title: Expansion of memory Vδ2 T cells following SARS-CoV-2 vaccination revealed by temporal single-cell transcriptomics

city: Rozzano, Milan

first: Sara

last: Terzoli

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Research Hospital

summary: γδ T cells provide rapid cellular immunity against pathogens. Here, we conducted matched single-cell RNA-sequencing and γδ-TCR-sequencing to delineate the molecular changes in γδ T cells during a longitudinal study following mRNA SARS-CoV-2 vaccination. While the first dose of vaccine primes Vδ2 T cells, it is the second administration that significantly boosts their immune response. Specifically, the second vaccination uncovers memory features of Vδ2 T cells, shaped by the induction of AP-1 family transcription factors and characterized by a convergent central memory signature, clonal expansion, and an enhanced effector potential. This temporally distinct effector response of Vδ2 T cells was also confirmed in vitro upon stimulation with SARS-CoV-2 spike-peptides. Indeed, the second challenge triggers a significantly higher production of IFNγ by Vδ2 T cells. Collectively, our findings suggest that mRNA SARS-CoV-2 vaccination might benefit from the establishment of long-lasting central memory Vδ2 T cells to confer protection against SARS-CoV-2 infection.

overall_design: Peripheral blood mononuclear cells were isolated from buffy coats of 6 healthy volunteers (3 males and 3 females, age range 25-50 years old) with two doses of mRNA COVID-19 (BNT162b2)–vaccine without previous SARS-CoV-2 infection. PB were longitudinally collecteded for each healthy donor 1 day before the first dose (P0; n=6), 3 days after the first vaccine dose (P1; n=6), 17 days after the first dose (P2; n=5), 3 days after the second dose (P3; n=6), and 3 months following the boost (P4; n=5). PB were analyzed using paired single-cell RNA-seq and γδ TCR-seq technics.

first: Paolo

last: Marzano

first: Valentina

last: Cazzetta

first: Rocco

last: Piazza

first: Inga

last: Sandrock

first: Sarina

last: Ravens

first: Likai

last: Tan

first: Immo

last: Prinz

first: Simone

last: Balin

first: Michela

last: Calvi

first: Anna

last: Carletti

first: Assunta

last: Cancellara

first: Nicolò

last: Coianiz

last: Franzese

first: Alessandro

last: Frigo

first: Antonio

last: Voza

first: Francesca

last: Calcaterra

first: Clara

last: Di Vito

first: Silvia

last: Bella

first: Joanna

last: Mikulak

first: Domenico

last: Mavilio


title: Symmetrically fated progenitors dynamically accommodate tissue maintenance in the esophagus [RNA-seq]

status: Public on Mar 07 2024

city: Stockholm

first: David

last: Grommisch

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: Progenitor cells adapt their behavior in response to tissue demands. However, the molecular mechanisms controlling esophageal progenitor decisions remain largely unknown. Here we demonstrate the presence of a Troy(Tnfrsf19)-expressing progenitor subpopulation localized to defined regions along the esophageal axis. Lineage tracing and mathematical modelling demonstrate that Troy-positive progenitor cells are prone to undergoing symmetrical fate choices and contribute to esophageal tissue homeostasis long-term. Functionally, TROY inhibits progenitor proliferation and enables commitment to differentiation without affecting fate symmetry. Whereas Troy expression is stable during esophageal homeostasis, progenitor cells downregulate Troy in response to tissue stress, enabling proliferative expansion of basal cells refractory to differentiation and reestablishment of tissue homeostasis. Our results demonstrate functional, spatially restricted, progenitor heterogeneity in the esophageal epithelium and unveil how dynamic regulation of Troy coordinates tissue generation.

overall_design: To investigate the effect of a Tnfrsf19 knockout on esophageal epithelial progenitor cells we recombined Troy expressing cells 24 hours prior to euthanasia and FACS isolated recombined cells of four TroyWT/KI and TroyKI/KI mice, respectively.

first: Menghan

last: Wang

first: Maria

last: Genander


title: Combination treatmetn of MRT68921 and all-trans retinoic acid in HL-60 human leukemia cells

status: Public on Mar 05 2024

city: Kanazawa

first: Tomohisa

last: Baba

address: Kakuma-machi

country: Japan

institute: Kanazawa University

summary: It was previously reported that inhibition of autophagosome formation by MRT68921 induced  accumulation of cytosolic dsDNA, which can activate cytosolic DNA-sensor signaling pathway, thereby reducing cell viability through reactive oxygen species generation in leukemia cells. Thus, we examined the effect of combination treatment of MRT68921 and a leukemia differentiation therapeutic drug, all-trans retinoic acid.

overall_design: HL-60 human leukemia cells were treated with all-trans retinoic acid alone or all-trans retinoic acid and MRT68921. Gene expression was determined 48 hours after treatment. There is single sample for each condition.

first: Naofumi

last: Mukaida


title: Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas [CapIG-seq]

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

country: USA

institute: Weill Cornell

summary: Mutations in chromatin modifiers are a hallmark of many tumors, especially lymphomas arising from germinal center (GC) B cells. Given that these lymphoma mutations all induce aberrant gene repression, it is surprising that they often co-occur in individual patients. The most common pairing are mutations affecting CREBBP and KMT2D. Both impair enhancer activity in overlapping pathways to facilitate lymphomagenesis, hence their co-occurrence is especially puzzling. Herein, we report that combined haploinsufficiency of CREBBP and KMT2D (C+K) do indeed accelerate lymphomagenesis (vs either allele alone) and confer a more malignant phenotype. Single cell RNA-seq analysis of GC reaction showed that C+K haploinsufficiency induced aberrant GC hyperplasia by altering cell fate decisions, skewing B cells away from memory B and plasma cell differentiation and favored instead expansion of centroblasts. Integrative epigenomic studies in murine and human B cells showed that C+K deficiency particularly impairs enhancer activation for immune synapse genes involved in exiting the GC reaction. This effect was especially severe at super-enhancers for genes governing cell fate decisions induced by T cell help, pointing to a particular dependency for both co-activators at these specialized regulatory elements. Mechanistically, CREBBP and KMT2D formed a complex, were highly co-localized on chromatin, and were required for each-other’s stable recruitment to enhancers. Given the impaired expression of immune synapse genes, it was notable that C+K lymphomas in mice and humans manifested significantly reduced CD8+ T cell abundance. This suggests that deficiency of the two chromatin modifiers cooperatively induced an immune evasive phenotype due to failure to activate key immune synapse super-enhancers, associated with altered immune cell fate decisions. These findings point to the potential need for epigenetic adjuvant therapy to augment reactivity with immunotherapy approaches in patients with C+K deficiency.

overall_design: CapIG-seq (aka, B cell receptor sequencing) for splenic germinal center B cells sorted from lymphoma-bearing mice at day 235 post bone marrow transplant. We sequenced 4 mice replicates for each genotype (i.e., BCL2, BCL2+C, BCL2+K, BCL2+CK)

first: Jie

last: Li

first: Wendy

last: Béguelin

first: Ari

last: Melnick


title: MERTK inhibition for the treatment of tissue fibrosis [CUT&Tag]

city: Westmead

first: Ziyan

last: Pan

state: NSW

address: 176 Hawkesbury Rd

department: Storr Liver Centre

country: Australia

institute: Westmead Institute for Medical Resea

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Fibrosis is a core pathway that drives the progression of multiple chronic diseases for which there is a paucity of safe and effective treatments. In these diseases, transforming growth factor–β (TGF-β)–driven scarring propels disease progression. However, targeting this ubiquitously expressed cytokine is unlikely to yield a viable and safe antifibrotic therapy; thus, identification of alternative mechanisms to inhibit TGF-β signalling is required. We identified Mer tyrosine kinase (MERTK) as a TGF-β–inducible nodal effector of fibrosis that is up-regulated with fibrosis in multiple organs in both mice and humans. MERTK also induces TGF-β expression and promotes it’s signalling resulting in a positive feedback loop that promotes fibrosis. Mechanistically, MERTK regulates both canonical and non-canonical TGFβ signalling. Further downstream, MERTK modulates the fibrotic regulatory gene transcription network by regulating chromatin accessibility, RNA polymerase II (pol II) pausing and reprograming the enhancer landscape. Using mouse models of kidney, lung, and liver fibrosis, we demonstrate that this fibrosis-promoting signalling loop can be interrupted by loss of MERTK expression, leading to marked attenuation of fibrosis. Pharmacologic MERTK inhibition reduced fibrosis either when initiated immediately after injury or when initiated after fibrosis is established. Together, this data suggests that MERTK plays a critical role in modulating organ fibrosis, while small-molecule MERTK inhibitors are an attractive target for the treatment of diseases characterized by fibrosis.

overall_design: Comparative histone modifications profiling analysis of Pol II, CTCF, H3K27ac, H3K4me1, H3K4me3, H3K27me3 in WT and Mertk knockout mice liver samples in liver fibrosis model.

first: Rasha

last: El Sharkway

first: Ali

last: Bayoumi

first: Mayada

last: Metwally

first: Brian

middle: S

last: Gloss

first: Robert

last: Brink

middle: B

last: Lu

last: Liddle

first: Jun

last: Yu

first: Philip

middle: J

last: O'Connell

first: Jacob

last: George

first: Mohammed

last: Eslam


title: PRMT1 promotes pancreatic cancer development and resistance to chemotherapy

status: Public on Mar 09 2024

city: Daejeon

first: Bomin

last: Ku

address: 335 Gwahak-ro

department: Biological Sciences

country: South Korea

institute: Korea advanced institute of science and technology (KAIST)

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal types of cancer, and novel treatment regimens are direly needed. Epigenetic regulation contributes to the development of various cancer types, but its role in the development of, and potential as a therapeutic target for, PDAC remains underexplored. Here, we show that PRMT1 is highly expressed in murine and human pancreatic cancer and is essential for cancer cell proliferation and tumorigenesis. Deletion of PRMT1 delays pancreatic cancer development in a KRAS-dependent mouse model, and multi-omics analyses reveal that the PRMT1 depletion leads to global changes in chromatin accessibility and transcription, resulting in reduced glycolysis and a decrease in tumorigenic capacity. Pharmacological inhibition of PRMT1 in combination with gemcitabine has a synergistic effect on pancreatic tumor growth in vitro and in vivo. Collectively, our findings implicate PRMT1 as a key regulator of pancreatic cancer development and a promising target for combination therapy.

overall_design: ATAC-seq data of PRMT1 knockdown from MiaPaca-2 cells

first: David

last: Eisenbarth

first: Dae-Sik

last: Lim


title: O-GlcNAcylation of CTCF regulates 3D chromatin structure [ChIP-seq]

status: Public on Mar 04 2024

city: Guanghzou

first: Zeng

last: Pengguihang

address: No.74, Zhongshan 2nd Road, Guangzhou, Guangdong

country: China

institute: Sun Yat-Sen University

summary: The goal of this study is to test whether the O-GlcNAcylation of CTCF plays a role in regulating chromatin structure.

