title: Life long effects of radiation and high fat dieat on the mouse left ventricular tissue

first: David

middle: A.

last: Goukassian

address: One Gustave L. Levy Place, Box 1014

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

summary: We studied the long-term effects of single whole-body gamma and simulated GCR irradiation (IR) and consumption of a Western Diet (WD) on the heart's left ventricle (LV). Three-month-old C57Bl/6J wild-type male and female mice were assigned to the following groups: 1) Gamma-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 2) simGCRsim-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 3) 270-days WD-fed animals with followup at 530 (males and females) and 750(males)/640(females). Control groups consisted of non-irradiated (non-IR) mice and normal diet-fed mice. Control groups were followed up similarly to the treatment groups.  LV tissues were collected at follow-up and subjected to bulk RNA sequencing analysis.  Total RNA was extracted from LV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use. A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit. The sequencing was performed on the Illumina NovaSeq-6000 platform to collect an average of 48 million 2x150bp paired-end reads per sample.FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) with STAR aligner (version 2.7.8a) with gene count quantification mode and obtained raw gene counts. Differential gene expression analysis and functional annotation were performed using DeSeq2 and fgsea R packages.  The results of the studies provide insight into the long-term transcriptome disturbance in response to irradiation and the Western diet, their association with structural and functional changes in LV, and implications in the development of cardiovascular disease (CVD). Furthermore, the study results pointed to the strong sex-biased pathophysiological and transcriptomic changes in LV.

first: Siras

last: Hakobyan

first: Roksana

last: Zakharyan

first: Ani

last: Stepanyan

first: Arsen

last: Arakelyan


title: Sexual dimorphism of the synovial transcriptome underpins greater PTOA disease severity in male mice following joint injury

status: Public on Jul 17 2024

city: Ann Arbor

first: Tristan

last: Maerz

state: MI

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Osteoarthritis (OA) is a disease with sex-dependent prevalence and severity in both human and animal models. We sought to elucidate sex differences in synovitis, mechanical sensitization, structural damage, bone remodeling, and the synovial transcriptome in the anterior cruciate ligament rupture (ACLR) mouse model of post-traumatic OA (PTOA).

overall_design: Male and female 12-week-old C57/BL6J mice were randomized to Sham or noninvasive ACLR with harvests at 7d or 28d post-ACLR. Ipsilateral (Sham, 7d or 28d ACLR) or contralateral knee synovium was dissected, then RNA was isolated from tissue for bulk RNA-sequencing and analysis.

first: Rachel

middle: F

last: Bergman

first: Lindsey

last: Lammlin

first: Lucas

last: Junginger

first: Easton

last: Farrell

first: Sam

last: Goldman

first: Rose

last: Darcy

first: Cody

last: Rasner

first: Alia

middle: M

last: Obeidat

first: Anne-Marie

last: Malfait

middle: E

last: Miller


title: Single-cell RNA transcriptome defines the signaling networks regulated by ACE2 in cornea

