title: Laser capture-microdissected islet transcriptomics

status: Public on Dec 31 2024

city: Gainesville

first: Alexandra

middle: E.

last: Cuaycal

state: FL

address: 1275 Center Drive

department: Infectious Diseases and Immunology/Biomedical Engineering

institute: University of Florida

summary: Type 1 Diabetes (T1D) is an autoimmune disease characterized by T cell-mediated destruction of insulin-producing pancreatic β-cells. The pathogenesis of T1D is not fully understood but involves development of autoantibodies (AAbs) followed by a progressive decline in first phase insulin response. Live imaging of T1D pancreatic slices has revealed β cell dysfunction irrespective of the acute presence or absence of CD3+ T cells. However, the mechanisms that drive this dysfunction in the prediabetic period remain unclear. In-situ longitudinal studies of human islet cell biology in the context of T1D are essentially impossible. Hence, we leveraged the availability of pancreas tissues from the Network for Pancreatic Organ donors with Diabetes (nPOD) program to phenotypically and transcriptionally characterize laser capture-microdissected islets across the natural history of T1D.

overall_design: Fresh frozen pancreas sections were obtained from donors with no diabetes (ND, n=16), single autoantibody positive (sAAb, n=6), multiple autoantibody positive (mAAb, n=5) and patients with Type 1 Diabetes (T1D, n=16). Blocks were selected based on immunohistochemistry staining and contained INS+ islets and/or T cell infiltration as defined by six or more CD3+ cells immediately touching the islet endocrine cells. Blocks were cut into thick (10 μm) serial (3-4) sections and placed onto PEN-slides (Leica) along with thin (4 μm) sections placed onto Superfrost slides (Thermofisher) before and after the thick sections. Thin pancreas sections were immunostained for insulin (INS), CD3, HLA class I and ATP5B to delineate islets with residual beta cells, T cell infiltration, antigen presentation and mitochondrial function. Thick sections were used to laser-microdissect single islets from dehydrated slides. Laser microdissections yielded 3-4 sections per islet captured into 0.6 mL RNAse-free tubes. Sets of 7-25 islets were laser-captured per donor. A total of 260 islets were obtained across the four different clinical phenotypes (ND=73, sAAb=40, mAAb=37, T1D=110). Microarray gene expression profiling of single islets was performed using the Affymetrix Human Gene 2.0 ST arrays.


title: The Expression profile of splenic/hepatic macrophages in RNaseT2 deficient mice

city: Tokyo

first: Ryota

last: Sato

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

type: Expression profiling by high throughput sequencing

summary: RNA stress caused by the loss of RNaseT2, which is localized in lysosomes, leads to macrophage accumulation in the spleen and liver. However, the underlying mechanism remained unclear. Here, we demonstrated that cell proliferation in Rnaset2 -/- mice is dependent on TLR13, an RNA sensor. In both organs, TLR13 was found to induce cell proliferation and survival signals. Notably, in the liver, the most accumulated Ly6Clow macrophages were found to resemble wild-type Kupffer cells. These cells were shown to exert hepatoprotective effects through the LXR-CD5L axis.

overall_design: To examine the characteristics of splenic macrophages that accumulate in Rnaset2–/– mice, we isolated Ly6C low or Ly6C high splenic macrophages from wild-type and Rnaset2–/– mice using FACS sorting. Similarly, to examine the characteristics of hepatic macrophages that accumulate in Rnaset2–/– mice, we isolated Kupffer cells, Ly6C low or Ly6C high splenic macrophages from wild-type and Rnaset2–/– mice using FACS sorting. Subsequently, we performed gene expression profiling analysis by employing RNA-seq data obtained from macrophage samples.

first: Kensuke

last: Miyake

first: Kiyoshi

last: Yamaguchi


title: Silencing of STEAP3 suppresses cervical cancer cell proliferation and migration via JAK/STAT3 signaling pathway

city: Shanghai

first: Zouyu

last: Zhao

address: 1508 Longhang Road

country: China

institute: Jinshan Hospital of Fudan University

summary: To investigate the mechanisms of STEAP3 in cervical cancer cell proliferation and migration, we established HeLa cell lines in which STEAP3 gene has been knocked down by shRNA. We then performed gene expression profiling analysis and enrichment analysis using data obtained from RNA-seq of NC and KD cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HeLa cells and its KD derivatives (shSTEAP3)

first: Panpan

last: Yu

first: Yan

last: Wang

first: Hong

last: Li

first: Hui

last: Qiao

first: Chongfeng

last: Sun

first: Lina

last: Zhu

first: Ping

last: Yang


title: Macrophage-induced enteric neurodegeneration leads to motility impairment during gut inflammation

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

country: Germany

institute: University Clinics Bonn

summary: Background: Current studies provide compelling evidence that the enteric nervous system and neighboring resident macrophages in the muscularis externa modulate neuroimmune processes in the gut after abdominal surgery. While substantial knowledge exists about macrophage-enteric glia interactions, the fate of enteric neurons, which have an indispensable role in gut homeostasis and gastrointestinal motility, has not been thoroughly investigated during enteric neuroinflammation. Therefore, we investigated the impact of enteric neuron-macrophage interactions on postoperative trauma and subsequent motility disturbances, i.e., postoperative ileus. Methods: Neuroinflammation and postoperative ileus were induced in various transgenic mice by surgical manipulation of the small intestine. We studied enteric neurons and macrophage-specific transcriptomes using bulk RNA-Seq in neuron-specific RiboTag mice and sorted CX3CR1-GFP+ macrophages. To investigate their intercellular communication, we treated CX3CR1-GFP+ mice with CSFR1-antibody to deplete macrophages and subsequently induce POI through surgical trauma. These mice were examined for gastrointestinal motility, immune cell infiltration, and neuronal function. Ultimately, we validated the murine data in human gut samples collected early and late during abdominal surgery to understand the impact of surgical manipulation on patients' enteric nervous system function. Results: We detected strong neuronal activation in the early postsurgical phase, followed, after 24h, by transcriptional signatures of neuronal proliferation, neuronal death, and synaptic degradation. Neuron-specific transcriptome analysis confirmed these changes and verified the neuronal responses to the inflammatory environment. Simultaneously, our study revealed a neurodegenerative profile in macrophage-specific transcriptomes during POI. Depletion of macrophages before surgical manipulation led to decreased neuronal death, less synaptic decay, and improved GI motility, emphasizing the essential role of macrophages in neurodegeneration during intestinal neuroinflammation. In human jejunal muscularis externa samples, taken at early and late stages of pancreatectomies, we detected reactive and dying neurons with dysregulated gene expression of synaptic signaling and neurogenic processes. Conclusion: Surgical trauma and acute intestinal inflammation activate enteric neurons and induce neurodegeneration with severe synaptic decay, predominantly mediated by resident macrophages. Future studies should focus on neuroprotective mechanisms to dampen neurodegeneration and promote faster recovery from postoperative inflammation and motility disturbances.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of enteric neurons during acute intestinal inflammation

first: Sven

last: Wehner


title: PD-L1 and IFN-γ modulate Non-Small Cell Lung Cancer (NSCLC) Cell Plasticity responsible for ICI-Resistance

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

country: Italy

institute: University of Verona

summary: Non-small cell lung cancer (NSCLC) is the leading cause of cancer death worldwide. Although immune checkpoint inhibitors (ICIs) have demonstrated outstanding clinical efficacy in the treatment of NSCLC patients, ICIs-based therapy has also been associated with a paradoxical acceleration of tumor growth defined as hyperprogressive disease (HPD). In this paper we evaluated distinct plasticity traits in a model of HPD-NSCLC, with the aim of clarifying the mechanisms contributing to ICI resistance that involve IFN-γ and PD-L1. For this purpose, primary cell cultures were established from two stage IV NSCLC samples obtained from a single patient: one, prior to ICI initiation (NSCLC-B, baseline) and the other at the time of radiological evidence of hyperprogression under ICI treatment (NSCLC-H, hyperprogression). Compared to NSCLC-B cells, NSCLC-H cells exhibited a more aggressive in vivo and in vitro behavior, higher MAPK activation and owned the ability to develop tumoroids. The 3500 differentially expressed transcripts, according to whole transcriptome analysis, well described the profound plastic evolution of cells from NSCLC-B to NSCLC-H culture, as well as the increase of CD44 in the NSCLC-H cell line model, in which transcripts of CD44 isoforms lacking the variant domain were abundant. Transcripts of genes involved in the cellular response to IFN-γ were down-modulated in NSCLC-H compared to NSCLC-B, together with CD274. Conversely, an up-regulation of genes related to inflammatory response, including IL1-𝛽 and IFNGR1, was found. In vitro response to IFN- γ was compromised in both NSCLC-B and NSCLC-H cells, since IFN- γ failed to exert its antiproliferative effect on these cells and to effectively induce PD-L1 expression in 2D-growth assays. Nevertheless, the cytokine induced the activation of both type I and type II IFN-pathway mediators. In addition, treatment with IFN-γ induced NSCLC-H traits in NSCLC-B cells, promoting a striking increase in the number of NSCLC-B 3D-soft agar colonies. Low IFN-γ doses or modulation of PD-L1 contributed to the evolution of NSCLC-B towards NSCLC-H phenotype through the augment of CD44 on cell membrane, cell morphological changes and increased cell growth or sphere formation ability.  In conclusion, we report a modulation of plasticity by PD-L1 modulation and IFN-γ in a NSCLC cell culture established from a treatment-naïve patient, who developed HPD under ICI therapy, suggesting an association between NSCLC plasticity and these main actors involved in ICI activity.