overall_design: We used HiC to test the changes of 3D chromtin sttucture after muating the O-GlcNAcylation of CTCF. ChIP-seq was used to test the function of O-GlcNAcylation in CTCF chromatin binding. RNA-seq was perforemed to test the changes of genes expression in same condition. ATAC-seq was used to test the change of the chromatin accessibility.

first: Junjun

last: Ding

first: Xiuxiao

last: Tang

first: Pengguihang

last: Zeng


title: O-GlcNAcylation of CTCF regulates 3D chromatin structure [RNA-seq]


title: O-GlcNAcylation of CTCF regulates 3D chromatin structure

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

overall_design: Refer to individual Series


title: Mesenchymal glioma stem cells trigger vasectasia, a distinct neovascularization process mediated by extracellular vesicles carrying EGFR [scRNA-seq]

city: Montreal

first: Janusz

last: Rak

state: Quebec

address: 1001 Decarie Blvd. Room E01.4366

department: Department of Pediatrics

country: Canada

institute: McGill University

summary:
To investigate the functional role of EGFR in the formation of large vessels, we established a mesenchymal glioma stem cell line (GSC83) with intact EGFR and knocked down EGFR by Crispr-Cas9.
We then performed single cells gene expression profiling analysis using data obtained from RNA-seq of 2 different tumours, derived by injection of GSC83 WT or GSC83 KO in NSG mice. In addition, GSC83 WT or GSC83 KO tumours in NSG mice  were subjected to spatial gene expression profiling in situ using GeoMX platform.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design:
Comparative single cells gene expression profiling analysis of RNA-seq data for 83 wild type EGFR and its EGFR knockdown derivative (GSC83 WT vs. GSC83 KO).
For GeoMX spatial analysis, regions-of-interest were designated using anti-CD31 immunofluorescent tissue staining. Cells within/proximal to CD31-positive areas were profiled for mRNA expression.

first: Cristiana

last: Spinelli

first: Lata

last: Adnani

last: Meehan

first: Laura

last: Montermini

first: Sidong

last: Huang

first: Minjun

last: Kim

first: Tamiko

last: Nishimura

first: Sidney

middle: E

last: Croul

first: Ichiro

last: Nakano

first: Yasser

last: Riazalhosseini


title: MERTK inhibition for the treatment of tissue fibrosis [RNA-seq]

first: Ziyan

last: Pan

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Mertk knockout mice liver, kidney tissue of liver, kidney fibrosis models. Comparative gene expression profiling analysis of RNA-seq data for WT and MERTK inhibitor (UNC569) injection mice liver, kidney, and lung tissue of liver, kidney, and lung fibrosis models.

first: Rasha

last: El Sharkway

first: Ali

last: Bayoumi

first: Mayada

last: Metwally

first: Brian

last: Gloss

first: Robert

last: Brink

last: Lu

first: Christopher

last: Liddle

first: Jun

last: Yu

first: Philip

last: O'Connell

first: Jacob

last: George

first: Mohammed

last: Eslam


title: Insights for disease modeling from single cell transcriptomics of iPSC-derived neurons and astrocytes across differentiation time and co-culture

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

summary: Trans-differentiation of human induced pluripotent stem cells into neurons (hiPSC-N) via Ngn2-induction has become an efficient system to quickly generate neurons for disease modeling and in vitro assay development, a significant step up from previously used neoplastic and other cell lines. Recent single-cell interrogation of Ngn2-induced neurons however, has revealed some similarities to unexpected neuronal lineages. Similarly, a straightforward method to generate hiPSC derived astrocytes (hiPSC-A) for the study of neuropsychiatric disorders has also been described. Here we examine the homogeneity and similarity of hiPSC-N and hiPSC-A to their in vivo counterparts, the impact of different lengths of time post Ngn2 induction on hiPSC-N (15 or 21 days) and of hiPSC-N / hiPSC-A co-culture. We explore how often genes differentially expressed between conditions relate to genetic risk for neuropsychiatric disease. Leveraging the wealth of existing public single-cell RNA-seq (scRNA-seq) data in Ngn2-induced neurons and in vivo data from the developing brain, we provide perspectives on the lineage origins and maturation of hiPSC-N and hiPSC-A. Both show heterogeneity and share similarity with multiple in vivo cell fates, and both cell types more precisely approximate their in vivo counterparts when co-cultured. hiPSC-A show more heterogeneity and similarities to other non-neural cell types, especially when cultured in isolation. Gene expression data from the hiPSC-N show excess of genes linked to schizophrenia (SZ) and autism spectrum disorders (ASD) as has been previously shown for neural stem cells and neurons. These overrepresentations of disease genes are strongest in our system at early times (day 15) in Ngn2-induction/maturation of neurons, which together with our observation of similarities with in vivo neurons earlier in development suggest they may be a better model for neurodevelopmental disorders. We have assembled this new scRNA-seq data along with the public data explored here as an integrated biologist-friendly web-resource for researchers seeking to understand this system more deeply: https://nemoanalytics.org/p?l=DasEtAl2022 .

overall_design: Lymphocyte derived iPS cells from a healthy human were differentiated to excitatory neurons for 15 or 21 days and also to astrocytes. There are 4 conditions and 8 samples analysed here, each from a cell culture well as follows. Neurons at day 21 (sample 1,2), neurons at day 15 (sample 7,8), astrocytes (sample 3,4) and neurons at day 21 mixed with astrocytes (sample 5,6).For detailes and protocols see our publication in bioRxiv 2022.06.15.495952; doi: https://doi.org/10.1101/2022.06.15.495952.

first: D

last: Das

first: S

last: Sonthalia

first: G

last: Stein-O'Brien

first: M

middle: H

last: Wahneh

first: K

last: Feuer

first: L

last: Goff

first: C

last: Colantuoni

first: V

last: Mahairaki


title: MERTK inhibition for the treatment of tissue fibrosis [ATAC-seq]

first: Ziyan

last: Pan

overall_design: Comparative chromatin accessibility profiling analysis of ATAC-seq data for WT and Mertk knockout mice liver, and kidney tissue of liver, kidney fibrosis models.

first: Rasha

last: El Sharkway

first: Ali

last: Bayoumi

first: Mayada

last: Metwally

last: Gloss

first: David


title: O-GlcNAcylation of CTCF regulates 3D chromatin structure [HiC]

first: Zeng

last: Pengguihang

first: Junjun

last: Ding

first: Xiuxiao

last: Tang

first: Pengguihang

last: Zeng


title: O-GlcNAcylation of CTCF regulates 3D chromatin structure [ATAC-seq]


title: Efficient trans-differentiation/ de-differentiation of mature intestinal cells in adult Drosophila midgut by depleting a single transcription factor

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

summary: The manipulation of cell identity by reprograming holds immense potential in regenerative medicine, but is often limited by the inefficient acquisition of fully functional cells. This problem can potentially be resolved by better understanding the reprogramming process using in vivo genetic models, which are currently scarce. Here we report that both enterocytes (ECs) and enteroendocrine cells (EEs) in adult Drosophila midgut show a surprising degree of cell plasticity. Depleting the transcription factor Tramtrack in the differentiated ECs can initiate Prospero-mediated cell transdifferentiation leading to EE-like cells. On the other hand, depletion of Prospero in the differentiated EEs leads to the loss of EE-specific transcription programs, allowing cell cycle re-entry or differentiation into ECs. We found that intestinal progenitor cells, ECs, and EEs have a similar chromatin accessibility profile, suggesting that cell plasticity is enabled by pre-existing chromatin accessibility with switchable transcription programs. In a pilot genetic screen using this system, we found that cell lineage confliction and epigenetic memory were potential barriers during the EC-to-EE transdifferentiation. The establishment of this genetically tractable in vivo model should facilitate mechanistic investigation of cell plasticity at the molecular and genetic level.

overall_design: Chromatin accessibility analysis by ATAC-seq, using FACS sorted normal EC, EE, progenitor and transformed EE-like and progenitor like cells

first: Xingting

last: Guo

first: Yongchao

last: Zhang

first: Ruxue

last: Wei

first: Rongwen

last: Xi


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [ATAC-seq]

status: Public on Mar 01 2024

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro-proliferative mutations. Under these conditions, many cases eventually develop genetic abnormalities endowing them with constitutive NF-κB activation. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a novel p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression.

overall_design: Assay for transposase-accessible chromatin with DNA-sequencing (ATAC-seq) in multiple myeloma cell lines KMS-11 and MM1.144 subjected to p52 knock down.

first: Daniel

middle: A

last: Ang

first: Jean-Michel

last: Carter

first: Kamalakshi

last: Deka

first: Joel

last: Tan

first: Jianbiao

last: Zhou

first: Qingfeng

last: Chen

first: Wee

last: Chng

first: Nathan

last: Harmston


title: Ex vivo lung perfusion with dialysis in pig (timepoints T0H, T6H and T12H)

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

summary: Ex vivo lung perfusion (EVLP) has extended the number of transplantable lungs by reconditioning marginal organs. However EVLP is performed at 37°C without homeostatic regulation leading to metabolic wastes accumulation in the perfusate, and as a corrective measure, the costly perfusate is repeatedly replaced during the standard of care procedure. As an interesting alternative, a hemodialyzer could be placed on the EVLP circuit, that was previously shown to rebalance the perfusate composition, maintain lung function and viability without appearing to impact the global gene expression in the lung. Here, we assessed the biological effects of a hemodialyzer during EVLP by performing biochemical and refined functional genomic analyses over a 12 h procedure in a pig model. We found that dialysis stabilized electrolytic and metabolic parameters of the perfusate but enhanced the gene expression and protein accumulation of several inflammatory cytokines, and promoted a genomic profile predicting higher endothelial activation already at 6 h and immune cytokine signaling at 12 h. Therefore epuration of EVLP with a dialyzer, while correcting features of perfusate composition and maintaining respiratory function, promotes inflammatory responses in the tissue. This finding suggests that modifying the metabolite composition of the perfusate by dialysis during EVLP can have detrimental effects on the tissue response and that this strategy should not be transferred as such to the clinic.

overall_design: 2 groups : Gold standard EVLP (GS ; 5 pigs)  vs Pediattric dialysis (PD ; 4 pigs) - 3 timepoints : T0H, T6H and T12H

first: Julien

last: de Wolf

first: Carla

last: Gouin

first: Luc

last: Jouneau

first: Yan

last: Jaszczyszyn

first: Yannick

last: Marie

first: Isabelle

last: Schwartz


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [RNA1]

overall_design: RNA-sequencing (RNA-seq) of multiple myeloma cell lines KMS-11 and MM1.144 subjected to p52 knock down.