status: Public on Jul 15 2024

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary: For decades, it has been well accepted that corneal epithelial stem cells and their immediate progeny, the early transit amplifying (eTA) cells, reside in the limbal epithelial basal layer. Activation of quiescent stem/eTA cells is required for proper re-epithelialization during wound healing. The molecular profile of activated stem/eTA cells remains unclear because of difficulties in obtaining discrete cell populations for analyses. Single cell RNA sequencing (scRNA-seq) technology can profile the transcriptome at a single cell level, providing information on how stem/eTA cell activation is regulated. Using this technology, we report that ACE2, a key component in the renin-angiotensin system (RAS), functions as a negative regulator of stem/eTA activation. Methods: Mouse corneal epithelium was exposed to 1M NaOH for 30s or mechanically removed with a diamond burr. Corneas were processed for scRNA-seq and data was analyzed using R with a Seurat package. Limbal epithelial cell proliferation was assessed using BrdU incorporation. RT-qPCR, western blotting and immunostaining were conducted to determine the change of gene expression. Results: ACE2 was predominantly expressed in the stem cell-enriched limbal basal epithelium. scRNA-seq combined with GO analysis suggested that ACE2 was involved in limbal stem/eTA cell proliferation. Interestingly, immunostaining and RT-qPCR indicated that ACE2 expression was reduced following corneal injuries. Reduction in ACE2 promoted proliferation in human limbal epithelial cell culture as well as in mouse limbal epithelium after corneal epithelial debridement. Significantly, the negative effect of ACE2 on proliferation was not reversed following treatment with the angiotensin II receptor blocker losartan, indicating that the function of ACE2 in limbal epithelium is independent of RAS. scRNA-seq also revealed that reduction of ACE2 caused activation of the TGFA/EGFR pathway, which reduced expression of Lcn2. Lcn2 is a negative regulator of proliferation in a variety of cells. Inhibition of EGFR or overexpression of Lcn2 reversed the increased proliferation in limbal epithelial cells lacking ACE2.  Conclusion: Our findings strongly support the idea that in response to corneal injury, ACE2 is downregulated, which results in the activation of stem/eTA cell proliferation via a novel TGFA/EGFR/Lcn2 signaling pathway in an angiotensin-independent way.

overall_design: Methods:We conducted scRNA-seq on ocular anterior segmental tissue from 3 wild-type and 3 Ace2 KO (Ace2-/−) mice, using a 10X Gemomics pipeline. Cell populations were distinguished byUMAP embedding. Seurat analysis was conducted to compare gene expression profiles between these two groups of mice.

first: Min

last: Liu

first: Robert

last: Lavker


title: Transcriptomic changes upon ESRRA loss in the small intestinal epithelium

status: Public on Jul 10 2024

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Rd

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: Amidst the obesity epidemic and advancements in satiety-targeting therapies, the transcriptional control of energy metabolism is crucial for managing obesity. The transcription factor Estrogen-related receptor α (ESRRA) regulates genes involved in mitochondrial biogenesis, gluconeogenesis, oxidative phosphorylation, and fatty acid metabolism. Although not essential for basic cellular function, ESRRA is vital for energy supply during physiological and pathological challenges. Studies show Esrra mutant mice have impaired fat metabolism and absorption, with germline Esrra loss conferring resistance to high-fat diet (HFD)-induced obesity. However, these studies often overlook tissue-specific roles. Esrra knockdown in the medial pre-frontal cortex reduces feeding and HFD-induced obesity, indicating possible neurological involvement. Notably, ESRRA is highly expressed in the gastrointestinal (GI) tract, a key player in dietary lipid metabolism and target of weight loss therapies.This study aims to investigate the impact of intestinal ESRRA and determine whether it contributes to resistance to diet-induced obesity.

overall_design: RNA-seq was performed in the duodenal epithelial cells of the small intestine upon loss of ESRRA.

first: Kiranmayi

last: Vemuri


title: Transcriptome sequence of intestinal tissues with LL and HH modes in the murine whole-body irradiation model

status: Public on Jul 08 2024

city: Guangzhou

first: Shihua

state: Guangdong

address: 651 Dongfeng East Road

department: Collaborative Innovation Center for Cancer Medicine

country: China

institute: Sun Yat-sen University Cancer Center

summary: To explore the molecular signaling pathways underlying different dose-rate modes, the intestinal tissues of mice were utilized to perform transcriptome sequencing. The result revealed that low mean dose-rate and low instantaneous dose-rate irradiation (LL mode) and ultra-high mean dose-rate and ultra-high instantaneous dose-rate irradiation (HH mode) evoked differential signaling pathways. Compared with LL mode, the signaling pathways of immune response were activated by HH, whereas the signals of mitochondrial metabolism and biogenesis, biological oxidation, amino acid metabolism and biosynthesis were suppressed under HH mode.

overall_design: Female C57BL6/J mice were subjected to 10 Gy whole-body irradiation using LL and HH modes. Mice were euthanized at 48h post IR and extracted intestines to perform transcriptome sequencing.

