADH4 is the most substantially downregulated gene, which affects both overall survival (OS) and disease-free survival (DFS) in liver cancer patients. Furthermore, a thorough investigation was previously conducted to identify possible biomarkers for predicting liver cancer recurrence. The results showed that in liver cancer, ADH4 was significantly downregulated and this downregulation indicated a higher likelihood of recurrence in liver cancer patients. As a consequence, further research was conducted on the role of ADH4 in liver cancer progression.

overall_design: Total RNA was extracted from ADH4-overexpressing or control hepatoma cell line HepG2.2.15, and RNA quality was evaluated with an Agilent 2100/4200 bioanalyzer. Qualified RNA was used to construct the common transcriptome library.

first: Yunhai

last: Luo


title: Single-cell transcriptomic sequencing identifies the genes related to polyfunctionality of persistent CAR-T cells targeting B7-H3 (CD276) in mice bearing human neuroblastoma xenografts

status: Public on Aug 17 2023

city: Bethesda

first: Mitchell

last: Ho

state: MD

address: 37 Convent Drive, Rm5002

department: LMB/CCR

institute: NCI

summary: To understand the molecular determinants of B12(VHH)-CAR-T polyfunctionality, we simultaneously measured the protein and RNA expression levels of 95 single CD4+ B12(VHH)-CAR-T cells isolated from IMR5 tumor-bearing mouse and re-stimulated with IMR5 tumor cells in vitro. We identified two CAR-T clusters, low polyfunctionality and high polyfunctionality subsets, in a 2D t-SNE plot. Moreover, our single-cell mRNA expression profiling revealed 32 genes that displayed statistically significant, concordant differences between the two cell subsets.

overall_design: IMR5 tumor-bearing mice persistent B12(VHH)-CAR-T CAR T cells were stimulated with IMR5 tumor cells in vitro,  then grouped into high-polyfunctionality and low-polyfunctionality subsets based on the cytokine secretion profile. Then scRNA-seq was used to analyze upregulated genes in each subset.

first: Dan

last: Li

first: Dana

last: Ashworth

first: Weiming

last: Ni

first: Jing

last: Zhou

first: David

last: Coit

first: Tenzin

last: Lhakhang

first: Jeff

last: Sabina


title: Human thymic putative CD8aa precursors exhibit a biased TCR repertoire in single cell AIRR-seq

status: Public on Aug 18 2023

city: Oslo

first: Benedicte

middle: Alexandra

last: Lie

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: University Of Oslo

summary: To explore the effect of the adaptive immune receptor repertoire on thymocyte developmental decisions, we performed single cell adaptive immune receptor repertoire sequencing (scAIRR-seq) of thymocytes from human young paediatric thymus and blood.

overall_design:
scAIRRseq of samples from young paediatric donors (n  = 5). For each donor, four samples were profiled: 1.) peripheral blood mononuclear cells (PBMC), 2.) unenriched thymic cells, 3.) thymic cells enriched for antigen-presenting cells by density gradient centrifugation, and 4.) thymic cells enriched for stromal cells by CD45-depletion.
Raw data files not included due to data sensitivity concerns

first: Heimli

last: Marte

first: Siri

last: Flåm

first: Hanne

last: Hjorthaug


first: Yunke

last: Zhu

overall_design: lncRNA-seq of Isoetes sinensis

first: Jinteng

last: Cui

first: Zhe

last: Liang


title: Transcriptomics and metabolomics study in mouse kidney of the molecular mechanism underlying energy metabolism response to hypoxic stress in highland areas