overall_design: Primary cell cultures from two stage IV NSCLC samples from same patient prior and after ICI treatment

first: Arianna

last: Palladini

first: Giulia

last: Lopatriello

first: Francesco

last: Lescai

first: Stefania

last: Angelicola

first: Francesca

last: Giunchi

last: Ruzzi

first: Mariateresa

last: Frascino

first: Mary

last: Pitzalis

first: Lorena

last: Landuzzi

first: Laura

last: Scalambra

first: Maria

middle: S

last: Semprini

first: Olga

middle: M

last: Pittino

first: Chiara

last: Cappello

first: Irene

last: Siracusa

first: Martina

last: Di Noia

first: Cristian

last: Turato

first: Silvia

last: De Siervi

first: Luca

last: Bertoli

first: Hugo

last: De Jonge

first: Luisa

last: Iamele

first: Annalisa

last: Altimari

first: Elisa

last: Gruppioni

first: Andrea

last: Ardizzoni

last: Gelsomino

first: Pier-Luigi

last: Lollini


title: IL-1β-driven NF-kB transcription of ACE2 as a Mechanism of Macrophage Infection by SARS-CoV-2

city: Providence

first: Alan

last: Morrison

state: RI

address: 830 Chalkstone Ave

country: USA

institute: Ocean State Research Institute

summary: Coronavirus disease 2019 (COVID-19), caused by infection with the enveloped RNA betacoronavirus, SARS-CoV-2, led to a global pandemic involving over 7 million deaths. Macrophage inflammatory responses impact COVID-19 severity; however, it is unclear whether macrophages are infected by SARS-CoV-2. We sought to identify mechanisms regulating macrophage expression of ACE2, the primary receptor for SARS-CoV-2, and to determine if macrophages are susceptible to productive infection. We developed a humanized ACE2 (hACE2) mouse whereby hACE2 cDNA was cloned into the mouse ACE2 locus under control of the native promoter. We validated susceptibility of hACE2 mice to SARS-CoV-2 infection relative to wild-type mice or an established K18-hACE2 model of acute fulminating disease. Intranasal exposure to SARS-CoV-2 led to pulmonary consolidations with cellular infiltrate, edema, and hemorrhage, consistent with pneumonia, yet unlike the K18-hACE2 model, hACE2 mice survived and maintained stable weight. Infected hACE2 mice also exhibited a unique plasma chemokine, cytokine, and growth factor, inflammatory signature relative to K18-hACE2 mice. Infected hACE2 mice demonstrated evidence of viral replication in infiltrating lung macrophages, and infection of macrophages in vitro revealed a transcriptional profile indicative of altered RNA and ribosomal processing machinery as well as activated cellular antiviral defense. Macrophage IL-1β-driven NF-B transcription of ACE2 appeared to be an important mechanism of dynamic ACE2 upregulation, promoting macrophage susceptibility to infection. Experimental models of COVID-19 that make use of native hACE2 expression will allow for mechanistic insight into factors that can either promote host resilience or increase susceptibility to worsening severity of infection.

overall_design: RNA-seq of BMDMs from hACE2 mice stimulated with LPS+IFNγ and then infected with SARS-CoV-2 (MOI=0.1) or with mock vehicle control.

middle: R


title: Tgfβ signaling hyperactivates glycolysis via positive feedback to promote interzone formation and joint tissue development

city: Philadelphia

first: Chao

last: Song

state: Pennsylvania

address: 4141 Spruce St., Room 308

institute: Children's Hospital of Philadelphia

summary: The role of bioenergetics in synovial joint development is unknown.  With single-cell RNA sequencing (scRNA-seq) in the knee joint primordia, we discover that the Gdf5-expressing interzone cells are enriched for the expression of glycolysis genes.

overall_design: Cartilage anlagen were isolated from the hindlimbs of E13.5 or E14.5 embryos, and cleaned of soft tissues by rolling on Kimwipe paper. Presumptive knee joint regions were excised under a dissecting microscope (Leica) and digested in 4 mg/ml collagenase D (Sigma-Aldrich, Cat# 11088858001) on an orbital shaker at 120 rpm, 37℃ for 20 mins.

first: Fanxin

last: Long


title: Convergent gene pairs restrict chromatin looping in Dictyostelium discoideum, acting as directional barriers for extrusion

city: Moscow

first: Irina

middle: V

last: Zhegalova

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology

summary: Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into largely consecutive, non-hierarchical and weakly insulated loops positionally conserved at the onset of multicellular development. The transcription level within loops tends to be higher than in adjacent regions. Loops frequently contain functionally linked genes and genes which coherently change expression level during development. Genes at loop anchors are predominantly in the convergent orientation. Our data suggest that the loop profile may arise from the interplay between transcription and cohesin-driven chromatin extrusion. In particular, a convergent gene pair serves as a bidirectional extrusion barrier or a “diode” that controls passage of the cohesin extruder by relative transcription level of paired genes.

overall_design: Refer to individual Series


title: Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [RNA-seq]

summary: Dictyostelium discoideum is a unicellular slime mold developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying rearrangements of chromatin structure remain unknown. Here, we report a unique Dictyostelium 3D genome organization represented by largely consecutive, non-hierarchical and weakly insulated loops of diverse morphology conserved at the onset of multicellular development. Loops are chromosomal neighborhoods facilitating transcription and frequently containing functionally-linked genes which coherently change expression level during development. Loop anchors are enriched with convergent gene pairs, putative enhancers and boundaries of synteny gene blocks that point at their role in genome function and evolution. Our data suggest that the loop profile arises from the interplay between transcription and cohesin-driven chromatin extrusion. In this confunction, a convergent gene pair serves as a “diode” effectively passing the extruder from upstream or downstream direction in dependence on transcription level of the paired genes.

overall_design: Total RNA-seq on developing D. discoideum

first: Sergey

last: Ulianov

first: Aleksandra

last: Galitsyna


title: Screening for transcriptomic associations with Swine Inflammation and Necrosis Syndrome

city: Giessen

first: Gerald

middle: Herbert

last: Reiner

address: Frankfurter Strasse 112

department: Veterinary Medicine

institute: Justus-Liebig-University Giessen

summary:
The recently identified swine inflammation and necrosis syndrome (SINS) affects tail, ears, teats, coronary bands, claws and heels of affected individuals. The primarily endogenous syndrome is based on vasculitis, thrombosis, and intimal proliferation, involving defence cells, interleukins, chemokines, and acute phase proteins and accompanied by alterations in clinical chemistry, metabolome, and liver transcriptome. The complexity of metabolic alterations and the influence of the boar led to hypothesize a polygenic architecture of SINS. This should be investigated by a transcriptome study. For this purpose, the four least affected (SINS-low) and the four most SINS affected (SINS-high) 3d-old piglets, each of three boars, a relatively SINS stable Duroc boar (DU), a relatively stable Pietrain boar (PI+) and a highly susceptible Pietrain boar (PI-) were selected from 27 litters of mixed semen to minimize environmental effects.
Results: A genome-wide expression experiment revealed a huge set of differentially expressed genes that are involved in vasculitis, inflammation and necrosis, keratinization and erythrocyte epitopes. Among them were CRP, GYPA, S100A12, and LIPK. The results confirm and complement previous studies to this topic.
Conclusion: The results confirm the outstanding importance of defence in the context of SINS. At the same time, for the first time, there is evidence for a direct involvement of the keratinisation capacity of the skin and various epitopes of the erythrocyte membrane, which seem to be associated with the severity of SINS. These genes could serve to clarify the pathogenesis of the syndrome and to develop diagnostic tools in future studies.

overall_design: For microarray analysis, n = 3 to 5 RNA samples each of the group SINS low and group SINS high from Duroc, vafourable Pietrain, and unfavourable Pietrain offspring were used for hybridization to the Affymetrix GeneChip Porcine Gene 1.0 Sense Target array.

first: Katharina

last: Gerhards

first: Sabrina

last: Becker

first: Josef

last: Kühling

first: Mirjam

last: Lechner

first: Hermann

last: Willems

first: Robert

last: Ringseis


title: Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [Hi-C]

overall_design: Hi-C on developing D. discoideum


title: Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Lineberger Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Annotation of the cis-regulatory elements mediating oncogenic transcription is essential to understanding breast cancer biology. In this work, we quantitatively linked variation in chromatin accessibility to gene expression within human breast tumors, normal mammary reduction tissue samples, and breast cancer cell lines using single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq). Our analysis resolved the underlying cellular heterogeneity in chromatin accessibility and transcriptional output for each patient sample. We also showed that our findings were recapitulated in the breast cancer cell line samples. These data will serve as an important resource for the single-cell genomics and breast cancer research communities.

overall_design:
Matched single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq) were performed for 12 human breast tumor samples, 4 human normal mammary reduction samples, and 4 human breast cancer cell lines (HCC1143, SUM149PT, MCF7, and T47D).

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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first: M

middle: J

last: Regner

first: H


title: RNA-seq analysis of miR-210 KO 293T cells

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

summary: To study the effects of miR--210 on 293T cells and hypoxia response, we used the CRISPR/Cas9 system to knockout (KO) the human miR-210 gene in 293T cells.  We then added DMOG to mimic hypoxia condition and analyzed the RNA expression profile of wildtype (WT) and KO cells under normal and hypoxic conditions.  DMOG treatment and RNA-seq were performed three times (experiment 1, 2, and 3).

overall_design: Total RNA was isolated after 48h treatment, and RNA-seq analysis was performed.


title: Tau-A152T linked to AD induces neuronal hyperexcitation through FYN-NMDAR in human iPSC-neurons

city: Shinjuku

first: Sumihiro

last: Maeda

state: Tokyo

address: 35 Shinanomachi, Tokyo

institute: Keio University School of Medicine

summary: Tau protein has critical roles in Alzheimer’s disease (AD) pathogenesis and neuronal excitation. Among tau gene mutations, A152T is reported to increase the risk of AD and neuronal excitability in mouse models. To examine the effects of tau gene mutations on neuronal excitability in human neurons, we introduced A152T or P301S mutation to induced pluripotent stem cells (iPSCs) using genome editing technology. To examine the effects of tau expression itself, we generated tau knockout or tau conjugate with a fluorescent protein. In excitatory neuronal culture, we found that the A152T mutation increases spontaneous neuronal excitation and the association of tau and Fyn. NMDAR antagonist blocked neuronal excitation in both the control and A152T neurons, indicating that the A152T mutation enhanced the intrinsic function of tau. Transcriptome analysis revealed structural changes by the A152T mutation. These data showed that the A152T tau gene mutation increases neuronal excitability through the tau-FYN-NMDAR pathway in excitatory neurons.

overall_design: hiPSC-derived neurons with MAPT mutants were compared with those of WT

first: Hirokazu

last: Tanabe

first: Takashi

last: Sasaki

first: Setsu

last: Endo

first: Hideyuki

last: Okano


title: Dissecting the role of CAR signaling architectures on T cell activation and persistence using pooled screening and single-cell sequencing

city: Basel

first: Rocio

last: Castellanos Rueda

state: --None--

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH

summary: Chimeric antigen receptor (CAR) T cells represent a promising approach for cancer treatment, yet challenges remain such as limited efficacy due to a lack of T cell persistence. Given its critical role in promoting and modulating T cell responses, it is crucial to understand how alterations in the CAR signaling architecture influence T cell function. Here, we designed a combinatorial CAR signaling domain library and performed repeated antigen stimulation assays, pooled screening and single-cell sequencing to investigate T-cell responses triggered by different CAR architectures. Parallel comparisons of CAR variants, at early, middle and late timepoints during chronic antigen stimulation systematically assessed the impact of modifying signaling domains on T cell activation and persistence. Our data reveal the predominant influence of membrane-proximal domains in driving T cell phenotype. Additionally, we highlight the critical role of CD40 costimulation in promoting potent and persistent T cell responses, followed by CTLA4, which induces a long-term cytotoxic phenotype. This work deepens the understanding of CAR T cell biology and may be used to guide the future engineering of CAR T cell therapies.

overall_design: Library CAR T cells derived from two healthy donors were subjected to a repeated antigen stimulation assay (co-cultured at 1:1 E:T ratio with SKBR3-GFP cells every 3 days). At days 0, 6 and 12 of the RAS assay, CAR library T cells were co-cultured with SKBR3-GFP cells for 6h in 30 IU/mL of IL-2. Following this time, the co-cultures were stained using DRAQ7, and the live GFP- negative population was sorted using a FACS. Cells were then stained using 20 Totalseq B antibodies and sequenced.