first: Hongyu

last: Zhu

first: Jiaqi

last: Qiu

first: Ankang

last: Hu

first: Wanyi

last: Zhou

first: Jian

last: Wang

first: Weihang

last: Gu

first: Yinuo

first: Hao

last: Zha

first: Rong

last: Xiang

first: Junli

last: Li

first: Rui

first: Peng

last: Huang

first: Xiaowu

last: Deng


title: Identification of targets for the transcription factor EFL-3 in the C. elegans epidermis

status: Public on Jul 02 2024

city: London

first: Michalis

last: Barkoulas

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study we employ NanoDam to identify targets within the epidermis for the transcription factor EFL-3 that we identified as a key epidermal development regulator.

overall_design: Identification of EFL-3 genome-wide binding by epidermis-specific expression of GFP-nanobody:Dam fusion combined with EFL-3:GFP knock-in in C. elegans. Two different configurations of the GFP-nanobody:dam fusions are included (C-terminal and N-terminal fusions). Samples containing the GFP-nanobody:dam fusion only constitute control samples.

first: Mar

last: Ferrando-Marco


title: IL-21 induces antitumor response in NK cells via CEBPD

status: Public on Jul 09 2024

city: HOUSTON

first: Katayoun

last: Rezvani

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: NK cells engineered to express IL-21 (IL-21 NK) acquire strong antitumor activity, with the ability to respond to glioblastoma (GBM) rechallenge in vitro and in vivo. IL-21 NK cells have a unique signature of chromatin accessibility, with CCAAT/Enhancer-Binding Protein (C/EBP), especially CEBPD, serving as key transcription factors regulating their memory response.

overall_design: The objective of this study was to investigate the epigenetic factors that contributing for memory formation in NK cells

first: Mayra

last: Shanley


title: The cholinergic receptor nicotinic α3 was reduced in the hippocampus of cognitively impaired old mice and upregulated by nicotine and cytisine in HT22 cells

status: Public on Jul 21 2024

city: Akita

first: Takako

last: Ohnuma

state: Akita

department: ARGG

country: Japan

institute: Akita University

summary:
Microarrays were performed to facilitate a comparative analysis of the hippocampi in old mice exhibiting normal versus declined cognitive function.
The results demonstrated that the expression of the cholinergic receptor nicotinic α3 subunit (Chrna3) was significantly reduced in old mice with cognitive decline compared to control.

overall_design: The hippocampus was extracted from C57BL7 mice.

first: Hidetaka

last: Ota

first: Ayuto

last: Kodama

first: Tatsunori

last: Shimizu

first: Kaoru

last: Sugawara

first: Fumio

last: Yamamoto


title: Dual targeting of EZH2 and Histone Deacetylases in hematological malignancies promotes transcriptional and metabolic deregulation leading to ferroptosis. [RNA-Seq]

status: Public on Jul 01 2024

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: The methyltransferase EZH2 functions as the enzymatic component of the PRC2 complex, which deposits methyl groups on H3K27, leading to chromatin condensation and gene repression. Recent studies have shown that EZH2 can also act as a transcriptional modulator outside of the PRC2 complex independent of its methyltransferase activity. In this study, we first aimed to investigate the effects of EZH2 enzymatic inhibition versus protein degradation. We demonstrate that EZH2 degradation is more effective in blocking cellular proliferation compared to EZH2 enzymatic inhibition, and that EZH2 targeting upregulates the cholesterol biosynthesis pathway. Combined targeting of EZH2 and HDACs showed synergistic effects in a broader spectrum of hematological malignancies. Mechanistically, combined targeting of EZH2 and HDACs induced increased levels of H3K27 acetylation and strong upregulation of cholesterol biosynthesis. This leads to metabolic stress due to acetyl-CoA depletion, ultimately inducing ferroptotic cell death.