city: Xining

first: yujie

last: gao

state: Qinghai

address: No.251 Ningda Road

institute: Qinghai university

summary: Exposure to hypoxia disrupts energy metabolism and induces inflammation. However, the pathways and mechanisms underlying energy metabolism disorders caused by hypoxic conditions remain unclear. In this study, we constructed a hypoxic animal model and applied transcriptomic and non-targeted metabolomics techniques to further investigate the pathways and mechanisms of hypoxia exposure that disrupt energy metabolism. Transcriptome results showed that 3007 genes were significantly differentially expressed under hypoxic exposure, and Gene Ontology (GO) annotation analysis and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis showed that the differentially expressed genes (DEGs) were mainly involved in energy metabolism and were significantly enriched in the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) pathway. Differential genes in the TCA cycle (IDH3A, SUCLA2, and MDH2) and OXPHOS pathway (NDUFA3, NDUFS7, UQCRC1, CYC1, and UQCRFS1) were validated using mRNA and protein expression, and the results showed downregulation. The results of non-targeted metabolomics showed that 365 significant differential metabolites were identified under plateau hypoxia stress. KEGG enrichment analysis showed that the differential metabolites were mainly enriched in metabolic processes, such as energy metabolism, nucleotide metabolism, and amino acid metabolism. Hypoxia exposure disrupted the TCA cycle and reduced the synthesis of amino acids and nucleotides by decreasing the concentrations of cis-aconitate, α-ketoglutarate, NADH, NADPH, most amino acids, purines, and pyrimidines. Bioinformatics analysis was used to identify inflammatory genes related to hypoxia exposure, and some inflammatory genes were selected for verification. We found that the mRNA and protein expression levels of IL1B, IL12B, S100A8, and S100A9 in kidney tissues were upregulated under hypoxic exposure. Our results suggest that hypoxia exposure inhibits the TCA cycle and OXPHOS signalling pathway by inhibiting IDH3A, SUCLA2, MDH2, NDUFFA3, NDUFS7, UQCRC1, CYC1, and UQCRFS1, thereby suppressing energy metabolism, inducing amino acid and nucleotide deficiency, and promoting inflammation, ultimately leading to kidney damage.

overall_design: In this study, C57BL/6 mice were raised at an altitude of 4200 meters (altitude hypoxia group, HKT) and 400 meters (altitude normoxic group, PKC), respectively. After 30 days, the kidney tissue of the mice was aseptically taken out. By measuring the blood gas analysis index and the mRNA and protein expression level of HIF-1α, it is proved that the establishment of hypoxic animal mouse model is successful. By comparing the renal index and HE staining results of two groups of mice, it was found that hypoxia induced renal tissue damage in mice. Furthermore, the two groups of kidney tissues were transcriptomically sequenced, and the reliability of sequencing results was verified by detecting differentially expressed genes (DEGs) by RT-QPCR technology. Through the enrichment analysis of DEGs, it was found that hypoxia induced changes in energy metabolism of mouse kidney tissues.

first: Yujie

last: Gao

first: Qifu

last: Long

first: Hui

last: Yang

first: Ying

last: Hu

first: Yuzhen

last: Xu

first: Chaoqun

last: Tang

first: Cunlin

last: Gu

first: Sheng

last: Yong


title: A Human Post-Implantation Embryoid Model Derived Ex Utero Solely from Genetically Unmodified Naive PSCs (scRNA-Seq I)

first: Noa

last: Novershtern

overall_design: Three scRNA-seq 10X Genomics samples of human synthetic embryo models (SEMs), taken on days 4,6 & 8 of the protocol. Each sample was generated from 50-80 SEMs.

first: Bernardo

last: Oldak

first: Emilie

last: Wildschutz

first: Vladyslav

last: Bondarenko

first: Jacob

last: Hanna


title: A Human Post-Implantation Embryoid Model Derived Ex Utero Solely from Genetically Unmodified Naïve PSCs

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

overall_design: Refer to individual Series


title: Gene Editing of Anp32a Confers Resistance to Avian Influenza in Chicken

status: Public on Aug 15 2023

city: London

first: Michael

middle: A

last: Skinner

address: St Mary's Campus, Norfolk Place

department: Faculty of Medicine, Section of Virology

institute: Imperial College London

summary: Comparison of transcriptomic profiles of primordial germ cells and derived fibroblast cell lines from homozygous, CRISPR/Cas9 gene-edited, ANP32A knockout and mutant chickens

overall_design: We used CRISPR/Cas9 to perform precise sequence changes in ANP32A to generate genome-edited PGC cell lines, which were also differentiated into fibroblast-like cell lines, all of which were subjected to RNA-seq in their native state.