first: Rocío

last: Castellanos-Rueda

first: Sai

middle: T

last: Reddy


title: Unraveling calcium dysregulation and autoimmunity in immune mediated rippling muscle disease

status: Public on Jan 10 2025

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Rippling Muscle Disease (RMD) is a rare skeletal myopathy characterized by abnormal muscular excitability manifesting with wave-like muscle contractions and percussion-induced muscle mounding. Hereditary RMD is associated with caveolin-3 or cavin-1 mutations. Recently we discovered anti-cavin 4 autoantibodies as a biomarker of immune-mediated RMD (iRMD), but the underlying disease-mechanisms are poorly understood. Transcriptomic studies were performed on muscle biopsies of 8 patients (5 males; 3 females; ages 26-to-80) with iRMD. Subsequent pathway analysis compared iRMD to human non-disease control and disease control (dermatomyositis) muscle samples. Transcriptomic studies demonstrated changes in key pathways of muscle contraction and development. All iRMD samples had significantly upregulated cavin-4 expression compared to controls, likely compensatory for autoantibody-mediated protein degradation. Proteins involved in muscle relaxation (including SERCA1, PMCA and PLN) were significantly increased in iRMD compared to controls. Comparison of iRMD to dermatomyositis transcriptomics demonstrated significant overlap in immune pathways, and the IL-6 signaling pathway was markedly increased in all iRMD patient muscle biopsies and increased in the majority of iRMD patients’ serum. This study represents the first muscle transcriptomic analysis of iRMD patients and dissects underlying disease mechanisms. Increase of sarcolemmal and cellular calcium channels as well as PLN, an inhibitor of the SERCA pump for calcium into the sarcoplasm, likely alters the calcium dynamics in iRMD. These changes in crucial components of muscle relaxation may underlie rippling by altering calcium flux. We propose a model in which autoantibody mediated cavin-4 destruction leads to RMD through alterations in key genes regulating muscle relaxation.

overall_design: To investigate the pathophysiologic changes underlying rippling muscle disease, patient skeletal muscle biopsies 8 iRMD patients were  collected and analyzed  in comparison to established non disease control muscle cohorts

first: Samir

last: Nath

first: Numrah

last: Fadra

first: Jason

last: Doles

first: Margherita

last: Milone


title: Microglial NLRP3-gasdermin D activation impairs blood-brain barrier integrity through interleukin-1β-independent neutrophil chemotaxis upon peripheral inflammation

status: Public on Dec 30 2024

city: Seoul

first: Seunghee

last: Hong

state: Seoul

address: 50, Yonsei-ro, Seodaemun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

summary: Blood-brain barrier (BBB) disintegration emerges as a significant contributor to neuroinflammation; however, the biological processes governing BBB permeability under physiological conditions remain unclear. Here, we examined the potential role of NLRP3 inflammasome in BBB disruption following peripheral inflammatory challenges. Systemic lipopolysaccharide administration caused an NLRP3-dependent increase in BBB permeability and myeloid cell infiltration into the brain. Using a cell-specific, hyperactive NLRP3-expressing mouse model, we found that microglial NLRP3 activation is crucial for peripheral inflammation-induced BBB disruption. In contrast, NLRP3 and microglial gasdermin D (GSDMD) deficiency remarkably attenuated lipopolysaccharide-induced BBB breakdown. Notably, IL-1 was unnecessary for this NLRP3-GSDMD-mediated BBB disruption. Instead, microglial NLRP3-GSDMD axis specifically upregulates CXCL chemokine around BBB via producing GDF-15, recruiting Cxcr2-containing neutrophils into the brain. Neutrophil depletion and Cxcr2 blockade significantly reduced NLRP3-mediated BBB impairment. Collectively, our findings unveiled the significant role of NLRP3-driven chemokine production for BBB disintegration, suggesting a potential therapeutic target to mitigate neuroinflammation.

overall_design: The brain tissues were collected from WT or Nlrp3-/- mice each treated with either single or double intraperitoneal injections of LPS (experimental group) in 24 hours of interval. The control groups were injected with PBS. The samples were collected 6 hours after the last injection. Single cell suspensions were acquired and analyzed using scRNA-seq.

first: Je-Wook

last: Yu

first: Sung-Hyun

last: Yoon

first: Chae-youn

last: Kim


title: WBSCR16 Deficiency Drives Adaptive Metabolic Flexibility Via Impaired Mitochondrial 16S rRNA Maturation

first: Shengjie

last: Zhang

address: No. 573, Xujiahui Road

institute: Shanghai Jiaotong University School of Medicine

summary: Mitochondrial rRNAs play important roles in regulating mtDNA-encoded gene expression and energy metabolism subsequently. However, the proteins that regulate mitochondrial 16S rRNA processing remain poorly understood. Herein, we generated adipose-specific Wbscr16-/- mice and cells, both of which exhibited dramatic mitochondrial changes. Subsequently, WBSCR16 was identified as a 16S rRNA-binding protein essential for the cleavage of 16S rRNA-mt-tRNALeu, facilitating 16S rRNA processing and mitochondrial ribosome assembly. Additionally, WBSCR16 recruited RNase P subunit MRPP3 to nascent 16S rRNA and assisted in this specific cleavage. Furthermore, evidence showed that adipose-specific Wbscr16 ablation promotes energy wasting via lipid preference in brown adipose tissue, leading to excess energy expenditure and resistance to obesity. In contrast, overexpression of WBSCR16 upregulated 16S rRNA processing and induced a preference for glucose utilization in both transgenic mouse models and cultured cells. These findings suggest that WBSCR16 plays essential roles in mitochondrial 16S rRNA processing in mammals, and is the key mitochondrial protein to balance glucose and lipid metabolism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Floxed brown adipose tissues and WBSCR16 knockout tissues (Floxed and AWBSCR16 KO).

first: Zi

last: Dong

first: Yang

last: Feng

first: Wei

last: Guo

first: Chen

first: Yifan

last: Shi

first: Zhiyun

last: Zhao

first: Jiqiu

last: Wang

first: Guang

last: Ning

first: Guorui

last: Huang


title: Interferon activation in bone marrow long-lived plasma cells in systemic lupus erythematosus

first: Aaron

last: Pennington

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: While durable antibody responses from long-lived plasma cell (LLPC) populations are important for protection against pathogens, LLPC may be harmful if they produce antibodies against self-proteins or self-nuclear antigens as occurs in autoimmune diseases such as systemic lupus erythematosus (SLE). Thus, the elimination of autoreactive LLPC may improve the treatment of antibody-driven autoimmune diseases. However, LLPC remain a challenging therapeutic target.  Here, we compare the matched bone marrow and blood plasma cell compartments of SLE and healthy donors (HD).  We show a similar distribution of CD138- and CD138+ plasma cells (PC), including putative LLPC (CD19- CD138+ CD38+), between SLE and HD bone marrow (BM).  For both SLE and HD, CD138+ PC are at a higher frequency in BM than peripheral blood (PBL). Expression of Ki-67 associates with the PBL compartment where it is found on all PC subsets regardless of CD19 or CD138 expression. Transcriptomic analysis identifies an interferon gene signature in transitional B cells in the SLE BM, but surprisingly also in the BM PC derived from SLE.  PC phosphorylate STAT1 in response to type I IFN stimulation in vitro. Circulating PC bind type I IFN receptor-blocking antibody anifrolumab, though to a lesser degree than circulating B cells. Anti-nuclear autoantibodies are found in the BM supernatant and PBL serum of SLE patients.  SLE BM-derived PC have increased survival compared to their PBL counterparts when treated with selinexor.  In summary, these findings show evidence of IFN activation in BM PC from SLE.

overall_design: To investigate transcriptomic profiles of plasmablast and plasma cells isolated from SLE patient compared to healthy controls and to compare plasma cells in blood and bone marrow. We FACS sorted plasmablast and plasma cells from blood and bone marrow of SLE patients and healthy controls. We then performed bulk RNA sequencing on the sorted cells

first: Diana

middle: F

last: Alzamareh

first: Nida

last: Meednu

first: Neha

last: Nandedkar-Kulkarni

first: Daria

last: Krenitsky

first: Jennifer

last: Barnard

first: Ken

last: Yasaka

first: Wesley

last: Durrett

first: Juilee

last: Thakar

first: Javier

last: Rangel-Moreno

middle: H

last: Anolik

last: Barnas


title: Characterizing the regulatory effects of H2A.Z and SWR1 on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae [RNA-Seq]

status: Public on Dec 29 2024

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Chromatin structure and DNA accessibility are partly modulated by the incorporation of histone variants. H2A.Z, encoded by the non-essential HTZ1 gene in S. cerevisiae, is an evolutionarily conserved H2A histone variant that is predominantly incorporated at transcription start sites by the SWR1-complex (SWR1-C). While H2A.Z has often been implicated in transcription regulation, htz1Δ mutants exhibit minimal changes in gene expression compared to wild-type. However, given that growth defects of htz1Δ mutants are alleviated by simultaneous deletion of SWR1-C subunits, previous work examining the role of H2A.Z in gene expression regulation may be confounded by deleterious activity caused by SWR1-C when its missing its H2A.Z substrate (apo-SWR1-C). Furthermore, as H2A.Z mutants only display significant growth defects in genotoxic stress conditions, a more substantive role for H2A.Z in gene expression may only be uncovered after exposure to cellular stress. To explore this possibility, we generated mRNA transcript profiles for wild-type, htz1Δ, swr1Δ, and htz1Δswr1Δ mutants before and after exposure to hydroxyurea (HU), which induces DNA replication stress. Our data showed that H2A.Z played a more prominent role in gene activation than repression during HU exposure, and its incorporation was important for proper upregulation of several HU-induced genes. We also observed that apo-SWR1-C contributed to gene expression defects in the htz1Δ mutant, particularly for genes involved in phosphate homeostasis regulation. Furthermore, mapping H2A.Z incorporation before and after treatment with HU revealed that decreases in H2A.Z enrichment at transcription start sites was correlated with, but generally not required for, the upregulation of genes during HU exposure. Together this study characterized the regulatory effects of H2A.Z incorporation during the transcriptional response to HU.

overall_design: To assess the impact H2A.Z incorporation has on gene expression in S. cerevisiae during HU exposure we sequenced poly(A)-enriched libraries from six biological replicates of wild-type, htz1Δ, swr1Δ, and htz1Δswr1Δ mutants before and after a 90 minute treatment with HU (200 mM).

first: Hilary

last: Brewis

first: Peter

middle: C

last: Stirling


title: Characterizing the regulatory effects of H2A.Z and SWR1 on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae