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the transcription factor p52 and the histone modification H3K27ac in multiple myeloma cell lines (MMCL): MM1.144, U266, KMS-11, MM1.S, JJN3 and LP1 as well as H3K27ac ChIP-seq for three MMCLs subjected to p52 knock down: KMS-11, MM1.144 and LP1. Control inputs for each MMCL are provided except MM1.144.


title: Heat-Resistant Inbred Lines Coordinate the Heat Response Genes Expression Remarkably in Maize

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

summary: High temperature is increasingly becoming one of the prominent environmental factors affecting the growth and development of maize (Zea mays L.). Therefore, it is critical to identify key genes and pathways related to heat stress (HS) tolerance in maize. Here, we identified a heat-resistant (Z58D) and heat-sensitive (AF171) maize inbred lines at seedling stage. Transcriptomic analysis identified 3,006 differentially expressed genes (DEGs) in AF171 and 4,273 DEGs in Z58D under HS treatments, respectively. Subsequently, GO enrichment analysis showed that shared upregulated genes in AF171 and Z58D involved in response to HS, protein folding, abiotic and temperature stimulus pathway. Moreover, the comparison between the two inbred lines under HS showed that response to heat and response to temperature stimulus significantly overrepresented for the 1,234 upregulated genes. Furthermore, commonly upregulated genes in Z58D and AF171 had higher expression level in Z58D than AF171. In addition, maize inbred CIMBL55 had been verified to be more tolerant than B73 and commonly upregulated genes  had higher expression level in CIMBL55 than B73 under HS. The consistent results indicated that heat-resistant inbred lines may coordinate the remarkable expression of genes in order to recover from HS. Additionally, 35 DEGs were conserved among 5 inbred lines by a comparative transcriptomic analysis. Most of them were more pronounced in Z58D than AF171 at expression level. Those candidate genes may confer thermotolerance in maize.

overall_design: Sequencing data of leaf of heat-sensitive and heat-resistant line under normalcondition and heat stress condition

first: Ming

last: Xue

first: Xiaoyue

last: Han

first: Luyao

last: Zhang

first: Saihua


title: Autophagy-enhancing ATG16L1 polymorphism improves clinical outcomes and promotes superior T-cell immunity in chronic HIV-1 infection

city: Amsterdam

last: Ribeiro

address: Meibergdreef 9

department: Experimental Immunology

country: Netherlands

institute: Amsterdam UMC

summary: Chronic HIV-1 infection is characterized by T-cell dysregulation that is partly restored by antiretroviral therapy. Autophagy is a critical regulator of T-cell function. Here, we demonstrate a protective role for autophagy in HIV-1 disease pathogenesis. Targeted analysis of genetic variation in core autophagy gene ATG16L1 revealed the previously unidentified rs6861 polymorphism, which correlated functionally with enhanced autophagy and clinically with improved survival of untreated HIV-1-infected individuals. T cells carrying ATG16L1 rs6861(TT) genotype displayed superior antiviral immunity, evidenced by increased proliferation, revamped immune responsiveness and suppressed exhaustion/immunosenescence features. In-depth flow-cytometric and transriptional profiling revealed T-helper-cell-signatures unique to rs6861(TT) individuals with enriched regulation of pro-inflammatory networks and skewing towards immunoregulatory phenotype. Therapeutic enhancement of autophagy recapitulated the rs6861(TT)-associated traits in non-carriers. These data underscore the in vivo relevance of autophagy for longer-lasting T-cell-mediated HIV-1 control, with implications towards development of host-directed antivirals targeting autophagy to restore immune function in chronic HIV-1 infection.

overall_design: We performed differential gene expression and gene-set enrichment analyses using data obtained from RNA-seq of fluorescence-activated cell-sorted T cells (CD3+CD4+CD8-) from n=4 rs6861(TT) n=4 rs6861(CC) genotyped individuals under 4 conditions (untreated [steady-state], or stimulated with anti-CD3/anti-CD28, anti-CD3/anti-CD28/IL-15, or anti-CD3/anti-CD28/IL-7 for 16 hours).

first: Renee

middle: R

last: Schreurs

first: Athanasios

last: Koulis

first: Thijs

last: Booiman

first: Brigitte

last: Boeser-Nunnink

first: Alexandra

middle: P

last: Cloherty

first: Anusca

middle: G

last: Rader

first: Kharishma

last: Patel

first: Neeltje

last: Kootstra

middle: M


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [HICHIP]

first: Yinghui

last: Li

overall_design: In situ chromatin conformation capture followed by chromatin immunoprecipitation DNA-sequencing for the histone modification H3K27ac (H3K27ac HiChIP) in multiple myeloma cell line KMS-11 subjected to p52 knock down.

first: Daniel

last: Ang

first: Jean-Michel

last: Carter

first: Kamalakshi

last: Deka

first: Joel

last: Tan

first: Jianbiao

last: Zhou

first: Qingfeng

last: Chen

first: Wee

last: Chng

first: Nathan

last: Harmston


title: Temporal and sex‑dependent gene expression patterns in a renal ischemia–reperfusion injury and recovery pig model

status: Public on Mar 02 2024

city: San Sebastian

first: Stéphane

last: Nemours

state: Guipúzcoa

address: Paseo Dr. Begiristain, s/n

country: Spain

institute: Biogipuzcoa

summary: Men are more prone to acute kidney injury (AKI) and chronic kidney disease (CKD), progressingto end-stage renal disease (ESRD) than women. Severity and capacity to regenerate after AKI are important determinants of CKD progression, and of patient morbidity and mortality in the hospital setting. To determine sex diferences during injury and recovery we have generated a female and male renal ischemia/reperfusion injury (IRI) pig model, which represents a major cause of AKI.  This study was conducted using farm pigs, hybrids between Large White and Landrace. Five females and five males of four months old, free of specifc pathogens, between 30 and 40 kg of weight were included in this study. This age range was chosen due to the sexual maturity of the animal, allowing hormone efects. Using microarray assays, global transcriptomic analyses of kidney biopsies from this IRI pig model was conducted and revealed a sexual dimorphism in the temporal regulation of genes and pathways relevant for kidney injury and repair. Overall, this study constitutes an extensive characterization of the time and sex diferences occurring during renal IRI and recovery at gene expression level.

overall_design: On the frst day of surgery, expert urology surgeons from the team practiced a laparoscopic lef nephrectomy followed by 30 min of warm ischemia in the right kidney. The lef kidney was defned as control tissue at basal state (PR), clear form injury. By performing a lef nephrectomy, the compensation of the other kidney to maintain renal function during ischemia–reperfusion injury was prevented. Upon ischemia, the lower pole of the kidney was removed (approximately 3  cm of kidney parenchyma) and afer suturing, and 5 more minutes of arterial reperfusion, an upper polar biopsy was obtained (approximately 1 cm of renal parenchyma). Animals were housed until day 7-post surgery, when a laparoscopic nephrectomy of the right kidney was performed. Pigs were then euthanized at that point. Overall, three kidney biopsies were collected for each animal: prior to injury (PR), 5 min following 30 min of ischemia (PS) and one week afer ischemia (WL).  RNA was extracted from the PR, PS and WL kidney biopsies from each animal. The extractions were performed starting from 50 mg of each biopsy performed with the NZyol Kit following manufacturer instructions (Nzytech genes & enzymes). Microarray hybridization was carried out at High Technology Unit (UAT) at the Vall d'Hebron Research Institute . RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, Ca). Only samples with similar RNA integrity number were accepted for microarray analysis. Gene Titan Afymetrix microarray platform and the Genechip Porcine Gene 2.1 ST 16-Array plate were used for this experiment.

first: Anna

last: Meseguer


title: KPT-330-modulated cold adaptation in various thermogenic organs of prediabetic mice

city: Guangzhou

first: Liu

last: Yasong

address: Tianhe District Tianhe Road, No. 600

institute: Third Affiliated Hospital Of Sun Yat-Sen University

summary: Transcriptomic analysis on white adipose tissues (WAT), brown adipose tissues (BAT), skeletal muscles and liver from cold-exposed obese mice treated with KPT-330 or DMSO, and those from obese mice housed at ambient temperature indicated that KPT-330 profoundly modulates immune responses in these thermogenic tissues and organs.

overall_design: To understand how KPT-330 elicits protective effects against acute cold exposure, Epididymal WAT, BAT, thigh skeletal muscle, and liver samples were collected and snap frozen in liquid nitrogen

first: Jingxing

last: Ou

first: Xiaomei

last: Zhang

first: Guanghui

last: Jin

first: Yasong

last: Liu


title: GAS41 modulates ferroptosis by anchoring NRF2 on chromatin

city: New York

first: Xin

last: Yang

address: 1130 Saint Nicholas Ave, ICRC building

department: Institute for Cancer Genetics

institute: Columbia University

summary: Here, through genome-wide CRISPR-Cas9 screenings, we identified GAS41, a well-known histone reader as a major repressor for ferroptosis. GAS41 interacts with NRF2 and is critical for NRF2 to activate its targets such as SLC7A11 for modulating ferroptosis. By recognizing the H3K27-acetylation (H3K27-ac) marker, GAS41 is recruited to the SLC7A11 promoter independent of NRF2 binding. Notably, by bridging the interaction between NRF2 and the H3K27-ac marker, GAS41 acts as an anchor for NRF2 on chromatin in a promoter-specific manner for transcriptional activation. Moreover, the GAS41-mediated effect on ferroptosis contributes significantly to its oncogenic role in vivo. These data demonstrate that GAS41 is an important target for modulating tumor growth through ferroptosis. Our study reveals a previously unanticipated mechanism for GAS41-mediated regulation in transcription by anchoring NRF2 on chromatin and provides a model that the DNA binding activity on chromatin by transcriptional factors (NRF2) can be directly regulated by histone markers (H3K27-ac).

overall_design: The CUT&RUN experiments were conducted in WT or GAS41 KO A549 cells. The commercial NRF2 antibody used CUT&RUN is purchased from Abcam (#62352)

first: Zhe

last: Wang

first: Wei

last: Gu


title: Generation of marmoset primordial germ cell-like cells under chemically defined conditions