overall_design: 3' end RNA sequencing of RPMI-8402 cells after treatment with DMSO, Romidepsin, MS1943, Romidepsion+MS1943 or Tazemetostat

first: Marlies

last: Vanden Bempt

first: Alexandra

middle: B

last: Veloso

first: Daan

last: Dierckx

first: Jan

last: Cools


title: Genome binding/occupancy profiling of ESRRA in the small intestinal epithelium

first: Michael

last: Verzi

overall_design: DNA binding patterns of ESRRA were assessed using ChIP-seq with an anti-ESRRA antibody in the small intestinal epithelium

first: Kiranmayi

last: Vemuri


title: ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers (postmortem cortex)

status: Public on Jul 19 2024

city: New York

first: Oliver

middle: H

last: Tam

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

summary: Amyotrophic Lateral Sclerosis (ALS) is a complex syndrome with multiple genetic causes and wide variation in disease presentation. Despite this general heterogeneity, several common factors have been identified. For example, nearly all patients show pathological accumulations of phosphorylated TDP-43 protein in affected regions of the motor cortex and spinal cord. Moreover, large patient cohort studies have revealed that most patient samples can be grouped into a small number of ALS subtypes, as defined by their transcriptomic profiles. These ALS molecular subtypes can be grouped by whether postmortem motor cortex samples display signatures of: mitochondrial dysfunction and oxidative stress (ALS-Ox), microglial activation and neuroinflammation (ALS-Glia), or dense TDP-43 pathology and associated transposable element de-silencing (ALS-TE). In this study, we have built a deep layer ALS neural network classifier (DANcer) that has learned to accurately assign patient samples to these ALS subtypes, and which can be run on either bulk or single-cell datasets. Upon applying this classifier to an expanded ALS patient cohort from the NYGC ALS Consortium, we show that ALS Molecular Subtypes are robust across clinical centers, with no new subtypes appearing in a cohort that has quadrupled in size. Signatures from two of these molecular subtypes strongly correlate with disease duration: ALS-TE signatures in cortex and ALS-Glia signatures in spinal cord, revealing molecular correlates of clinical features. Finally, we use single nucleus RNA sequencing to reveal the cell type-specific contributions to ALS subtype, as determined by our single-cell classifier (scDANCer). Single-cell transcriptomes reveal that ALS molecular subtypes are recapitulated in neurons and glia, with both ALS-wide shared alterations in each cell type as well as ALS subtype- specific alterations. In summary, ALS molecular subtypes: (1) are robust across large cohorts of sporadic and familial ALS patient samples, (2) represent a combination of cellular, genetic, and pathological features, and (3) correlate with clinical features of ALS.

overall_design: To determine the ALS molecular subtypes of post-mortem cortex samples through transcriptomic analysis of genes and TE, and correlate with molecular and clinical features

first: Kathryn

last: O'Neill

first: Hemali

last: Phatnani

first: Molly

last: Gale-Hammel


title: The Retinal Determination Gene Network can confer chemoresistant properties to AML

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

summary: Acute Myeloid Leukaemia (AML) is a highly heterogeneous disease characterised by an abnormal transcriptional landscape that results in a block in normal blood cell differentiation and aberrant self-renewal. Dysregulation of Homeobox A9 (HOXA9) expression is a hallmark of multiple AML subsets. Although HOXA9 is critical for maintaining leukaemic transformation, it has proven to be a challenging druggable target, and the underpinning molecular mechanisms through which it promotes leukaemogenesis remain elusive. Here, we report the existence of a dichotomous expression profile between sine oculis homeobox 1 SIX1 and the well known HOXA9 interactors MEIS1 in monocytic zinc finger (MOZ) and mixed-lineage leukaemia (MLL) rearranged AMLs. We employed ChIP-seq, together with RNA-seq, to identify regions bound and transcriptionally upregulated in a MOZ-TIF2 driven model of AML. Using RNA-seq, we demonstrated that SIX1 and EYA1 (the well known SIX1 partner) potentiates the transforming capacity of HOXA9 to confer a greater level of differentiation block via suppression of myelo-monocytic programmes. We next sought to define the impact of pharmacologically destabilising the EYA1/SIX1 complex using Benzarone. Through a single cell RNA-Seq timecourse following treatment of MOZ-TIF2 cells with Benzarone, we provide evidence that disruption of EYA1 and its interactions results in differentiation of these cells. To prove the specificity of Benzarone towards EYA1, we also conducted RNA-Seq on cells expressing EYA1 and HOXA9 or HOXA9 alone.