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


title: Characterizing the regulatory effects of H2A.Z and SWR1 on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae [ChIP-seq]

overall_design: H2A.Z incorporation before and after a 90 minute treatment with HU (200 mM), was mapped using MNase Native Chromatin Immunoprecipitation of FLAG tagged H2A.Z followed by high-throughput sequencing (MNase-NChIP-seq) of both the solubilized chromatin (INPUT) and H2A.Z enriched (IP) fractions.


title: An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants

city: Pittsburgh

first: Quasar

last: Padiath

state: PA

address: 130 DeSoto St., Dept. of Human Genetics

department: Human Genetics

institute: University of Pittsburgh

summary: Autosomal Dominant Leukodystrophy (ADLD) is a fatal, adult-onset neurological disorder characterized by extensive CNS demyelination. Most cases of ADLD are caused by tandem genomic duplications involving the lamin B1 gene (LMNB1), while a small subset result from genomic deletions upstream of the gene. However, recently identified families carrying the LMNB1 gene duplication, but lacking demyelination, have been found, suggesting the involvement of a non-coding regulatory element. To investigate this, a LMNB1-specific aCGH was conducted using DNA from these newly discovered families and canonical ADLD cases. This approach identified a genomic region, belonging to a silencer element, that is absent in ADLD cases with a LMNB1 duplication or deletion.

overall_design:
Genomic DNA was isolated from whole blood from individuals with LMNB1 duplications or deletions. The DNA was analyzed using a custom 8×15K HD-CGH microarray designed to detect copy number variations specifically within the LMNB1 gene (Design# 035726_20110728). DNA isolation (Gentra Puregene kit (Qiagen)) and preparation (Agilent SureTag DNA Labeling Kit) were performed according to the manufacturer’s protocols. Test DNA was labeled with Cy5-dUTP, and control DNA with Cy3-dUTP. The samples were hybridized and scanned at 5 µm resolution using the Agilent G2565CA microarray scanner. Image data was extracted using Agilent’s Feature Extraction program, then normalized and analyzed with Agilent CytoGenomics v. 4.0.3.12. All genome coordinates were based on the human genome assembly GRCh37/hg19.

Please note that the raw data file for GSM8703288 has been updated on Jan 3, 2024.

first: Nmezi

last: Bruce

first: Padiath

last: Quasar


title: Epidermal growth factor dampens pro-inflammatory gene expression induced by interferon-gamma in global transcriptome analysis of keratinocytes

status: Public on Jan 09 2025

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The impact of EGFR ligands (i.e. EGF) on interferon signaling is unclear. The purpose of this study was to investigate the impact of EGF on IFN-γ transcriptional responses on a genome-wide scale in keratinocytes. RNA-seq was performed in human keratinocyte (HaCaT) cells treated with IFN-γ, EGF, both, or neither (control).  Differentially expressed genes (DEGs) in each treatment group, relative to control, were identified using DESeq2. Our findings suggest that the pro-inflammatory IFN-γ-induced transcriptome may be globally attenuated by EGF in keratinocytes, supporting an anti-inflammatory role of EGF in the skin.

overall_design: Expression profiling by high throughput sequencing of three replicates each of untreated, EGF treated, IFNgamma treated and EGF plus IFNgamma treated cells.

first: Brian

last: Pollack

first: David

last: Gibbs


title: Analysis of mRNA profiling in sinonasal inverted papilloma

status: Public on Dec 27 2024

city: Kaohsiung

first: Yi-Fang

last: Yang

address: No. 386, Dajhong 1st Rd., Zuoying Dist., Kaohsiung City 813414, Taiwan.

department: Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary: Sinonasal papilloma is the most common type of sinonasal tumor, with the inverted variant being the most frequent subtype. This variant is known for its potential for recurrence and propensity for malignant transformation. The aim of this study is to investigate the biomarkers and regulatory pathways involved in the development of sinonasal inverted papilloma (SNIP).

overall_design: To determine the roles of these biomarkers, we performed RNA exome sequencing on two SNIP samples and their paired normal tissues to analyze gene expression differences.

first: Yu-Hsuan

last: Lin


title: Parishin B Blocking TRIB3-AKT1 interaction inhibits Breast cancer Lung Metastasis

city: Changsha

first: Xiongtao

last: Cheng

address: Graduate School, Hunan University of Chinese Medicine, Changsha, Hunan 410208, P. R. China

institute: Department of Oncology, The First Hospital of Hunan University of Chinese Medicine

summary: TRIB3 has been reported to mediate breast cancer (BC) proliferation and metastasis by interacting with AKT1, and blocking the interaction between TRIB3 and AKT1 can inhibit the progression of BC. Besides, inhibiting TRIB3 to turn “cold tumor” hot has also been proved to be an effective therapeutic strategy for BC. Thus, this study aim to find drugs that can bind to TRIB3 to inhibit BC progression, and further elucidate its mechanism.

overall_design: The possible inhibitors of TRIB3 were screened by high-throughput molecular docking, CETSA, and CO-IP assay. Then, the effect of TRIB3 inhibitor anti BC was assessed by CCK-8 assay, flow cytometry, plate colony formation assay, and transwell assay; and the RNA-seq was empolyed to study the potential mechanism of Parishin B (PB) anti-BC. Finally, the effect of TRIB3 inhibitor on BC lung metastasis in vivo was evaluated..

first: Xiongta

first: Jianguo

last: Sun

first: Shouhong

last: Chen


title: Neutrophils-derived itaconate facilitates viral infection via alkylating GDI2 [RNA-seq]

status: Public on Dec 25 2024

city: Shanghai

first: Shulei

last: Yin

state: Shanghai

address: No.800 Xiangyin Road, Yangpu District

department: Department of Immunology

institute: Naval Medical University

summary: The objective was to investigate the disparity in gene expression between DMSO-treated group and OI-treated group following VSV infection.

overall_design: Macrophages were treated with DMSO or OI (itaconate) for 12 hours following infection with VSV for 8 hours, and then subjected to RNA-seq.

first: S

first: Y

last: Tao

last: Xu

last: Yu


title: Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KvPC organoids in nu/nu mice

status: Public on Dec 24 2024

city: Cambridge

first: Giulia

last: Biffi

address: Robinson way

country: United Kingdom

institute: University of Cambridge

summary: We investigated the effect of SMAD4 loss in KvPC PDAC tumors

overall_design:
Single-cell RNA-sequencing (scRNA-seq) of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KvPC (i.e. KRASG12v; p53 mutant) organoids in nu/nu mice
8 samples in total - 4 Smad4 WT KvPC tumors; 4 Smad4 KO KvPC tumors

first: Eloise

last: Lloyd

first: Muntadher

last: Jihad


title: Low avidity T cells drive endogenous tumor immunity in mice and humans

city: Farmington

first: Summit

last: Singhaviranon

state: Connecticut

address: 263 Farmington Ave

institute: University of Connecticut School of Medicine

summary: CD8 T cells which recognize neoepitopes are central to immune control of cancers. T cells, through T cell receptors, recognize neoepitope peptide-MHC I on cancer cells. The strength (or avidity) of the T cell receptor- peptide-MHCI interaction is a critical variable in immune control of cancers in vivo. Here, analyzing neoepitope-specific CD8 cells of distinct avidities to validated neoepitopes of a mouse tumor, low avidity T cells are observed to be the sole mediators of cancer control in vivo. Low avidity cells are also observed to be solely responsive to checkpoint blockade in mice and in humans. High avidity T cells are not only ineffective but suppress immune response. The mechanistic basis of the differences in the anti-tumor activity of cells of low and high avidities, lies in the higher exhaustion status of high avidity cells. High avidity T cells have a distinct transcriptomic profile which creates an Avidity Score, used here to identify in silico, the low and high avidity T cell populations in mice and humans. Surprisingly, CD8 T cells with identical TCRs exhibit a wide variation in avidities, suggesting a novel level of regulation of T cell activity. These observations, and the mechanisms that underlie them, shed new light on the endogenous T cell response to cancer and suggest new avenues in cancer immunotherapy.

overall_design:
Low, med, or high avidity CD8 TILs specific to the MethA neoepitope PDPRMUT were isolated for 10x multiomic sequencing.
The processed data files generated from both GEX and FBC raw data are linked to the corresponding GEX sample records.

first: Joseph

last: Dempsey

first: Adam

last: Hagymasi

first: Ion

last: Mandoiu

first: Pramod

last: Srivastava


title: TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders

status: Public on Dec 28 2024

city: Zwijnaarde

first: Kevin

last: Verstaen

address: Technologiepark-Zwijnaarde 71

department: VIB Single Cell Core

country: Belgium

institute: VIB

summary: Since the precursor frequency of naïve T cells is extremely low, investigating the early steps of antigen-specific T cell activation is challenging. To overcome this detection problem, adoptive transfer of a cohort of T cells purified from T cell receptor (TCR) transgenic donors has been extensively used but is not readily available for emerging pathogens. Constructing TCR transgenic mice from T cell hybridomas is a labor-intensive and sometimes erratic process, since the best clones are selected based on antigen-induced CD69 upregulation or IL-2 production in vitro, and TCR chains are PCR-cloned into expression vectors. Here, we exploited the rapid advances in single cell sequencing and TCR repertoire analysis to select the best clones without hybridoma selection, and generated CORSET8 mice (CORona Spike Epitope specific CD8 T cell), carrying a TCR specific for the Spike protein of SARS-CoV-2. Implementing newly created DALI software for TCR repertoire analysis in single cell analysis enabled the rapid selection of the ideal responder CD8 T cell clone, based on antigen reactivity, proliferation and immunophenotype in vivo. Identified TCR sequences were inserted as synthetic DNA into an expression vector and transgenic CORSET8 donor mice were created. After immunization with Spike/CpG-motifs, mRNA vaccination or SARS-CoV2 infection, CORSET8 T cells strongly proliferated and showed signs of T cell activation. Thus, a combination of TCR repertoire analysis and scRNA immunophenotyping allowed rapid selection of antigen-specific TCR sequences that can be used to generate TCR transgenic mice.

overall_design: We immunized C57BL/6 mice with Spike protein every 14 days for a total of three immunisations. From these mice, we sorted splenic T cells and used an MHC class I tetramer to discriminate Spike-reactive and non-reactive T cells. The tetramer identifies CD8 T cells directed to a conserved and highly immunogenic epitope (VNFNFNGL) of the SARS-CoV-2 spike protein. A naïve mouse was taken along as a backdrop for the cellular phenotypes. Ultimately, we subjected 3 samples for single cell sequencing: Tetramer positive T cells originating from the immunised mice, Tetramer negative T cells originating from the immunized mice, and tetramer negative T cells originating from the naïve control mouse.