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

country: Germany

institute: University of Goettingen

summary: Primordial germ cells (PGCs) are the embryonic precursors of sperm and oocytes and are responsible for the transmission of genetic and epigenetic information across generations. The development of mouse gametes from PGCs can be reconstituted from pluripotent stem cells in vitro, opening up new avenues for the study of germ cell biology in biomedical research. However, the development of germ cells exhibits molecular and morphological differences between rodents and humans. Therefore, to establish an in vitro model system that is closely related to humans, we studied PGC development in vivo and in vitro in the common marmoset Callithrix jacchus (cj), a New World monkey. Post-migratory cjPGCs in gonads at embryonic day 74 express the germ cell-related genes SOX17, AP2Ɣ, BLIMP1 and the pluripotency markers NANOG and OCT4A (POU5F1), which is reminiscent of human PGCs. We established transgene-free induced pluripotent stem cell (cjiPSC) lines from foetal and postnatal fibroblasts. These cjiPSCs, cultured in a defined medium and in feeder-free conditions, can be differentiated into precursors of mesendoderm and subsequently into cjPGC-like cells (cjPGCLCs) with a transcriptome similar to human PGCs/PGCLCs. Our results not only pave the way to study PGC development in a non-human primate in vitro under experimentally controlled conditions without foetal calf serum and feeder cells, but also provide the opportunity to derive functional marmoset gametes in vitro in future studies.

overall_design: Two biological replicates of each cell type analyzed: iPSCs cultured in different media (TESR and cjPSCM), Precursor of mesendoderm induced with or without Activin A, CXCR4&INTalpha6 double-positive and double-negative cells from day 4 embryoid bodies

first: Julia

last: Kurlovich

first: Ignacio

last: Rodriguez Polo

first: Oleksandr

last: Dovgusha

first: Yuliia

last: Tereshchenko

first: Carmela Rieline

middle: V

last: Cruz

first: Rüdiger

last: Behr


title: Single-cell gene expression profiling of SOXC-mutant bone and bone marrow cells

city: Philadelphia

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

institute: The Children's Hospital of Philadelphia Research Institute

summary: SOXC genes (i.e., SOX4, SOX11 and SOX12) encode for transcription factors controlling survival, proliferation, commitment and differentiation of several cell types from development onwards. Although human diseases indicate crucial roles for SOXC in bone development and maintenance, SOXC activities in osteoblastic cells remain elusive. Here, we used a mouse model to inactivate SOXC genes in the osteoblast lineage cells using an OsxCre transgene (Sox4fl/fl Sox11fl/fl Sox12fl/fl OsxCre mice referred to as SOXCOsxCre mice) and we used single-cell RNA-sequencing assays to characterize gene expression changes in bone and bone marrow cells in adulthood.

overall_design: Femurs and tibiae were collected from 7- and 13-week-old female SOXCOsxCre and control mice (2 mice per genotype and age). After periosteum removal and bone marrow flushing, bones were digested with LiberaseTM and EDTA to release bone and endosteal bone marrow cells. Hematopoietic cells were removed by immunomagnetic sorting, while remaining cells were used for scRNA-seq analysis.

first: Marco

last: Angelozzi


title: Reprograming human fibroblasts into Sertoli cells:  a tool for personalized medicine

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

summary: Differences of Sex Development (DSD) are a set of conditions where development of chromosomal, gonadal, or anatomical sex is atypical. With overlapping phenotypes and multiple genes involved, poor diagnostic yields are achieved for many of these conditions. The current DSD diagnostic regimen can be augmented by investigating transcriptome/proteome in vivo, but it is hampered by the unavailability of affected gonadal tissue at the relevant developmental stage. We try to mitigate this limitation by reprogramming readily available skin tissue-derived dermal fibroblasts into Sertoli cells (SC), which could then be deployed for different diagnostic strategies. SCs form the target cell type of choice because they act like an organizing center of embryonic gonadal development and many DSD arise when these developmental processes go awry. Methods: We employed a computational predictive algorithm for cell conversions called Mogrify to predict the transcription factors (TFs) required for direct reprogramming of human dermal fibroblasts into SCs. We established trans-differentiation culture conditions where stable transgenic expression of these TFs was achieved in 46, XY adult dermal fibroblasts using lentiviral vectors. The resulting Sertoli like cells (SLCs) were validated for SC phenotype using several approaches.  Results: SLCs exhibited Sertoli-like morphological and cellular properties as revealed by morphometry and xCelligence cell behavior assays. They also showed Sertoli-specific expression of molecular markers such as SOX9, PTGDS, BMP4, or DMRT1 as revealed by IF imaging, RNAseq and qPCR. The SLC transcriptome shared about two thirds of its differentially expressed genes with a human adult SC transcriptome and expressed markers typical of embryonic SCs. Notably, SLCs lacked expression of most markers of other gonadal cell types such as Leydig, germ, peritubular myoid or granulosa cells.  Conclusions: The trans-differentiation method was applied to a variety of commercially available 46, XY fibroblasts derived from patients with DSD and to a 46, XX cell line. The DSD SLCs displayed altered levels of trans-differentiation in comparison to normal 46, XY-derived SLCs, thus showcasing the robustness of this new trans-differentiation model.

overall_design:
To investigate the molecular mechanism underlying the cellular reprogramming of of human fibroblast cells to sertoli like cells, we performed differential expression analysis between control male  (46,XY) fibroblast treated  with 2 different Transcription Factor (TF) sets (6TF and 8TF) independently and their Wild type (GFP).
To further investigate the effects of the cellular reprogramming in affected 46,XY cell lines (WT1 deletion, 46,XY female, and campomelic dysplasia) and a control female sample (46,XX), we performed differential expression,  between samples treated with 6TF and 8TF independently, and their respective no treatment (GFP) control.

first: Abhinav

last: Parivesh

first: Emmanuèle

middle: C

last: Délot

first: Alejandra

last: Reyes

first: Janelle

last: Ryan

first: Surajit

last: Bhattacharya

first: Vincent

last: Harley

first: Eric

last: Vilain


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [RNA2]

first: Yinghui

last: Li

overall_design: RNA-sequencing (RNA-seq) of CD138 positive plasma cells purified from BM aspirates obtained from multiple myeloma patients.

first: Daniel

last: Ang

first: Jean-Michel

last: Carter

first: Kamalakshi

last: Deka

first: Joel

last: Tan

first: Jianbiao

last: Zhou

first: Qingfeng

last: Chen

first: Wee

last: Chng

first: Nathan

last: Harmston


title: Genomic analyses of H1 cells induced by FOXO1

first: Liu

last: Yasong

summary: Insufficient understanding on cold adaptation technically restricts donor tissue banking. Here we identify FOXO1 as a conserved transcription factor for cell cold survival, relocating from cytosol to nucleus when temperature drops. FOXO1 small ubiquitin-like modifiers (SUMO) -interacting motif (SIM) antagonizes FOXO1-Importin-7 interaction regardless of temperature. At 37°C, SIM enhances FOXO1 interactions with SUMO E3 ligase RANBP2 and Exportin-1, FOXO1 hence cytoplasmic; at 4°C, FOXO1-Importin-7 interaction increases probably via RANBP2, making FOXO1 nuclear. These features enable fine-tuned FOXO1 regulations on chromatin folding and subsequent gene expression. Using these key factors as readouts, a ‘hibernation solution’ was developed, enabling long-term pancreatic islet cold storage and transplantation to cure diabetes. Henceforth, targeting FOXO1 SIM or the SUMO machinery may aid tissue/organ survival from long-term cold and other stresses.

overall_design: Examination of FOXO1 binding in H1 cells, including two replicates in H1.

first: J

last: Ou

first: X

last: Zhang

first: Y

last: Liu

first: W

last: Yang


title: Chromatin Landscape Analysis of H1 cells with different temperature.

overall_design: Examination of Chromatin Landscape in H1 cells, including two replicates.


title: Tgfb in AT1 cells

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Premature birth disrupts normal lung development and places infants at risk for bronchopulmonary dysplasia (BPD), a disease increasing in incidence which disrupts lung health throughout the lifespan. The TGFβ superfamily has been implicated in BPD pathogenesis, however, what cell lineage it impacts remains unclear. We show that the primary TGFβ receptor, Tgfbr2, is critical for AT1 cell fate maintenance and function. Loss of Tgfbr2 in AT1 cells during late lung development leads to AT1-AT2 cell reprogramming and altered pulmonary architecture, which persists into adulthood. Restriction of fetal lung stretch and associated AT1 cell spreading through a model of oligohydramnios enhances AT1-AT2 reprogramming. Transcriptomic and proteomic analysis reveal that expression of extracellular matrix components by AT1 cells is attenuated with loss of Tgfbr2. Cell spreading assays shows that TGFβ signaling regulates integrin transcription to alter AT1 cell morphology, which further impacts ECM expression through changes in mechanotransduction. These data reveal the cell intrinsic necessity of TGFβ signaling to maintain AT1 fate and define this cell lineage as a major orchestrator of the alveolar matrisome, which, if altered, may predispose to BPD.

overall_design: To determine the role of Tgfbr2 in AT1 cells, we generated HopxCreERT2+/-;Tgfbr2 fl/+; eYFP-/-  and HopxCreERT2+/-;Tgfbr2 fl/fl; eYFP-/- mice, allowing us to inactivate one or two copies of Tgfbr2 in AT1 cells and trace their fate from P0 to P5.

first: Danielle

last: Callaway

first: Apoorva

last: Babu

first: Edward

last: Morrisey


title: Deficiency of lncRNA MERRICAL abrogates macrophage chemotaxis and alleviates diabetes-associated atherosclerosis

city: Boston

first: Jingshu

address: 77 Avenue Louis PasteurBoston

department: Medicine

institute: Harvard Medical School

summary: 1) Differential gene expression profiling of bone marrow derived macrophage treated with GapmeR NS (control) or MERRICAL (KD) in both M0 and M1 phase

overall_design: M0 and M1 phase bone marrow derived macrophage was treated with GapmeR (NS) and (MERRICAL) for 16 hours, and RNA was collected to compare the transcriptome difference between KD and NS.

first: Mark

middle: W

last: Feinberg


title: An endosomal toll-like receptor inhibitor drug with therapeutic effects in autoimmune diseases

status: Public on Feb 29 2024

city: Suwon-si

first: Uisuk

last: Jeong

state: Gyeonggi-do

address: 206, World cup-ro

department: Molecular Science and Engineering

institute: Ajou university

summary: Autoimmune disease is a systemic inflammatory response of immune blood cells caused by self-tolerance dysfunction, due to genetic or environmental factors or a combination thereof. Studies on autoimmune disease regarding the inhibition of toll-like receptor (TLR)7/9-MyD axis or the regulation of plasmacytoid dendritic cells (pDCs) and Th17 comprising an abundance of respective receptors have shown improvements in phenotypes or molecular markers, providing clues to the practicality of the inhibitors of endosomal TLRs. This study discovered several small-molecule compounds in endosomes exerting specific inhibitory effects on SITE1 shared among TLR 3, 7, 8, and 9, named endosomal TLR inhibitors (ETIs). The drug discovery process involved identifying lead compounds optimized to the receptors using a quantitative structure-activity relationship model and subsequent modification of the compounds to improve their binding affinity to target proteins. To propose a method of verifying the drug effects against side or placebo effect arising from false positives, the drug evaluation process converged from cellular response to signaling process to protein binding. Drug values on the inhibition of endosomal TLRs in autoimmune disease were assessed based on the onset of mild-to-life-threatening autoimmune disease including psoriasis, systemic lupus erythematosus, and multiple sclerosis. Complete healing was achieved for psoriasis through direct or indirect association with TLRs. Therapeutic potential of the novel ETIs for psoriasis was verified and is considered an effective drug for other autoimmune diseases associated with the TLR7/9-MyD axis.