first: Alewo

last: Idoko-Akoh

last: McGrew


title: Infiltrating CD8+ T cells exacerbate Alzheimer’s disease pathology in a novel 3D human neuroimmune axis model

status: Public on Aug 14 2023

city: Charlestown

first: Joseph

last: Park

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital/Harvard Medical School

summary: T cells have been proposed to play a role in Alzheimer’s disease (AD) pathology by infiltrating the brain and interacting with resident cells.  Here, we describe a novel three- dimensional (3D) human neuroimmune axis model comprised of human stem cell-derived neurons, astrocytes, and microglia, together with human peripheral immune cells. We used this neuroimmune axis model to examine the infiltration of peripheral immune cells into AD versus control neural-glial cell cultures. Using single-cell RNA- sequencing, we identified that infiltrating T cells into AD cultures led to induction of interferon-gamma and neuroinflammatory-associated pathways in microglial cells.

overall_design: To compare T cell mediated glial actvation various conditions such as 3D culture (Neuron/astrocyte),  3D triculture (Neuron/Astrocyte/Microglia), 3D PiChip (Neuron/Astrocyte/Microglia/T cells), and 3D culture  with T cells (Neuron/Astrocyte/T cells) in CTRL and AD prepared accoding to the timeline and  isolated  from central chamber (brain compartment) for the Droplet-based single cell RNAseq (InDrop method)

first: Mehdi

last: Jorfi

first: Dmitry

last: Prokopenko

first: Younjung

last: Choi

first: Doo Yeon

last: Kim

first: Rudolph

middle: E

last: Tanzi


title: Metastatic competency and tumor spheroid formation are independent cell states governed by RB in lung adenocarcinoma

city: Philadelphia

first: Nelson

last: Freeburg

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: Inactivation of the retinoblastoma (RB) tumor suppressor in lung adenocarcinoma is associated with the rapid acquisition of metastatic ability and the loss of lung cell lineage commitment. We previously showed that restoration of RB in advanced lung adenocarcinomas in the mouse was correlated with a decreased frequency of lineage de-committed tumors and overt metastases. To identify a causal relationship for RB and its role in reprogramming lineage commitment and reducing metastatic competency in lung adenocarcinoma, we developed multiple tumor spheroid forming lines where RB restoration could be achieved after characterization of the degree of each spheroid’s lineage commitment and metastatic ability. Surprisingly, we discovered that RB inactivation dramatically promoted tumor spheroid forming potential in tumors that arise in the KrasLSL-G12D/+; p53flox/flox lung adenocarcinoma model. However, RB reactivation had no effect on the maintenance of tumor spheroid lines once established. Additionally, we show that RB-deficient tumor spheroid lines are not uniformly metastatically competent but are equally likely to be non-metastatic. Interestingly, unlike tumor spheroid maintenance, RB restoration could functionally revert metastatic tumor spheroids to a non-metastatic cell state. Thus, strategies to reinstate RB-pathway activity in lung cancer may reverse metastatic ability and have therapeutic potential. Finally, the acquisition of tumor spheroid forming potential reflects underlying cell state plasticity, which is often predictive of, or even conflated with metastatic ability. Our data support that each is a discrete cell state restricted by RB and question the suitability of tumor spheroid models for their predictive potential of advanced metastatic tumor cell states.

overall_design: Group 1 samples express markers of EMT and metastatic competency. They form lung metastases upon intravenous injection. Group 2 samples do not show transcriptomic evidence of metastatic competency and are minimally capable of forming tumors in mice upon intravenous injection.  All samples are RB-deficient.

first: Nia

last: Peterson

first: Dain

last: Ruiz

first: Amy

last: Gladstein

first: David

last: Feldser