first: Nincy

last: Debeuf

first: Sahine

last: Lameire

first: Stijn

last: Vanhee

first: Bart

middle: N

last: Lambrecht


title: Fatty acid synthase (Fasn) inhibition improves hypertension-induced erectile dysfunction by suppressing oxidative stress and NLRP3 inflammasome-dependent pyroptosis through activating the Nrf2/HO-1 pathway

first: Jiaochen

last: Luan

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Background: Erectile dysfunction (ED) is a prevalent male sexual disorder, commonly associated with hypertension, though the underlying mechanisms remain poorly understood. Objective: This study aims to explore the role of Fatty acid synthase (Fasn) in hypertension-induced ED and evaluate the therapeutic potential of the Fasn inhibitor C75. Materials and Methods: Erectile function was assessed by determining the intracavernous pressure/ mean arterial pressure (ICP/MAP) ratio, followed by the collection of cavernous tissue for transcriptomic and non-targeted metabolomic analyses. In vitro, a concentration of 10-6 M angiotensin II (Ang II) was applied to rat aortic endothelial cells (RAOECs) to establish a model of hypertension. In vivo, spontaneously hypertensive rats (SHR) were randomly divided into two groups. The SHR+C75 group received intraperitoneal injections of C75 at a dose of 2 mg/kg once a week. After five weeks of treatment, the erectile function of the rats was assessed, and penile tissues were harvested for further analysis. Molecular and protein expression were assessed using Western blotting, qRT-PCR, immunofluorescence staining, and immunohistochemistry. Results: The SHR exhibited ED, indicated by reduced maximum ICP/MAP ratios. Histologically, corpus cavernosum tissue of SHR showed elevated fibrosis and endothelial dysfunction. Additionally, increased expression of the NLRP3 inflammasome, Caspase-1, GSDMD, and the pro-inflammatory cytokines IL-1β and IL-18 was observed. Multi-omics analysis revealed significant enrichment in lipid metabolic pathways, with Fasn identified as a hub gene. In vitro, siFasn and C75 enhanced antioxidant markers Nrf2 and HO-1, reduced ROS accumulation, and suppressed NLRP3 and GSDMD levels. In vivo, C75 treatment restored endothelial function and reversed erectile dysfunction, accompanied by decreased oxidative stress and pyroptosis in the penile corpus cavernosum. Conclusion: These findings suggest that Fasn inhibition may offer a promising therapeutic strategy for hypertension-induced ED by alleviating oxidative stress and suppressing NLRP3 inflammasome-dependent endothelial cell pyroptosis via activation of the Nrf2/HO-1 pathway.

overall_design: RNA-seq profiles of penile cavernous tissue of spontaneously hypertensive rats (SHR) and normal controls (Norm)

first: Mengchi

first: Qi

last: Gu

first: Xuan

last: Zhou

first: Yunqiang

last: Shao

first: Tong

last: Chen

first: Jiayi

last: Zhang

first: Zheng

last: Zhu

first: Ninghong

last: Song

first: Jie

last: Yang


title: Neutrophils-derived itaconate facilitates viral infection via alkylating GDI2

first: Shulei

last: Yin

overall_design: Refer to individual Series


title: Neutrophils-derived itaconate facilitates viral infection via alkylating GDI2 [scRNA-seq]

summary: The purpose is to investigate alterations in gene expression across diverse cellular subsets within the pulmonary tissue of mouse infected with VSV.

overall_design: 8-week old WT C57BL/6J mice were infected (i.p.) with VSV. 12 hours after infection, mouse was euthanized and their lungs were harvested.

first: S

first: Y

last: Tao

last: Xu

last: Yu


title: Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [ChIP-seq]

status: Public on Dec 22 2024

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: RBFox2 ChIP-seq in WT, ActD, RIN, RNase treated C2C12 cells.

overall_design: ChIP-seq

first: Huating

last: Wang

first: Qiang

last: Sun

first: Qin


title: Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [Hi-C]

summary: Hi-C in RBFox2 knockdown K562 and RBFox2 knockout C2C12 cells, Hi-C in ActD, RNase, and RNase inhibitor (RIN) treated C2C12 cells.

overall_design: Hi-C


title: Nuclear translocation of TfR1 facilitating tumor progression via p53-mediated gene regulation

city: Beijing

first: Qizhi

address: Chaoyang District

institute: Chinese Academy of Sciences


title: Q11, a CYP2E1 inhibitor, exerts anti-hepatocellular carcinoma effect by inhibiting M2 macrophage polarization

status: Public on Dec 26 2024

city: zhengzhou city

first: Cunzhen

state: Henan Province

address: 100 No, kexue road

institute: Zhengzhou university

summary: Despite significant advancements in cancer immunotherapy, many patients continue to respond poorly. Novel therapeutic strategies and drugs are urgently needed. Here, we found that CYP2E1 is significantly upregulated in M2 macrophages. The CYP2E1 inhibitor, Q11, could inhibit M2 macrophage polarization, while CYP2E1 overexpression could promote it. Increased levels of CYP2E1 and M2 macrophages in the tumor microenvironment of HCC patients correlate with poor prognosis. Q11 could inhibit tumor cells by targeting M2 macrophages rather than directly attacking tumor cells. Both Q11 and Cyp2e1 knockout could effectively suppress tumor growth. Q11 reduces the production of CYP2E1 metabolites (±)9(10)-DiHOME and (±)12(13)-DiHOME, thus attenuating PPARγ activation and M2 macrophage polarization. In summary, our findings suggest that Q11 could suppress M2 macrophage polarization by modulating the CYP2E1/(±)9(10)-DiHOME or (±)12(13)-DiHOME/PPARγ axis, indicating that CYP2E1 inhibition may be a novel therapeutic strategy for HCC and positioning Q11 as a promising therapeutic agent.

overall_design: The experiment was divided into three groups: control group, model group, and drug treatment group. J774A.1 cells were used. Cells in the control group were cultured under normal conditions. Cells in the model group were induced into M2 macrophages by treatment with 10 ng/mL IL-4 and IL-13, respectively. In the Q11 group, Q11 was added simultaneously with IL-4 and IL-13 during the induction process.

first: Yan

last: Fang

first: Hailing

last: Qiao


title: A Transcriptomic Dataset of Liver Tissues from Global and Liver-Specific Bmal1 Knockout Mice

status: Public on Dec 23 2024

city: YANGLING

first: Guohao

last: Han

address: NWAFU

institute: NWAFU

summary: The circadian clock system regulates a wide range of physiological processes in mammals, and the core circadian clock gene Bmal1 is crucial for maintaining the oscillations of circadian clock system by controlling the rhythmic expression of numerous clock-controlled genes. These data offer a valuable resource for researchers studying the role of BMAL1 in liver physiology and pathology, as well as the broader field of circadian biology.

overall_design:
To explore the transcriptional changes associated with Bmal1 deletion in liver tissues, we collected the liver tissues of global and liver-specific Bmal1 knockout mice at two circadian time points (CT2 and CT14), and used them for RNA-seq analysis. Bmal1+/−mice on C57BL/6J background were bred to generate Bmal1+/+ and Bmal1-/- mice . The Bmal1f/f (F) and Alb-Cre mice were bred to generate L-Bmal1−/− (liver- specific Bmal1 knockout, LKO) mice.

KO = global Bmal1 knockout
LKO = liver-specific Bmal1 knockout
F (Bmal1f/f) = the control mice for LKO (liver-specific Bmal1 knockout, Alb-Cre; Bmal1f/f );  These mice  (Bmal1f/f) have a floxed Bmal1 genotype but do not express Cre, serving as appropriate controls for the liver-specific knockout.


title: BBOX1 restrains TBK1-mTORC1 oncogenic signaling in clear cell renal cell carcinoma

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: Clear cell renal cell carcinoma (ccRCC) is a metabolic disease that is believed to arise from renal proximal convoluted tubule (PCT) epithelial cells. However, the signaling events leading to ccRCC development are not completely understood. Here, we report that a carnitine synthesis enzyme predominantly expressed in PCT cells, γ-butyrobetaine hydroxylase 1 (BBOX1), is a novel ccRCC tumor suppressor. BBOX1 expression is lost in transformed primary renal epithelial cells and ccRCC patient tumors. Restoring BBOX1 expression in ccRCC tumor cells suppresses cell viability in physiological conditions as well as tumor growth and metastasis in xenograft models. Conversely, BBOX1 inhibition increases ccRCC tumor growth. To dissect the mechanism, we performed mass spectrometry analysis of BBOX1 interacting proteins and identified TANK-binding kinase 1 (TBK1). Binding was abrogated by introducing a mutation in BBOX1 that rendered the enzyme inactive. Mechanistically, BBOX1 loss leads to TBK1-dependent mTORC1 activation and increased glycolysis. Thus, the BBOX1-TBK1 axis represents a novel mechanism of dysregulated metabolic signaling offering potential new therapeutic strategies to target ccRCC.

overall_design: Clear cell renal cell carcinoma cells grown in culture or in xenografts, with or without restoring BBOX1 expression, followed by RNA-seq. Three replicates per experimental group.

first: Chengheng

last: Liao

first: Qing


title: mRNA-seq of AID-expressing cells from mice infected with WT or M2.Stop 73.Bla MHV68

status: Public on Dec 20 2024

city: Little Rock

first: Mark

last: Manzano

state: AR

address: 4301 W Markham St

department: Microbiology & Immunology

institute: University of Arkansas for Medical Sciences

summary: Gammaherpesviruses (GHV) are DNA tumor viruses that establish lifelong latent infections in lymphocytes. For viruses such as Epstein-Barr virus (EBV) and murine gammaherpesvirus 68 (MHV68), this is accomplished through a viral gene-expression program that promotes cellular proliferation and differentiation, especially of germinal center (GC) B cells. Intrinsic host mechanisms to control virus-driven cellular expansion are incompletely defined. Using a small-animal model of GHV pathogenesis, we identify the B cell-specific latency gene M2, an MHV68 mediator of GC B cell differentiation, as a viral gene product that is sufficient to induce p53 in a manner that is dependent on Src kinase activity. To understand the function of M2 in germinal center B cells in vivo, we infected AID-cre tdTomato reporter mice with WT or M2.Stop 73.Bla MHV68. At 16 dpi, draining lymph nodes were harvested and treated with CCF4-AM. AID+ and AID+Bla+ lymphocytes were sorted from WT and M2.Stop MHV68 infected tissue and sent for ultra-low input RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of ultra-low input RNA-seq data for uninfected and infected AID+ lymphocytes at 16 dpi with WT or M2.Stop (frameshift stop) 73.Bla MHV68.

first: J Craig

last: Forrest

first: Shana

last: Owens


title: Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice.

first: Giulia

last: Biffi

summary: We investigated the effect of SMAD4 loss in KPC PDAC tumors

overall_design:
Single-cell RNA-sequencing (scRNA-seq) of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC (i.e. KRASG12D; p53 mutant) organoids in nu/nu mice. These data have been sequenced twice and the 2 sequenced datasets were merged in the final paper. Batch 1 (SLX-21116) has reads from 2 lanes, and Batch 2 (SLX-21289) has reads from 1 lane.
9 samples in total - 3 KPC SMAD4 WT; 6 KPC SMAD4 KO

first: Eloise

last: Lloyd

first: Muntadher

last: Jihad


title: Association between Activated Loci of HML-2 Primate-Specific Endogenous Retrovirus and Newly Formed Chromatin Contacts in Human Primordial Germ Cell-like Cells