overall_design: Gene expression profiling analysis of RNA-seq data to verify the effect of ETI41 or ETI60 treatment in TLR7 activation situation

first: Yangseon

last: Choi

first: Hongjun

first: Muhammad

last: Haseeb

first: Mahesh

last: Patra

first: Sangdun


title: Myeloid-derived suppressor cells mitochondrial fitness governs chemotherapeutic efficacy in hematologic malignancies

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Myeloid derived suppressor cells (MDSCs) are key regulators of immune responses and correlated with poor outcomes in hematologic malignancies.  Here, we identify the mitochondrial fitness in MDSCs controlling the efficacy of doxorubicin chemotherapy for lymphoma.  Mechanistically, we show that triggering STAT3 signaling via β2-adrenergic receptor (β2-AR) activation leads to metabolic reprograming of MDSCs, marked by sustained mitochondrial respiration (OX/PHOS) and higher ATP generation which reduces the AMPK signaling. Furthermore, induced STAT3 signaling in MDSCs enhanced glutamine consumption via the tricarboxylic acid (TCA) cycle.  Metabolized glutamine generates itaconate which downregulates mitochondrial reactive oxygen species (mROS) via regulation of nuclear factor erythroid 2-related factor 2 (Nrf2) and the antioxidant machinery.  We found that targeting the STAT3 pathway or ATP/Itaconate metabolites by blocking β2-AR signaling, the electron transport chain and ATP generation, or itaconate generation, results in disrupted MDSC mitochondrial fitness. This disruption increases the in vivo response to doxorubicin, delaying lymphoma progression.

overall_design: WT and β2AR-/- MDSCs were generated in vitro in presence of rmIL-6 and rmGM-CFS (40 ng/mL each) and 10 µM isoproterenol (ISO).  On day 4, single cell libraries were generated using the 10X Genomics platform.  First, Feature Barcode conjugated molecules were bound to cell surface proteins.  Then live-CD11b+ cells were isolated using the SONY MA900 cell sorter (Sony Biotechnology).  Sorted cells were subjected to scRNA-Seq.

first: Saeed

last: Daneshmandi

first: Hemn

last: Mohammadpour


title: A Negative Feedback Loop Between TET2 and Leptin in Adipocyte Regulates Body Weight

city: Changsha

first: Qin

last: Zeng

address: Renmin Middle Road

institute: The Second Xiangya Hospital of Central South University

summary: Ten-eleven translocation (TET) 2 is an enzyme that catalyzes DNA demethylation to regulate gene expression by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine, functioning as an essential epigenetic regulator in various biological processes. However, the regulation and function of TET2 in adipocytes during obesity are poorly understood. In this study, we demonstrate that leptin, a key adipokine in mammalian energy homeostasis regulation, suppresses adipocyte TET2 levels via JAK2-STAT3 signaling. Adipocyte Tet2 deficiency protects against high-fat diet-induced weight gain by reducing leptin levels and further improving leptin sensitivity. By interacting with C/EBPα, adipocyte TET2 increases the hydroxymethylcytosine levels of the leptin gene promoter, thereby promoting leptin gene expression. A decrease in adipose TET2 is associated with obesity-related hyperleptinemia in humans. Inhibition of TET2 suppresses the production of leptin in mature human adipocytes.Our findings support the existence of a negative feedback loop between TET2 and leptin in adipocytes and reveal a novel compensatory mechanism for the body to counteract the metabolic dysfunction caused by obesity.

overall_design: Chromatin Immunoprecipitation DNA sequencing (ChIP-seq) for TET2 in differentiated primary adipocytes.

first: Tuo

last: Deng

first: Jianfeng

last: Song


title: The RANBP2/Importin-7-FOXO1 axis provides superior cold protection to aid islet transplantation

first: Liu

last: Yasong

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Hif1a-deficient sympathetic system and maternal diabetes exposure reprogram the developing heart

city: Vestec

first: Valéria

last: Fabríciová

address: Průmyslová 595

country: Czech Republic

institute: Institute of biotechnology CAS

summary: Maternal diabetes is a recognized risk factor for both short-term and long-term complications in offspring. Beyond the direct teratogenicity of maternal diabetes, the intrauterine environment can influence offspring cardiovascular health. Abnormalities in the cardiac sympathetic system are implicated in conditions such as sudden infant death syndrome, cardiac arrhythmic death, heart failure, and certain congenital heart defects in children from diabetic pregnancies. However, the mechanisms by which maternal diabetes affect the development of the cardiac sympathetic system and consequently, heightening health risks and predisposing to cardiovascular disease remain poorly understood. In this study, we present a comprehensive analysis of the combined impact of a Hif1a-deficient sympathetic system and the maternal diabetes environment on both heart development and the formation of the cardiac sympathetic system. The synergic negative effect of exposure to maternal diabetes and Hif1a deficiency resulted in the most pronounced deficit in cardiac sympathetic innervation and the development of adrenal medulla. Abnormalities in the cardiac sympathetic system were accompanied by a smaller heart, reduced ventricular wall thickness, dilated subepicardial veins, and coronary arteries in the myocardium, along with anomalies in the branching and connections of the main coronary arteries. Transcriptional profiling by RNA-seq revealed significant transcriptome changes in Hif1a-deficient sympathetic neurons, primarily associated with cell cycle regulation, proliferation, and mitosis, explaining the shrinkage of the sympathetic neuron population. Our data demonstrate that a failure to adequately activate HIF-1α regulatory pathway, particularly in the context of maternal diabetes, may contribute to abnormalities in the cardiac sympathetic system. In conclusion, our findings indicate that the interplay between deficiencies in the cardiac sympathetic system and subtle structural alternations in the vasculature, microvasculature, and myocardium during heart development not only increases the risk of cardiovascular disease but also diminishes the adaptability to the stress associated with the transition to extrauterine life, thus, increasing the risk of neonatal death.

overall_design: Hif1a plays important role in development of cardiac sympathetic innervation.To analyze changes resulting from elimination of Hif1a in sympathetic neurons we established mouse model of conditional knockout (Hif1aCKO). We evaluated embryos at age E14.5 Hif1aCKO (genotype Isl1 tm1(cre)Sev/+;Hif1a loxP/loxP) and controls (genotype Hif1a loxP/+ or Hif1a loxP/loxP without the Isl1-Cre).

first: Hana

last: Kolesova

first: Petra

last: Hrabalova

first: Romana

last: Bohuslavova

first: Pavel

last: Abaffy

first: Valeria

last: Fabriciova

first: David

last: Sedmera

first: Gabriela

last: Pavlinkova


title: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma

first: Yinghui

last: Li


title: Reactivation of memory-encoding dentate gyrus neurons during memory consolidation is associated with subregion-specific, learning- and sleep-mediated biosynthetic changes [spatial RNA expression level]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Post-learning sleep plays an important role in hippocampal memory processing, including contextual fear memory (CFM) consolidation. Here, we used targeted recombination in activated populations (TRAP) to label context-encoding engram neurons in the hippocampal dentate gyrus (DG) and assessed reactivation of these neurons during post-learning sleep. We find that post-learning sleep deprivation (SD), which impairs CFM consolidation, selectively disrupts reactivation in inferior blade DG engram neurons. This change was linked to more general suppression of neuronal activity markers in the inferior, but not superior, DG blade by SD. To further characterize how learning and subsequent sleep or SD affect these (and other) hippocampal subregions, we used subregion-specific spatial profiling of transcripts and proteins. We found that transcriptomic responses to sleep loss differed greatly between hippocampal regions CA1, CA3, and DG inferior blade, superior blade, and hilus. Critically, learning-driven transcriptomic changes, measured 6 h following contextual fear learning, were limited to the two DG blades, differed dramatically between the blades, and were absent from all other regions. Similarly, protein abundance in these hippocampal subregions were differentially impacted by sleep vs. SD and by prior learning, with the majority of alterations to protein expression restricted to DG. Together, these data suggest that the DG plays an essential role in the consolidation of hippocampal memories, and that the effects of sleep and sleep loss on the brain are highly subregion-specific, even within the DG itself.

sample_organism:
Mus musculus
blank sample

platform_organism:
Mus musculus
blank sample

overall_design: This dataset contains RNA expression levels from spatially resolved regions of interest (ROIs) of mice that received CFC+sleep, CFC+SD, No_CFC+Sleep (Home Cage+Sleep), and No_CFC+SD (Home Cage+SD). ROIs were collected from both hemispheres of the brain, including 5 different subregions of the brain (CA1, CA3, DG-superior blade, DG-inferior blade, and DG-hilus).

first: Lijing

first: Lauren

last: Park

first: Weisheng

last: Wu

first: Dana

last: King

first: Alexis

last: Medina

first: Frank

last: Raven

first: Jessy

last: Martinez

first: Amy

last: Ensing

first: Katherine

last: McDonald

first: Zhongying

last: Yang

first: Sha

last: Jiang

first: Sara

last: Aton


title: Reactivation of memory-encoding dentate gyrus neurons during memory consolidation is associated with subregion-specific, learning- and sleep-mediated biosynthetic changes [spatial protein expression level]

overall_design: This dataset contains protein expression levels from spatially resolved regions of interest (ROIs) of mice that received CFC+sleep, CFC+SD, No_CFC+Sleep (Home Cage+Sleep), and No_CFC+SD (Home Cage+SD). ROIs were collected from both hemispheres of the brain, including 5 different subregions of the brain (CA1, CA3, DG-superior blade, DG-inferior blade, and DG-hilus).