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: The pluripotent stem cell (PSC)-derived human primordial germ cell-like cells (PGCLCs) are a cell culture-derived surrogate model of embryonic primordial germ cells. Upon differentiation of PSCs to PGCLCs, multiple loci of HML-2, the hominoid-specific human endogenous retrovirus (HERV), are strongly activated, which is necessary for PSC differentiation to PGCLCs. In PSCs, strongly ac-tivated loci of HERV-H family HERVs create chromatin contacts, which are required for the plu-ripotency. Chromatin contacts in the genome of human PSCs and PGCLCs were determined by Hi-C sequencing, and their locations were compared with those of HML-2 loci strongly activated in PGCLCs but silenced in the precursor naïve iPSCs. In both iPSCs and PGCLCs, the size of chromatin contacts were found to be around one megabase, which corresponds to the Topologically Associ-ated Domains in the human genome but is slightly larger in PGCLCs than iPSCs. The number of small-sized chromatin contacts diminished while numbers of larger-sized contacts increased. The distances between chromatin contacts newly formed in PGCLCs and the degrees of activation of the closest HML-2 loci showed significant inverse correlation. Our study provides evidence that strong activation of HML-2 provirus loci may be associated with newly formed chromatin contacts in their vicinity, potentially contributing to PSC differentiation to the germ cell lineage.

overall_design: Hi-C sequencing of proximally ligated DNA isolated from human naïve iPSCs and PGCLCs

first: Vargas

last: Bianca Cordazzo

first: Shioda

last: Toshihiro


title: Gene expression changes in human pluripotent and fibroblast cells  and mouse embryonic fibroblasts upon NORAD lncRNA knockdown

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

summary: RNA sequencing data from knockdowns of the long non-coding RNA NORAD in human foreskin fibroblasts (HFFs), human embryonic stem cells (hESCs), and mouse embryonic fibroblasts (MEFs) for varying durations (8–72 hours, depending on the cell type). Total RNA was purified using TRI-reagent, and libraries were prepared using the CEL-seq2 protocol. RNA-seq data were processed with cutadapt, aligned to the reference genome using RNA-STAR, and gene expression counts were generated with HTSEQ count.

overall_design: Human embryonic stem cells, human foreskin fibroblasts, and mouse embryonic fibroblasts were transfected with siRNA against NORAD lncRNA and compared to control siRNA. Transfected cells were incubated for different time periods and then subjected to RNA sequencing. Each experiment was performed in several replicates.

first: Amir

last: Argoetti

first: Dor

last: Shalev

first: Galia

last: Polyak

first: Noa

last: Shima

first: Hadas

last: Biran

last: Hashimshony

first: Yael

last: Mandel-Gutfreund


title: Neuroprotective role of sialic-acid-binding immunoglobulin-like lectin-11 in humanized transgenic mice

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

summary: Brain aging is a chronic process linked to inflammation, microglial activation, and oxidative damage, which can ultimately lead to neuronal loss. Sialic acid-binding immunoglobulin-like lectin-11 (SIGLEC-11) is a human lineage-specific microglial cell surface receptor that recognizes α-2-8-linked oligo-/polysialylated glycomolecules with inhibitory effects on the microglial inflammatory pathways. Recently, the SIGLEC11 gene locus was prioritized as a top tier microglial gene with potential causality to Alzheimer’s disease, although its role in inflammation and neurodegeneration remains poorly understood. In this study, aged Siglec-11 transgenic (tg) mice, which expressed the human SIGLEC-11 receptor on microglia and tissue macrophages, were investigated. The brains of the Siglec-11 tg mice were analyzed in 6-month-old mature mice and 24-month-old aged mice using immunohistochemistry and transcriptomics. Results showed decreased density and fewer clusters of ionized calcium binding adaptor molecule 1 (Iba1)-positive microglial cells in the hippocampus and substantia nigra, as well as less lipid-laden microglia in the Siglec-11 tg in comparison to wildtype (WT) controls. Additionally, Siglec-11 tg mice exhibited less age-related neuronal loss in the substantia nigra pars compacta in comparison to WT mice. Transcriptome analysis revealed suppression of oxidative phosphorylation and inflammatory pathways in Siglec-11 tg brains at 6 months, with further suppression of complement and coagulation cascades at 24 months of age in comparison to WT mice. Gene transcript levels of the pro-inflammatory cytokines tumor necrosis factor alpha (Tnf) and interleukin 1 beta (Il-1b),  as well as the oxidative stress markers cytochrome b-245 alpha and beta (Cyba and Cybb) and the nitric oxide synthase 2 (Nos2) were reduced in the brains of 24-month-old Siglec-11 tg mice relative to WT controls. Brains of 24-month-old Siglec-11 tg mice also exhibited lower gene transcription of complement component 4 and integrin alpha M (C4 and Itgam), along with the complement C1q subcomponents a and c (C1qa and C1qc). In summary, aged Siglec-11 tg mice displayed reduced brain inflammation and oxidative stress, as well as protection against age-related neuronal loss in the substantia nigra.

overall_design: To investigate the effects of the human Siglec-11 receptor on brain aging, we aged Siglec-11 transgenic mice to two different age groups of 6- and 24- months of age, and sacrificed them at those ages, comparing each to its respective age group wildtype BL6 mice. We collected the brain and did bulk-RNA sequencing at both time points

first: Tawfik

last: Abou Assale

first: negin

last: Afrang

first: Jannis

last: Wissfeld

first: German

last: Cuevas-Rios

first: Christine

last: Klaus

first: Bettina

last: Linnartz-Gerlach


title: Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers

status: Public on Dec 21 2024

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Cis-regulatory elements (CREs), such as enhancers and promoters, are fundamental regulators of gene expression and, across different cell types, the MYC locus utilizes a diverse regulatory architecture driven by multiple CREs. To better understand differences in CRE function, we performed pooled CRISPR inhibition (CRISPRi) screens to comprehensively probe the 2.8Mb topologically-associated domain containing MYC in 6 human cancer cell lines with nucleotide resolution. We map 32 CREs where inhibition leads to changes in cell growth, including 8 that overlap previously identified enhancers.  Targeting specific CREs decreased MYC expression by as much as 60%, and cell growth by as much as 50%. Using 3-D enhancer contact mapping, we found that these CREs almost always contact MYC but less than 10% of total MYC contacts impact growth when silenced, highlighting the utility of our approach to identify phenotypically-relevant CREs. We also detect an enrichment of lineage-specific transcription factors (TFs) at MYC CREs and, for some of these TFs, find a strong, tumor-specific correlation between TF and MYC expression not found in normal tissue. Taken together, these CREs represent systematically identified, functional regulatory regions and demonstrate how the same region of the human genome can give rise to complex, tissue-specific gene regulation.

overall_design:
H3K27ac HiChIP for 6 cancer cells lines: A375, A549, HT29, K562, MDAMB231, and PC9
H3K27ac HiChIP after CCAT1 knockdown with Cas13d

first: Christina

last: Caragine

first: Victoria

last: Le

first: Meer

last: Mustafa

first: Bianca Jay

last: Diaz

first: John

middle: A

last: Morris

first: Simon

last: Müller

first: Alejandro

last: Mendez-Mancilla

first: Evan

last: Geller

last: Liscovitch-Brauer

middle: E


title: Chimeric antigen receptor macrophages (CAR-M) sensitize HER2+ solid tumors to PD1 blockade [TCR-Seq]

city: Philadelphia

first: Michael

last: Klichinsky

address: 3675 Market Street Ste. 401

institute: Carisma Therapeutics

summary: We previously developed human CAR macrophages (CAR-M) and demonstrated redirection of macrophage anti-tumor function leading to tumor control in immunodeficient xenograft models. Here, we developed clinically relevant fully immunocompetent syngeneic models to evaluate the potential for CAR-M to remodel the tumor microenvironment (TME), induce T cell anti-tumor immunity, and sensitize solid tumors to PD1/PDL1 checkpoint inhibition. In vivo, anti-HER2 CAR-M significantly reduced tumor burden, prolonged survival, remodeled the TME, increased intratumoral T cell and natural killer (NK) cell infiltration, and induced epitope spreading. CAR-M therapy protected against antigen-negative relapse in a T cell dependent fashion, confirming long-term anti-tumor immunity. In HER2+ solid tumors resistant to anti-PD1(aPD1) monotherapy, the combination of CAR-M and aPD1 significantly improved tumor growth control, survival, and remodeling of the TME. These results demonstrate synergy between CAR-M and T cell checkpoint blockade and provide a strategy to enhance response to aPD1 therapy for patients with non-responsive tumors.

overall_design:
CT26 BALB/c mice were either untreated, administered anti-PD1 alone,  treated with CAR macrophages alone, or treated with CAR Macrophages and anti-PD1. Tissue and blood were harvested 13 days after treatment for TCR sequencing by Adaptive Biotechnologies

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Adaptive Biotechnologies does not provide raw data.
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first: Stefano

last: Pierini

first: Rashid

last: Gabbasov

first: Maria

last: Oliveira-Nunes

first: Rehman

last: Qureshi

first: Alison

last: Worth

first: Shuo

last: Huang

first: Karan

last: Nagar

first: Crystal

last: Griffin

first: Lurong

last: Lian

first: Yumi

last: Ohtani

first: Kayleigh

last: Ross

first: Christopher

last: Sloas

last: Ball

first: Benjamin

last: Schott

first: Poonam

last: Sonawane

first: Linara

last: Cornell

first: Daniel

last: Blumenthal

first: Sotheavy

last: Chhum

first: Nicholas

last: Minutolo

first: Kerri

last: Ciccaglione

first: Lauren

last: Shaw

first: Isaac

last: Zentner

first: Hyam

last: Levitsky

first: Olga

last: Shestova

first: Saar

middle: I

last: Gill

first: Bindu

last: Vargese

last: Cushing

first: Sabrina

last: DeLong

first: Sascha

last: Abramson

first: Thomas

last: Condamine


title: MAP3K1 mutations confer tumor immune heterogeneity in hormone receptor-positive HER2-negative breast cancer

first: Yuwen

last: Cai

institute: Fudan University Shanghai Cancer Center

summary: Hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) breast cancer, the most common type of breast cancer, is facing challenges such as endocrine therapy resistance and distant relapse. Immunotherapy has shown progress in treating triple-negative breast cancer, but immunological research on HR+/HER2- breast cancer is still in its early stages. Here, we performed a multi-omics analysis of a large cohort of HR+/HER2- breast cancer patients (n = 351) and revealed that HR+/HER2- breast cancer possessed a highly heterogeneous tumor immune microenvironment. Notably, the immunological heterogeneity of HR+/HER2- breast cancer was related to MAP3K1 mutation and we validated experimentally that MAP3K1 mutation could attenuate CD8+ T cell-mediated antitumor immunity. Mechanistically, MAP3K1 mutation suppressed MHC-I-mediated tumor antigen presentation through promoting the degradation of antigen peptide transporter 1/2 (TAP1/2) mRNAs, thereby driving tumor immune escape. In preclinical models, the postbiotics tyramine could reverse the MAP3K1 mutation-induced MHC-I reduction, thereby augmenting the efficacy of immunotherapy.

overall_design: 67NR mouse breast cancer cell lines were knocked out for Map3k1 expression. The knocked-out cell lines were then overexpressed with either Map3k1-WT (WT) or Map3k1-Mut (Mut: 1-1222 aa), and then orthotopically injected into BALB/c mice (randomly assigned). When the tumor volume reached 1000 mm3, mice were euthanized using the carbon dioxide method, and tumors were dissected and sent for RNA sequencing.

first: Yu-Wen

first: Cui-Cui

last: Liu

first: Yan-Wu

last: Zhang

first: Lie

last: Chen

first: Yi-Ming

first: Xin

last: Xiong

first: Zhi-Ming

last: Shao

first: Ke-Da

last: Yu


title: Spatial transcriptomic analysis of liver-innervating vagal sensory neurons

city: Bronx

first: Jeffrey

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: We report the effect of ablating liver-innervating vagal sensory neurons in diet-induced obese male mice

overall_design: Examination of diet-induced obese male mice in either Advillin-cre/ERT2 Control or Advillin-cre/ERT2 Casp3

first: Jiyeon

last: Hwang

first: Junichi

last: Okada

first: Li

first: Young-Hwan

last: Jo


title: Multichrome encoding-based multiplexed, spatially resolved imaging reveals single-cell RNA epigenetic modifications heterogeneity

first: Xiaochen

last: Tang

address: 1678 Dongfang Road, Pudong New Area, Shanghai

institute: Shanghai Jiao Tong University

summary: Understanding the heterogeneity of epigenetic modifications within single cells is pivotal for unraveling the nature of the complexity of gene expression and cellular function. In this study, we have developed a strategy based on multichrome encoding and “AND” Boolean logic recognition for multiplexed, spatially resolved imaging of single-cell RNA epigenetic modifications, termed as PRoximity Exchange-assisted Encoding of Multichrome (PREEM). Through the implementation of this strategy, we can now map the expression and nuclear distribution of multiple site-specific RNA epigenetic modifications at the single-molecule resolution level in single-cells, and reveal the previously unknown heterogeneity. Notably, we demonstrate how these patterns change after treatment with various drugs. Moreover, cyclic imaging with tailed DNA self-assembly further suggest the scalability and adaptability of PREEM’s design. As an innovative epigenetic modification imaging tool, PREEM not only broadens the horizons of single-cell epigenetics research, enabling joint analysis of multiple targets beyond the limitations of imaging channels, but also reveals cell-to-cell variability, thereby enhancing our capacity to explore cellular functions.

overall_design: To investigate the expression change of corresponding RNAs after drug treated, we established HeLa cell lines treated with six drugs, and we then performed gene expression profiling analysis using data obtained from RNA-seq at three time points.

first: Qiuhui

last: Pan

first: Xiaoli

last: Zhu


title: An Optimised Faecal microRNA Sequencing Pipeline Reveals Fibrosis in Trichuris muris Infection

city: Manchester

first: Emma

last: Layton

address: Dover street

institute: University of Manchester

type: Non-coding RNA profiling by high throughput sequencing

summary: The intestine is a site of diverse functions including digestion, nutrient absorption, immune surveillance, and microbial symbiosis. As such, intestinal homeostasis is vital for overall wellbeing. Faecal microRNAs (miRNAs) offer valuable non-invasive insights into the transcriptional state of the intestine. However, typical faecal miRNA yields and profiles remain incompletely characterised. Here, we develop an optimised protocol for faecal miRNA detection, and describe a reproducible murine faecal miRNA profile across several studies by performing a meta-analysis. By examining faecal miRNA changes during chronic infection with the gastrointestinal helminth, Trichuris muris, we identify the altered expression of miRNAs associated with fibrosis, barrier integrity and wound healing. Fibrosis was confirmed in vivo, suggesting a role for these miRNAs in regulating wound healing during chronic infection where the production of classical wound healing Th2 cytokines are low. Further implementations of this technique can identify novel hypotheses and therapeutic strategies in diverse disease contexts.

overall_design: 7 mice were gavaged with a low dose of Trichuris muris (mouse whipworm) eggs. 5 mice were gavaged with water as a control. Faecal samples were collected for small RNA sequencing at 21 and 35 days post-treatment for all mice. An additional collection was taken from the infected mice immediately prior to gavage with eggs / infection (I0).


title: Co-methylation Networks Associated with Cognition and Structural Brain Development During Adolescence

city: Atlanta

first: Dawn

middle: Marie

last: Jensen

state: Georgia

address: 55 Park Place

department: TReNDS Center

institute: Georgia State University

type: Methylation profiling by genome tiling array

summary: Typical adolescent neurodevelopment is marked by decreases in grey matter (GM) volume, increases in myelination, measured by fractional anisotropy (FA), and improvement in cognitive performance. To understand how epigenetic changes, methylation (DNAm) in particular, may be involved during this phase of development, we studied cognitive assessments, DNAm from saliva, and neuroimaging data from a longitudinal cohort of normally developing adolescents, aged nine to fourteen. We extracted networks of methylation with patterns of correlated change using a weighted gene correlation network analysis (WCGNA). Modules from these analyses, consisting of co-methylation networks, were then used in multivariate analyses with GM, FA, and cognitive measures to assess the nature of their relationships with cognitive improvement and brain development in adolescence. This longitudinal exploration of co-methylated networks revealed an increase in correlated epigenetic changes as subjects progressed into adolescence. Co-methylation networks enriched for pathways involved in neuronal systems, potassium channels, neurexins and neuroligins were both conserved across time as well as associated with maturation patterns in GM, FA, and cognition, revealing epigenetic mechanisms that could be involved in adolescent neural development.

overall_design: Networks of correlated methylation change were calculated using a WCGNA on difference scores of beta values collected from three time points. Modules of DNAm change with significant gene enrichment results were included in a multivariate analysis as the independent variable, while changes in gray matter volume, fractional anisotropy, and cognitive performance were the dependent variables.  Baseline age and sex were included as covariates, after ruling out significant effects for race, SES, and family ID.

first: Jiayu

first: Jessica

last: Turner

first: Julia

last: Stephen

first: Yu-Ping

last: Wang

first: Tony

last: Wilson

first: Vince

last: Calhoun

first: Jingyu


title: T helper 2 cell–directed immunotherapy eliminates precancerous skin lesions

first: Tomonori

last: Oka

department: CBRC

institute: Massachusetts general hospital

overall_design: Actinic keratoses were treated with either calcipotriol plus 5-FU or vaseline plus 5-FU in the randomized clinical trial. We have Day 0 before treatment samples and Day 5 after treatment samples in two groups. Total 4 groups.

first: Shadmehr

last: Demehri

first: Heehwa

middle: G

last: Son

first: Jongho

last: Park


title: An integrative multiparametric approach stratifies distinct phenotypes of blast phase chronic myelomonocytic leukemia with differential maturation status and drug sensitivity profiles

first: Kiran

last: Batta

address: The University of Manchester

summary: Approximately 30% of chronic myelomonocytic leukemia patients undergo transformation to a chemo-refractory blastic phase (BP-CMML). Seeking novel therapeutic approaches we profiled blast transcriptomes from 42 BP-CMMLs, observing extensive transcriptional heterogeneity and poor alignment to current AML classifications. BP-CMMLs displayed distinctive transcriptomic profiles, including enrichment for quiescence and variability in drug response signatures. Integrating clinical, immunophenotype and transcriptome parameters, RandomForest unsupervised clustering distinguished immature and mature subtypes characterized by differential expression of transcriptional modules, oncogenes, apoptotic regulators and patterns of surface marker expression. Subtypes differed in predicted response to AML drugs, validated ex vivo in primary samples. Iteratively refined stratification resolved a classification structure comprising five subtypes along a maturation spectrum, predictive of response to novel agents including consistent patterns for RTK, CDK, MTOR and MAPK inhibitors. Finally, we generated a clinically-applicable decision tree to stratify BP-CMML with high specificity and sensitivity, and potentially guide personalized drug selection for improved outcomes.

overall_design: RNA sequencing was performed on the available cryopreserved primary samples from BP-CMML and healthy control donors. Samples were enriched for live cells and FACS sorted for isolation of cell types of interest, followed by RNA extraction and subsequent library preparation and sequencing.

first: Kristian

last: Gurashi

first: Daniel

last: Wiseman


title: Mitochondrial haplotype dependant T cell activity

status: Public on Dec 19 2024

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

institute: Weizmann Institute

overall_design: Differential expression between mice with activated and non-activated T-cells, in two different mitochondrial background models

first: Tal

last: Yardeni


title: Schwann cell-specific ablation of Beclin 1 impairs peripheral myelination and leads to a progressive motor and sensory neuropathy

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
The core component of the class III phosphatidylinositol 3-kinase complex, Beclin 1, takes part in different protein networks, thus switching its role from inducing autophagy to regulating autophagosomal maturation and endosomal trafficking. While assessed in neurons, astrocytes and microglia, its role was far less investigated in myelinating glia, including Schwann cells (SCs), responsible for peripheral nerve myelination. Remarkably, the dysregulation in endosomal trafficking is emerging as a pathophysiological mechanism underlying peripheral neuropathies, such as demyelinating Charcot-Marie-Tooth diseases. By knocking out Beclin 1 in SCs we here generated a novel mouse model (Becn1 cKO), developing a severe and progressive neuropathy, accompanied by involuntary tremors, body weight loss and premature death. Ultrastructural analysis revealed abated myelination and SCs displaying enlarged cytoplasm with progressive accumulation of intracellular vesicles. Transcriptomic and histological analysis from sciatic nerves of 10-day and 2-month-old mice revealed pro-mitotic gene deregulation and increased SCs proliferation at both stages with axonal loss and increased immune infiltration in adults, well reflecting the progressive motor and sensory functional impairment that characterizes Becn1 cKO mice, compared to controls. Our study establishes a further step in understanding key mechanisms in SC development and points to Beclin 1 and its regulated pathways as targets for demyelinating CMT forms.
A novel conditional gene knockout  was generated to investigate the role that Beclin 1 exerts in Schwann cells and in myelination. The newly generated mouse line resulted in a model for severe and progressive peripheral neuropathy. Together with defective myelination, we described radial sorting defects, motor and sensory neuron impairments, immune infiltrate in adults and a huge transcripts deregulation. The emerged deregulated signalling pathways  highlighted how Beclin 1 is able to coordinate integrated signaling pathways essential for Schwann cell maturation and nerve development and homeostasis.