last: Wang


title: Uterine macrophages and NK cells exhibit population-and gene-level changes after implantation but maintain pro-invasive properties

first: James

last: Garifallou

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Prior to pregnancy, hormonal changes lead to cellular adaptations in the endometrium allowing for embryo implantation. Critical for successful pregnancy establishment, innate immune cells constitute a significant proportion of uterine cells prior to arrival of the embryo and throughout the first trimester in humans and animal models. Abnormal uterine immune cell function during implantation is believed to play a role in multiple adverse pregnancy outcomes. Current work in humans has focused on uterine immune cells present after pregnancy establishment, and limited in vitro models exist to explore unique functions of these cells. With single-cell RNA-sequencing (scRNAseq), we comprehensively compared the human uterine immune landscape of the endometrium during the window of implantation and the decidua during the first trimester of pregnancy. We uncovered global and cell-type-specific gene signatures for each timepoint. Immune cells in the endometrium prior to implantation expressed genes associated with immune metabolism, division, and activation. In contrast, we observed widespread interferon signaling during the first trimester of pregnancy. We also provide evidence of specific inflammatory pathways enriched in pre- and post-implantation macrophages and natural killer (NK) cells in the uterine lining. Using our novel implantation-on-a-chip (IOC) to model human implantation ex vivo, we demonstrate for the first time that uterine macrophages strongly promote invasion of extravillous trophoblasts (EVTs), a process essential for pregnancy establishment. Pre- and post-implantation uterine macrophages promoted EVT invasion to a similar degree as pre- and post-implantation NK cells on the IOC. This work provides a foundation for further investigation of the individual roles of uterine immune cell subtypes present prior to embryo implantation and during early pregnancy, which will be critical for our understanding of pregnancy complications associated with abnormal trophoblast invasion and placentation.

overall_design: Sort-purified CD45+ cells from mid-secretory (implantation window) endometrium were compared to Sort-purified CD45+ cells from first-trimester elective termination decidua

first: Sneha

last: Mani

first: Se-jeong

last: Kim

first: Michael

middle: K

last: Simoni

first: Dan

middle: D

last: Huh

first: Scott

last: Gordon

first: Monica

last: Mainigi


title: Studying human embryonic stem cell reveals molecular mechanisms of cold resistance

first: Liu

last: Yasong

summary: we investigated transcriptomes of  H1 ESCs in the response to cold treatment.

overall_design: Cultures of human embryonic stem cell in three conditions : 37 °C ctrl, 4 °C  for 4 hours, and 37 °C 2h after 4 °C for 4 hours. The  H1 ESCs have four celllines. Totally, we obtained 12 transcriptomes, including 4 replicates of human_4c_4h, 4 of human_37c, and 4 of human_4c_4h_37c_2h.

first: J

last: Ou

first: X

last: Zhang

first: Y

last: Liu

first: W


title: Genome-wide transcriptome and epigenome data analysis of kaku4-2 mutant and WT plants

city: Beijing

first: Zhen

last: Su

address: #2 Yuanmingyuan Xilu

department: College of Biological Sciences

institute: China Agricultural University

summary: We conducted ChIP-seq technology to generate epigenomic profiles of H3K4me3, H3K27me3 and H3K9me2 in Arabidopsis leaves for the mutant (kaku4-2) and wild-type (WT) plants. The results showed that knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least effect on H3K4me3, leading to significant change of chromatin states in Arabidopsis genome. KAKU4 may affect the switch between active and repressive chromatin states, especially knockdown of KAKU4 caused the transition between H3K9me2 and H3K27me3 in some specific PLAD regions. The combination analysis of epigenomic and transcriptomic data between kaku4-2 mutant and WT suggested that KAKU4 may regulate some key biological processes, especially programmed cell death and hormone signaling pathways.

overall_design: The ChIP-seq analyses of H3K4me3, H3K27me3 and H3K9me2 were conducted using the 4th-week rosette leaves of kaku4-2 mutant and WT. Rosette leaves of the 30-day-old kaku4-2 mutant and WT plants were sampled for RNA-seq with three independent biological replicates.

first: Yaxin

last: Cao

first: Hengyu

last: Yan

first: Minghao

last: Sheng

first: Wenying

last: Xu


title: Utilization of Tagged Transgenic Mouse Lines to Study the Molecular Roles of SMAD1/5 in Mediating Signaling Crosstalk During Early Pregnancy II

city: Houston

first: Martin

last: Matzuk

state: TX

address: One Baylor Plaza

department: Pathology and Immunolodgy

institute: Baylor College of Medicine

summary: In this study, we generated two novel transgenic mouse lines with HA- or PA- affinity tags in the SMAD1 and SMAD5 loci (Smad1HA/HA and Smad5PA/PA) to define how these proteins integrate BMP signaling in the uterus during early pregnancy. Using CUT & RUN, we provided genomic evidence demonstrating the unique and shared roles of SMAD1 and SMAD5 during the window of implantation.

overall_design: We performed Cleavage Under Targets & Release Using Nuclease (CUT&RUN-seq) for SMAD1 and SMAD5 proteins in the mouse mouse uterus at 4.5 days post coitus timepoint.

first: Zian

last: Liao

first: Suni

last: Tang

first: Kaori

last: Nozawa

first: Keisuke

last: Shimada

first: Masahito

last: Ikawa

first: Diana

last: Monsivais


title: Macrophage specific Mafb deficiency effects brown adipose tissue's cold adaptability

city: Tsukuba

first: Michito

last: Hamada

state: Ibaraki

address: 1-1-1 Tennodai,

department: Department of Anatomy and Embryology

institute: University of Tsukuba

summary: To investigate the Cold exposure adaptation under macrophage-specific Mafb deficiency, we put the Mafbf/f (Control) mice and Mafbf/f::LysM-cre (Macrophage specific Mafb deficient) under cold exposure for 10 days and collected the interscapular brown adipose tissue (iBAT) of these mice to compare the changes using RNA sequencing.

overall_design: We divided 8 week age mice littermate into two groups, Mafbf/f, and macrophage-specific Mafb deficient  Mafbf/f::LysM-cre mice, and performed RNA sequencing of iBAT collected after 10 days cold exposure.

first: Manoj

last: Yadav

first: Megumi

last: Ishida

first: Natalia

last: Gogoleva

first: Ching

first: Filiani

middle: N

last: Salim

first: Maho

last: Kanai

first: Akihiro

last: Kuno

first: Takuto

last: Hayashi

first: Zeynab

last: Shahri

first: Kaushalya

last: Kulathunga

first: Omar

last: Samir

first: Wenxin

last: Lyu

first: Olivia

last: Olivia

first: Evaristus

last: Mbanefo

first: Satoru

last: Takahashi


title: Maternal IL-10 restricts fetal emergency myelopoiesis [scATAC-seq]

first: Melissa

last: Proven

institute: Columbia Unversity

summary: We investigated how late fetal liver (FL) mouse hematopoieitic stem and progenitor cells (HSPC) respond to inflammation, with the hypothesis that deficits in engagement of emergency myelopoiesis (EM) pathways could limit neutrophil output and contribute to perinatal neutropenia, ultimately explaining the susceptibility of neonates to inflammation and infection. We show that fetal HSPCs are biased toward erythroid and lymphoid cell production at steady state and fail to mount classical EM responses in vivo. Despite being capable of responding to EM-inducing stimuli in vitro, we find that maternal factors like interleukin-10 (IL-10) restrict fetal HSPCs from activating EM pathways in utero. Accordingly, we find that loss of maternal IL-10 restores EM activation in fetal HSPCs but at a cost of premature parturition. These results reveal the evolutionary trade-off inherent in maternal anti-inflammatory responses that maintain pregnancy but render the fetus susceptible to infection.

overall_design: We sorted lineage negative, c-Kit positive cells from fetal liver of embryonic day 18.5 (E18.5) mice and bone marrow of adult mice.

first: Amelie

last: Collins

first: James

last: Swann

first: Emmanuelle

last: Passegue


title: Maternal IL-10 restricts fetal emergency myelopoiesis [Bulk RNA-seq]

overall_design: We sorted HSPC populations from fetal liver of embryonic day 18.5 (E18.5) mice, and bone marrow of 2 week old and adult (8-12 weeks) mice.


title: Comparison of SARS-CoV-2 variants in primary human nasal cultures indicates Delta as most cytopathic and Omicron as fastest replicating

first: David

middle: Michael

last: Renner

address: 3610 Hamilton Walk

department: Microbiology

institute: University of Pennsylvania

summary: The SARS-CoV-2 pandemic was marked with emerging viral variants, some of which were designated as variants of concern (VOCs) due to their selection and rapid circulation in the human population. Here we elucidate functional features of each VOC linked to variations in growth during infection. Patient-derived primary nasal cultures grown at air-liquid-interface (ALI) were used to model upper-respiratory infection and human lung epithelial cell lines used to model lower-respiratory infection. All VOCs replicated to higher titers than the ancestral virus, suggesting a selection for replication efficiency. In primary nasal ALI cultures, Omicron replicated to the highest titers at early time points, followed by Delta, paralleling comparative studies of patient samples. All SARS-CoV-2 viruses entered the cell primarily via a transmembrane serine protease 2 (TMPRSS2)-dependent pathway, and Omicron was more likely to use an endosomal route of entry. All VOCs activated and overcame dsRNA-activated cellular responses including interferon signaling, oligoadenylate ribonuclease L (OAS-RNase L) degradation and protein kinase R (PKR) activation. Among the VOCs Omicron expressed the most interferon and interferon stimulated genes. Infections in nasal ALI resulted in damage to nasal cells such as a compromise of cell-barrier integrity and loss of nasal cilia and ciliary beating function, especially with Delta infections. Overall, Omicron replication was optimized for growth in the upper-respiratory system and least-favorable in the lower-respiratory cell line; and Delta was the most cytopathic for both upper and lower respiratory cells. Our findings highlight the functional differences among VOCs and illuminate distinct mechanisms of pathogenesis in infected individuals.

overall_design:
To investigate differences in nasal cell responses to infections with SARS-CoV-2 variants, we pooled primary nasal epithelial cells from four donors and grew them in air-liquid interface cultures. These cultures were then mock infected or infected with SARS-CoV-2 variants at MOI = 0.1 for 96 hours.
We examined differences in gene expression using data obtained from bulk RNA sequencing from each infection in triplicate.
Differential gene expression analysis was done by comparing gene expression levels in each infection condition compared to mock infection (WT vs. Mock, Alpha vs. Mock, etc.).

first: Nikhila

middle: S

last: Tanneti

first: Susan

last: Weiss

first: Noam

last: Cohen


title: SOX17 initiates an immune evasion program in early colorectal cancers [RNAseq_230707Yil]

status: Public on Feb 28 2024

city: Cambridge

first: Norihiro

last: Goto

state: MA

address: 500 Main Street, Building 76

department: Department of Biology

institute: Massachusetts Institute of Technology

summary: In addition to accumulation of step-wise genetic mutations, epigenetic alterations play critical roles in the evolution of colon cancers. However, distinct mutational patterns and patient backgrounds render it challenging to distinguish driver epigenetic alterations from passenger epigenetic alterations. To address this, we combined the colon cancer organoid orthotopic transplantation approach with comprehensive epigenomic and transcriptomic analyses. We found that an in vivo environment induces epigenetic alterations with fetal intestinal features that converge on SOX17, a transcription factor that is required for endoderm development. Surprisingly, SOX17 knockout leads to tumour rejection in immunocompetent mice, but not in immunodeficient mice, by turning immune cold tumours into hot with robust infiltration of activated CD8+ T cells. Mechanistically, SOX17 suppresses Ifngr1-mediated MHC-I expression to evade CD8+ T cell-mediated tumour cell killing. At the tumour initiation, SOX17 expression is induced by APC loss, and SOX17 facilitates the production of LGR5- cells with low MHC-I expression to evade immune surveillance. Together, our result reveals that SOX17 is a master transcriptional factor that induces in vivo epigenetic reprograming of tumours, which provides fundamental understanding of how an immune evasion program is initiated at the early stages of colon cancer development.

overall_design: We performed RNA-seq in naïve AKP organoids, bulk primary tumours, and flow cytometry-sorted tdTomato+ tumour cells from primary tumours. Furthermore, we employed Villin-CreERT2; Apc f/f; Kras LSL-G12D; P53 f/f; Rosa LSL-tdTomato (AKPVT) mice to generate autochthonous tumours by colonoscopy-guided 4-OH-Tamoxifen injection into the colonic mucosa. We perfomed RNA-seq in these endogenous AKPVT tumours and normal colonic crypts.

first: Saori

first: Judith

last: Agudo

first: Omer

last: Yilmaz


title: OCT4 and YY1 ChIP-seq in iXist-ChrX mESCs (d0 and d6 Xist induction)

city: Oxford

first: Joseph

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary:
X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions in cis to silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. Chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing.