overall_design: Gene expression was measured using Affymetrix platform in sciatic nerve derived from Becn1 wild-type or conditional KO in 10 days old and 2 months old mice

first: Silvia

last: Bresolin

first: Luca

last: Persano

first: Matilde

last: Cescon


title: Effect of form derivation on mouse retinal transcriptome

first: Teele

last: Palumaa

address: 1365 Clifton Rd NE Building B

department: Ophthalmology

institute: Emory University

summary: The underlying molecular mechanisms resulting in myopia development are unknown. Here, we employed a mouse model of experimental myopia, inducing form-deprivation myopia using a diffuser goggle. We then analysed retinal transcriptome of form-deprived retinas and contralateral control retinas with RNA sequencing.

overall_design: Three male C57BL/6J mice were housed in a standard 12-12 hour light-dark cycle.From postnatal day (P) 28, mice were exposed to form-deprivation myopia (FDM) by surgically attaching a head-mounted diffuser goggle over the right eye. The left eye remained uncovered and served as an internal control. Refractive error, corneal curvature and axial length were measured at P28, P35, and P42. Myopic shift was confirmed in the goggled eye. Retinal tissue was collected at P42, RNA was extracted and mRNA levels analyzed using RNA-Seq.

first: Machelle

last: Pardue

first: Shruti

last: Balamurugan


title: The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases (Exp 4)

city: Marseille

first: Pierre

last: Milpied

address: Parc Scientifique de Luminy, case 906

country: France

institute: Centre d'Immunologie de Marseille-Luminy (CIML)

summary: Autoimmune liver diseases (AILD) are immune-mediated disorders in which CD4 T cells play a central role. However, the link between circulating self-antigen-specific CD4 T cells and the targeted tissue has not been extensively studied in AILD. We hypothesized that circulating autoreactive CD4 T cells were clonally and functionally related to dominant intra-hepatic pathogenic CD4 T cell clones. Single cell transcriptomic analysis of circulating self-antigen-specific CD4 T cells revealed a specific B-helper and immuno-exhausted transcriptional profile, which was conserved for different autoantigens, but distinct from several other types of foreign antigen specificities. In the blood, the dominant hepatic CD4 T cell clones had a similar transcriptomic signature and were enriched in the PD-1+ TIGIT+ HLA-DR+ CD4 T cell subset. In a mouse model, antigen-specific CD4 T cells acquired the immuno-exhausted transcriptional profile when they accumulated in the liver after local antigen reactivity. Locally, immune checkpoint molecules controlled the response of antigen-specific CD4 T cells responsible for liver damage. Our study reveals the origin and biology of liver-derived autoreactive CD4 T cells in the blood of AILD patients that are imprinted by the liver environment, and suggest a dysregulation of the immune checkpoint molecules pathways. Our study enables tracking and isolating circulating autoreactive CD4 T cells for future diagnostic and therapeutic purposes.

overall_design: For scRNA-seq analysis of peptide-restimulated CD4 T cells, CD154+ memory CD4 T cells were first sorted on BD FACSAriaII, one cell per well, in 96-well plates containing specific lysis buffer at the CRTI, Nantes. Plates were immediately frozen for storage at −80°C, and sent on dry ice to the Genomics core facility of CIML, Marseille, for further generating scRNAseq libraries with the FB5P-seq protocol as described22,58. Briefly, mRNA reverse transcription (RT), cDNA 5’-end barcoding and PCR amplification were performed with a template switching (TS) approach. After amplification, barcoded full-length cDNA from each well were pooled for purification and library preparation. For each plate, an Illumina sequencing library targeting the 5’-end of barcoded cDNA was prepared by a modified transposase-based method incorporating a plate-associated i7 barcode. Resulting libraries had a broad size distribution, resulting in gene template reads covering the 5’-end of transcripts from the 3rd to the 60th percentile of gene body length on average. As a consequence, sequencing reads covered the whole variable and a significant portion of the constant region of the TCRα and TCRβ expressed mRNAs, enabling assembly and reconstitution of TCR repertoire from scRNAseq data. Libraries prepared with the FB5P-seq protocol were sequenced on Illumina NextSeq2000 platform with P2 100-cycle kits, targeting 5×105-1×106 reads per cell in paired-end single-index mode with the following configuration: Read1 (gene template) 103 cycles, Read i7 (plate barcode) 8 cycles, Read2 (cell barcode and Unique Molecular Identifier) 16 cycles. We then used a custom bioinformatics pipeline to process fastq files and generate single-cell gene expression matrices and TCR sequence files, as described22,58.

first: Chuang

last: Dong

first: Amedee

last: Renand


title: The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases (Exp 3)


title: The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases (Exp 2)


title: Single-cell analysis of circulating autoreactive CD4 T cells of autoimmune hepatitis patients

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

overall_design: Refer to individual Series


title: The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases (Exp 1)


title: Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

institute: The Chinese University of Hong Kong


title: Transcriptomic analysis of  antigen-specific CD4 T cells infiltrating the liver (Figure 6)

city: Nantes

address: 30 Bd Jean Monnet

institute: CR2TI UMR1064

summary: Antigen-specific CD4 T cells immuno-exhausted transcriptional profile after local antigen reactivity in the liver.

overall_design: we designed a non-TCR-transgenic mouse model that allows the analysis of the emergence and modulation of CD4 T cell responses against a model antigen expressed by hepatocytes. We used a model of Balb/c mice in which the hemagglutinin (HA) expression was restricted to hepatocytes, by an inducible Cre recombinase under the control of hepatocyte-specific mTTR (transthyretin) promotor (HA/iCre). Experimental Design:   HA-specific CD4 T cells were isolated from the spleen and/or the liver: Group1 (HA i.m /Spleen): Mice immunized against HA (intra muscular immunization with Adenovirus-Cre; HA i.m); cells from spleen (n=4). Group2 (i HA i.m + Tamoxifen /Spleen): Mice expressing HA in the liver (Tamoxifen) and immunized against HA (AdCre i.m); cells from spleen (n=5). Group3 (HA i.m + Tamoxifen + Tamox/Liver): Mice expressing HA in the liver (Tamoxifen) and immunized against HA (Ad cre i.m and Plasmid HA); cells from liver (n=7)

first: Richard

last: Danger

first: Anaïs

last: Cardon

first: Thomas

last: Guinebretière


title: GATA6 is a Novel Regulator of Gene Expression and 3D Genome in Colorectal Cancer (HiC patient samples)

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern university

summary: Colorectal cancer (CRC) is one of the most lethal and prevalent malignancies with elusive molecular causes. While the abnormal activity of transcription factors has been reported as a vital component of cancer progression, the mechanism through which they function remains unclear. Here, through the analysis of primary human CRC tissue data, we identified GATA6 as a CRC specific regulator, whose expression upregulation is potentially associated with promoter hypomethylation. In the human genome, GATA6 showed preferential binding at tumor specific active enhancers. Through both auxin-inducible degron (AID) and CRISPR knockout, we showed that GATA6 depletion severely impaired clonogenicity and proliferation. GATA6 depletion caused the loss of CRC specific open chromatin, suggesting a specific regulatory role of GATA6 in CRC pathogenesis. Interestingly, we also discovered the co-occupancy of GATA6 with CTCF and its direct involvement in promoter enhancer loops, suggesting the possibility that GATA6 mediate transcriptional regulation through 3D genome. The loss of GATA6 led to alterations in E-P chromatin interactions of a panel of oncogenes, accompanied by the oncogene downregulation. Finally, we showed that GATA6 loss is detrimental to the xenograft tumor growth and thereby rescued mice survival. Taken together, we unrevealed a novel mechanism by which GATA6 contributes to CRC.

overall_design:
DLD1-GATA6-AID-IAA7 cell lines were established using the auxin-inducible degron(AID) system, in which target gene GATA6 has been degraded. DLD-1 cells were also engineered to knockout target gene GATA6 using CRISPR/cas9 system.
-----------------------------
Authors indicate "patient samples".

first: Huijue

last: Lyu

first: Xintong

last: Chen

first: Yang

last: Cheng

first: Te

last: Zhang

first: Ping

last: Wang

first: Josiah

last: Wong

first: Juan

first: Lena

last: Stasiak

first: Leyu

last: Sun

first: Guangyu

last: Yang

first: Lu


title: GATA6 is a Novel Regulator of Gene Expression and 3D Genome in Colorectal Cancer (CUT&Tag)

overall_design:
DLD1-GATA6-AID-IAA7 cell lines were established using the auxin-inducible degron(AID) system, in which target gene GATA6 has been degraded. DLD-1 cells were also engineered to knockout target gene GATA6 using CRISPR/cas9 system.
Cleavage Under Targets and Tagmentation (CUT&Tag) targeted for GATA6, CTCF, and histone marks H3K27ac, H3K4me3, H3K27me3 in DLD1-GATA6-AID-IAA7 cells.


title: GATA6 is a Novel Regulator of Gene Expression and 3D Genome in Colorectal Cancer


title: Cloning and comparison of human P63+ progenitor cells from various lung diseases [bulkRNA-seq]

city: Shanghai

first: Wei

last: Zuo

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: KRT5+P63+ progenitor cells located in the basal layer of the airway epithelium have been identified as a promising candidate for lung epithelium repair. To investigate P63+ progenitor cells in human, we cloned KRT5+P63+ progenitors from both healthy donors and patients with various lung diseases.

overall_design: Via bronchoscopy, a small amount of 3-5th level bronchi tissue sample were collected from patients. The obtained tissue was washed and enzymatically digested to form a single-cell suspension, which was then cultured under regenerative cell cloning system. In total, we conducted whole-genome RNA sequencing to analyze the transcriptome of P63+ progenitors from 44 donors, including 6 healthy controls and 12 patients with IPF, 13 with COPD, and 13 with non-cystic fibrosis bronchiectasis for comparative analysis.

first: Yueqing

last: Zhou

first: Yu

last: Zhao

first: Weipan


title: Fate mapping of human P63+ progenitor in vivo by single cell transcriptomic analysis [scRNA_seq]

summary: KRT5+P63+ progenitor cells located in the basal layer of the airway epithelium have been identified as a promising candidate for lung epithelium repair. To gain molecular insights into the fate specification process of human P63+ progenitor cells in the lung, we sorted the transplanted GFP+ cells at different time points using flow cytometry, followed by 10x Genomics single-cell RNA sequencing analysis. Unsupervised clustering of the cells resulted in the identification of 7 distinct populations.

overall_design: We isolated the human P63+ progenitors and transplanted the GFP-labelled P63+ progenitors into the bleomycin-injured mouse lung by intratracheal instillation. Mice were sacrificed at 8 and 35 days post transplantation and their lung tissue were harvest to detect GFP signal by fluorescence stereomicroscope, the region of which was dissect for single cell-RNA-seq (scRNA-seq). We utilized scRNA-seq to trace the fate of transplanted human P63+ progenitors at 8 days and 35 days post transplantation, which revealed cell types differentiated from the transplanted P63+ progenitors.