In this study, we examine mouse embryonic stem cell lines with an inducible Xist allele (iXist-ChrX mESCs) and integrate allele-specific data of gene silencing and decreasing inactive X (Xi) chromatin accessibility over time-courses of Xist induction with cellular differentiation. Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results suggest that YY1 acts as barrier to Xist-mediated silencing until late stages of the XCI process.

overall_design: This series contains data from ChIP-seq experiments conducted in iXist-ChrX mESCs with ChIP antibodies raised against endogenous OCT4A protein (Cell Signaling C3OA3C1) and YY1 protein (Cell Signaling D5D9Z). 2 replicates are performed in iXist-ChrX-Cast mESCs at day 0 and day 6 of Xist induction. Peaks were called across all 4 samples to generate a consensus set of OCT4 peaks.

first: Mafalda

last: Almeida

first: N

last: Brockdorff


title: YY1 ChIP-seq (T7 Ab) over a time course of Xist induction and NPC differentiation in iXist-ChrX YY1-FKBP-T7 cell lines

overall_design:
This series contains data from ChIP-seq experiments performed in iXist-ChrX YY1-FKBP12-3xT7 cells over a time course of Xist induction with mESC to NPC differentiation. ChIP-seq was performed with an antibody raised against the T7 tag, which generates data of superior signal:noise than endogenous YY1 antibodies.

Timecourses of 0, 3, 5, 7 and NPC (d18 or d28) were performed for each of two biological replicate YY1-FKBP12-3xT7 clones, aF1 and cC3. Clone aF1 derives from the iXist-ChrX-Dom line, so inducible Xist silences from the the Domesticus/129/Sv allele and only ChrX sequence proximal to the Xist locus (0-103Mb) is amenable to allelic analysis. Clone cC3 derives from the iXist-ChrX-Cast line, so inducible Xist is on the reciprocal Castaneous allele and the whole chromosome can be analysed allelically.

The series also contains YY1 ChIP from aF1 and cC3 mESCs with 6 days of Xist induction but no NPC differentiation, which show considerably more remaining YY1 binding on Xi than samples with differentiation.

first: Neil


title: Chromatin RNA-seq of Xist-mediated silencing upon YY1 degradation in iXist-ChrX YY1-FKBP12-T7 mESCs

overall_design: This series contains data from Chromatin RNA-seq experiments performed in iXist-ChrX YY1-FKBP12-3xT7 mESCs. Two clones (aF1 and cC3) were analysed as biological replicates. Clone aF1 derives from the iXist-ChrX-Dom line so harbours inducible Xist on the Domesticus/129/Sv allele and X-linked genes preceding the Xist locus (0-103Mb) are amenable to allelic silencing analysis. Clone cC3 derives from the iXist-ChrX-Cast line so has inducible Xist on the Castaneous allele and all X-linked genes can be analysed. Silencing is assayed at 0, 2 and 6 days of Xist induction, with and without treatment with 100nM dTAG-13 52 hours before sample collection. Hence, in the day 2 timepoints YY1 degradation occurs 4 hours prior to Xist induction, whereas in the day 6 timepoint YY1 is degraded at a stage where silencing has initiated and progressed substantially but is not fully complete.


title: YY1 ChIP-seq (endogenous YY1 Ab) in non-induced iXist-ChrX mESCs

overall_design: This series contains data from ChIP-seq experiments conducted in iXist-ChrX mESCs with a ChIP antibody raised against endogenous YY1 protein (Cell Signaling D5D9Z). It contains 2 replicates in iXist-ChrX-Cast mESCs and 2 replicates in iXist-ChrX-Dom mESCs. Peaks were called across all 4 samples to generate a consensus set of YY1 peaks.


title: Functional studies of TP63-affected ESCC tumor immune microenvironment

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

summary: Our preliminary data from unbiased analyses of both ESCC patient samples and cell lines identified interferon-γ (IFN-γ) signaling pathway as the most significantly enriched pathways suppressed by TP63. To validate the activation of IFN pathways and the immune responses upon silencing of TP63, we utilized immune-competent mice to conduct allograft experiments. To analyze the effect of TP63 on ESCC tumor microenvironment, resected tumors were then collected to perform scRNA-seq.

overall_design: Excised tumors were dissociated into single cells and enriched with CD45 microbeads, then rendered to scRNA-seq.

first: Yanyi

last: Jiang

first: Yuan


title: Disease-associated astrocyte epigenetic memory promotes CNS pathology [H3K27ac Chip-seq]

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: We identify H3K27ac peaks regulated by p300 in astroctyes during EAE

overall_design: H3K27ac Chip-seq analysis of scramble and p300 KD astrocytes during EAE in B6 mice.

first: Hong-Gyun

last: Lee

first: Francisco

middle: J

last: Quintana


title: Mitochondrial regulator CRIF1 deficiency induces Foxp3low inflammatory non-suppressive regulatory-T cells in tumors

city: Seoul

first: Sangsin

address: Daehakro

institute: Seoul National University

overall_design: Refer to individual Series


title: Mitochondrial regulator CRIF1 deficiency induces Foxp3low inflammatory non-suppressive regulatory-T cells in tumors [ATAC-seq]

summary: Foxp3low inflammatory non-suppressive (INS)-regulatory T cells (Tregs) were discovered recently. Unlike conventional Tregs, they produce proinflammatory-cytokines, exhibit reduced suppressiveness, and promote rather than impair anti-tumor immunity. The role of mitochondria in Foxp3low INS-Treg formation in vivo is unclear. We showed that the Foxp3low INS-Treg equivalents in human tumors demonstrate attenuated expression of CRIF1, a vital mitochondrial regulator. Mice with CRIF1 deficiency in Tregs bore Foxp3low INS-Tregs with mitochondrial dysfunction. The -ketoglutarate-mTORC1 axis was enhanced in these cells. This promoted proinflammatory-cytokine expression by inducing EOMES and SATB1 expression. Moreover, chromatin openness of the regulatory regions of the Ifng and Il4 genes was increased, which facilitated EOMES/SATB1 binding. The increased -ketoglutarate-derived 2-hydroxyglutarate downregulated Foxp3 expression by methylating the Foxp3-gene regulatory regions. Furthermore, CRIF1-deficiency-induced Foxp3low INS-Tregs suppressed tumor growth in an IFN- dependent manner. Thus, CRIF1-mediated mitochondrial homeostasis is critical for inducing Foxp3low INS-Tregs that promote anti-tumor immunity.

overall_design: Tregs were sorted by flow cytometry, and RNA-seq and ATAC-seq was performed.

first: Gwanghun

last: Kim

first: Hyun

last: Shin

first: Doo

last: Chung


title: YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing

summary:
X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions in cis to silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. Chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing.

In this study, we examine mouse embryonic stem cell lines with an inducible Xist allele (iXist-ChrX mESCs) and integrate allele-specific data of gene silencing and decreasing inactive X (Xi) chromatin accessibility over time-courses of Xist induction with cellular differentiation. Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results suggest that YY1 acts as barrier to Xist-mediated silencing until late stages of the XCI process.

This SuperSeries is composed of the SubSeries listed below.


title: Mitochondrial regulator CRIF1 deficiency induces Foxp3low inflammatory non-suppressive regulatory-T cells in tumors [RNA-seq]


title: SOX17 initiates an immune evasion program in early colorectal cancers [ATAC-seq]

first: Norihiro

overall_design: We orthotopically transplanted naïve AKP organoids to immunocompetent mice by colonoscopy, generated organoids from the primary tumours, and passaged several times until only cancer cells are present in the culture.

first: Saori


title: SOX17 initiates an immune evasion program in early colorectal cancers [scRNA-seq]

overall_design: Tumours from five mice were pooled for each condition (Control and SOX17KO) and 7-AAD-negative EpCAM-negative CD45-positive cells were sorted.

first: Judith

first: Omer


title: SOX17 initiates an immune evasion program in early colorectal cancers [RNAseq_201102YilA]

overall_design: To investigate the role of SOX17 in colon cancer, we deleted SOX17 in the in vivo tumour-derived AKP organoids by CRISPR-Cas9.


title: SOX17 initiates an immune evasion program in early colorectal cancers [RNAseq_200615Yil]

overall_design: We orthotopically transplanted naïve AKP organoids to immunocompetent and immunodeficient mice by colonoscopy, generated organoids from the primary tumours, and passaged several times until only cancer cells are present in the culture. In addition, to recapitulate the upregulation of SOX17 expression that occurs in vivo, we introduced dox-inducible and constitutive SOX17OE construct to the naïve AKP organoids by lentivirus transduction.


title: Maternal IL-10 restricts fetal emergency myelopoiesis [scRNA-seq]

city: New York

first: Melissa

last: Proven

overall_design: We sorted lineage negative, c-Kit positive cells from fetal liver of E18.5 mice and bone marrow of adult (8-12 weeks) mice. We compared wild-type fetuses to wild-type adults exposed to either PBS or LPS. We compared IL10+/- fetuses carried by wild-type mothers to IL10+/- fetuses carried by IL10-/- mothers, exposed to either PBS or LPS.

first: Amelie

last: Collins

first: James

last: Swann

first: Emmanuelle

last: Passegue


title: TIM-3, LAG-3, or 2B4 gene disruptions increase the anti-tumor  response of engineered T cells

status: Public on Feb 27 2024

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

institute: Consiglio Nazionale delle Ricerche

summary: In adoptive T cell therapy, the long term therapeutic benefits in patients treated with engineered tumor specific T cells are limited by the lack of long term persistence of the infused cellular products and by the immunosuppressive mechanisms active in the tumor microenvironment. Exhausted T cells infiltrating the tumor are characterized by loss of effector functions triggered by multiple inhibitory receptors (IRs). In patients, IR blockade reverts T cell exhaustion but has low selectivity, potentially unleashing autoreactive clones and resulting in clinical autoimmune side effects. Furthermore, loss of long term protective immunity in cell therapy has been ascribed to the effector memory phenotype of the infused cells.   We simultaneously redirected T cell specificity towards the NY-ESO-1 antigen via TCR gene editing (TCRED) and permanently disrupted LAG3, TIM-3 or 2B4 genes (IRKO) via CRISPR/Cas9 in a protocol to expand early differentiated long-living memory stem T cells.  The effector functions of the TCRED-IRKO and IR competent (TCRED-IRCOMP) cells were tested in short-term co-culture assays and under a chronic stimulation setting in vitro. Finally, the therapeutic efficacy of the developed cellular products were evaluated in multiple myeloma xenograft models.  Results: We show that upon chronic stimulation, TCRED-IRKO cells are superior to TCRED-IRCOMP cells in resisting functional exhaustion through different mechanisms and efficiently eliminate cancer cells upon tumor re-challenge in vivo. Our data indicate that TIM-3 and 2B4-disruption preserve T-cell degranulation capacity, while LAG-3 disruption prevents the upregulation of additional inhibitory receptors in T cells.  These results highlight that TIM-3, LAG-3, and 2B4 disruptions increase the therapeutic benefit of tumor specific cellular products and suggest distinct, non-redundant roles for IRs in anti-tumor responses.

overall_design:
To shed lights on the mechanisms underlying the functional advantage of TCRED-IRKO cells compared to IRCOMP counterparts, we compared the transcriptional profiles of our cellular products upon 24 hrs co-culture with MM1.s A2posESO-1pos multiple myeloma cells or left unstimulated.
We generated engineered T cells by using CRISPR/Cas9 nucleases. Briefly, we disrupted the endogenous TCR ⍺-chain in combination (TCRED-IRKO) or not (TCRED-IRCOMP) with TIM-3, LAG-3 or 2B4.T cell specificty was re-addressed upon lymphocyte transduction with a lentiviral vector encoding for a HLA-A2 restricted NY-ESO-1 specific TCR.
We analyzed differentially upregulated or downregulated genes in each TCRED-IRKO vs TCRED-IRCOMP cells after stimulation with cancer cells.

first: Beatrice

last: Cianciotti

first: Zulma

middle: I

last: Magnani

first: Alessia

last: Ugolini

first: Barbara

last: Camisa

first: Valentina

last: Vavassori

last: Potenza

first: Antonio

last: Imparato

first: Francesco

last: Manfredi

first: Danilo

last: Abbati

first: Laura

last: Perani

first: Antonello

last: Spinelli

first: Eric

last: Shifrut

first: Fabio

last: Ciceri

first: Luca

last: Vago

first: Raffaella

last: Di Micco

first: Luigi

last: Naldini

first: Pietro

last: Genovese

first: Eliana

last: Ruggiero

first: Chiara

last: Bonini


title: PGCC development and recovery within a prostate cancer cell population

city: Charleston

first: Christina

last: Voelkel-Johnson

state: SC

address: 173 Ashley Ave, MSC 250504 room 201

institute: Medical University of South Carolina

summary: Polyploid Giant Cancer Cells (PGCC) are increasingly being studied for their role in cancer recurrence and mortality.  PGCC arise from cancer cells in response to stress such as radiation, chemotherapy, or hypoxia. PGCC remain viable but do not divide by mitosis. However, upon cessation of stress, PGCC are capable of progeny formation via primitive, amitotic mechanisms akin to budding or bursting. In this study, the initial PGCC offspring are referred to as “early progeny”.  As early progeny cells resume proliferation they generate “late progeny”. This study assessed the transcriptional changes that occur as parental cancer cells progress to PGCC in response to radiation stress, escape as early progeny, and resume proliferation.

overall_design: The experiment included four conditions.  For each, 7 X 10^5 PPC1 cells were plated on day 1 in 100 mm plates.  Condition 1 (UT) were simply harvested on day 4 with trypsinization, processed using a Qiagen RNAEasy kit, purity assessed with a Nanodrop, and packaged for delivery to Novogene for analysis.  Condition 2 (Gi) were irradiated with 8 Gy on day 2 and on day 4 trypsinized, passed through a 20 micron PluriSelect cell filter, and the captured cells eluted.  Condition 3 (ErD) were irradiated on day 2 and on day 8 trypsinized, passed through a 20 micron PluriSelect cell filter, and the flowthrough processed for analysis.  Condition 4 (Late) were irradiated on day 2 and on day 20 trypsinized, passed through a 20 micron PluriSelect filter, and the flowthrough processed. The experiment was performed with 6 replicates, for a total of 24 samples.

first: Shai

last: White-Gilbertson

first: Ping

last: Lu


title: SOX17 initiates an immune evasion program in early colorectal cancers.

first: Norihiro

last: Goto

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


title: Transcriptome and Proteome Analysis Reveals Upregulation of GSTM2 by Allisartan Improving Cardiac Remodeling and Dysfunction in Hypertensive Rat

city: Tianjin

first: Hao

last: Wu

address: No.190 Jiaoyuan Road, Hongqiao District

department: Department of Cardiology

institute: Tianjin Union Medical Center

summary: Abstract Background: Long-term hypertension can lead to hypertensive heart disease, which ultimately progresses to heart failure. As an angiotensin receptor blocker (ARB) antihypertensive drug, allisartan can control blood pressure and improve cardiac remodeling and cardiac dysfunction caused by hypertension. The objective of this study is to investigate the protective effects of Allisartan on the heart of spontaneously hypertensive rats (SHRs) and the underlying mechanisms. Methods: We used spontaneously hypertensive rats (SHRs) as an animal model of hypertensive heart disease and treated them with allisartan orally at a dose of 25 mg/(Kg·day). We continuously monitored the rats' blood pressure levels, measured their body and heart weights, and evaluated their cardiac structure and function using echocardiography. WGA staining and Masson trichrome staining were employed to assess the morphology of the myocardial tissue. We performed transcriptome and proteome analysis using the Solexa/Illumina sequencing platform and tandem mass tag (TMT) technology, respectively. We used immunofluorescence co-localization to analyze Nrf2 nuclear translocation, and TUNEL to detect the level of cell apoptosis. The protein and mRNA levels were determined by Western blotting and qRT-PCR, respectively. Results: Allisartan lowered blood pressure, attenuated cardiac remodeling, and improved cardiac function. Allisartan alleviated cardiomyocyte hypertrophy and cardiac fibrosis. Allisartan significantly affected the pentose phosphate pathway, fatty acid elongation, valine, leucine and isoleucine degradation, glutathione metabolism, and amino sugar and nucleotide sugar metabolism pathways in the hearts of SHRs, and upregulated the expression level of GSTM2. Allisartan activated the PI3K-AKT-Nrf2 signaling pathway and inhibited cardiomyocyte apoptosis. Conclusions: Our study determined that allisartan effectively controls blood pressure in SHRs and improves cardiac remodeling and cardiac dysfunction. Allisartan upregulates the expression level of GSTM2 in the hearts of SHRs and significantly affects glutathione metabolism shown by transcriptomics and proteomics analysis. The cardioprotective effect of allisartan may be mediated through activation of the PI3K-AKT-Nrf2 signaling pathway, upregulation of GSTM2 expression, and reduction of SHRs cardiomyocyte apoptosis.

overall_design: To investigate the cardioprotective effects of Allisartan on spontaneously hypertensive rats (SHRs), the experiment involved three groups: WKY (W), SHR (M), and SHR+Allisartan (B). Transcriptome sequencing of cardiac tissues was conducted at 48-week-old.

first: Yajun

last: Zhai

first: Jing

last: Yu

first: Liping

last: Wei

first: Xin

last: Qi


title: Maternal IL-10 restricts fetal emergency myelopoiesis

first: Melissa

last: Proven

state: NY


title: The NF-κB RelA transcription factor is dispensable for CD8+ T-cell function in acute viral infection and cancer [human]

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

institute: Cancer Research Center of Lyon

summary: CD8+ T cells are critical mediators of pathogen clearance and anti-tumor immunity. Although signaling pathways leading to the activation of NF-B transcription factors have crucial functions in the regulation of immune responses, the CD8+ T cell-autonomous roles of the different NF-B subunits, are still unresolved. Here, we investigated the function of the ubiquitously expressed transcription factor RelA in CD8+ T-cell biology using a novel mouse model and gene-edited human cells. We found that CD8+ T cell-specific ablation of RelA markedly altered the transcriptome of ex vivo stimulated cells, but maintained the proliferative capacity of both mouse and human cells. In contrast, in vivo experiments showed that RelA deficiency did not affect the CD8+ T-cell response to acute viral infection or transplanted tumors. Our data suggest that in CD8+ T cells, RelA is dispensable for their protective activity in pathological contexts.

overall_design: CD8+ T cells cells were isolated from heathy donors' PBMCs, stimulated with anti-CD3/CD28 and IL-2 for 3 days and electroprated with Cas9 RNPs. After another 3 days of culture, ATTO550+ cells were sorted and stimualted as above for 4 hours. Cells were then subjected to bulk mRNAseq

first: Grinberg-Bleyer

last: Yenkel

first: Voisin

last: Allison

first: Tonon

last: Laurie


title: Allele-specific ATAC-seq over a timecourse of inducible XCI in mESCs

first: Joseph

last: Bowness

overall_design: This series contains data of ATAC-seq from a timecourse of inducible XCI in iXist-ChrX-Dom mESCs. The genotype of this model cell line is a female interspecific hybrid between M.m.Domesticus and M.m.Castaneous mouse strains, with dox-inducible Xist on the Domesticus allele. In this timecourse, we induce Xist with differentiation from mESCs to NPCs and perform ATAC-seq at days 0,1,3,6 and 17. Regulatory elements on Xi largely lose accessibility as the chromosome is silenced over the timecourse.

first: Tatyana

middle: B

last: Nesterova

first: Neil

last: Brockdorff


title: The NF-κB RelA transcription factor is dispensable for CD8+ T-cell function in acute viral infection and cancer


title: The NF-κB RelA transcription factor is dispensable for CD8+ T-cell function in acute viral infection and cancer [mouse]

overall_design: CD8+ T cells were isolated from spleen and LNs of control and cKO mice, and stimulated with anti-CD3/CD28 and IL-2 for 4 hours. Cells were then subjected to bulk RNAseq