overall_design:
ChIP Seq using Ty1 tag on c-Kit+ haematopoietic and stem progenitor cells (HSPCs) transduced with Ty1.MOZ-TIF2
ChIP Seq for H3K9/14Ac on freshly isolated c-Kit+ HSPCs or c-Kit+ HSPCs transduced with MOZ-TIF2 or empty vector
Poly(A) RNA-sequencing on freshly isolated c-Kit+ HSPCs or c-Kit+ HSPCs transduced with MOZ-TIF2 or empty vector
Poly(A) RNA-sequencing on established EYA1+HOXA9 and HOXA9 cell lines treated with either DMSO or Benzarone for 72 hours
Single cell profiling (10x platform) of MOZ-TIF2 cells treated with either DMSO (Days 1 and 5) or Benzarone (Days 1, 3 and 5)

Please note that the Series title and summary have been updated on Mar 4, 2025.

first: Liam

last: Clayfield

first: Divya

last: Mailk

first: Anne

last: Largeot

first: Renaud

last: Mevel

first: Muhammad

middle: Z

last: Fadlullah

first: Rahima

last: Patel

first: Martyna

last: Szpakowska

middle: A

last: Maqbool

last: Lie-a-ling

first: Andy

last: Chevigne

first: Jessica

last: Whittle

first: Pascal

last: Maire

first: Tim

middle: C

last: Somervaille

first: Heide

middle: L

last: Ford

first: Valerie

last: Kouskoff


title: RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection

status: Public on Jul 03 2024

city: Tampere

first: Sanna-Kaisa

middle: Emilia

last: Harjula

address: Arvo Ylpön katu 34

country: Finland

institute: University of Tampere

summary: Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish (Danio rerio) has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation, haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls.

overall_design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed, three biological replicates in two groups, fish homozygous for pycardtpu4 mutation and wild type (WT) control.

first: Meri

last: Uusi-Mäkelä

first: Maiju

last: Junno

first: Alina

last: Sillanpää

first: Reetta

last: Nätkin

first: Mirja

middle: T

last: Niskanen

first: Matti

last: Nykter

first: Mika

last: Rämet


title: Cigarette smoking prolongs immune responses against influenza and delays its clearance in mice

status: Public on Jun 21 2024

city: Groningen

first: Jelmer

last: Vlasma

state: Groningen

department: Pathology and Medical Biology

country: Netherlands

institute: UMCG

summary:
Introduction
Epidemiological studies have shown that smoking is associated with increased incidence of severe viral infections leading to hospitalisation. Moreover, studies in experimental models have identified impaired antiviral responses and altered inflammatory responses, yet it is unclear which immune cells are involved and whether this varies over the course of infection.
Methods
To test how cigarette smoking affects the response to influenza viral infection over time, female BALB/c mice were exposed to cigarette smoke or air twice a day for 24-28 days and infected with H3N2 influenza or mock infection on day 21. Three and seven days after infection, changes in immune cell populations, and mRNA expression/viral clearance in lung tissue were analysed.
Results
Smoke-exposed mice lost significantly more weight than air-exposed controls after influenza infection, indicating that smoking resulted in more severe disease. Immune cell and lung tissue transcriptome analysis revealed that neutrophil infiltration was prolonged and macrophage activation dysregulated after infection in smoke-exposed mice compared to air-exposed controls. Expression of genes in IL-6 and interferon pathways was similarly longer active. In parallel, we observed lower clearance of viral RNA in smoke-exposed mice after infection compared to air-exposed controls, indicating ineffective antiviral responses. Adaptive immune responses were unchanged in infected smoking animals compared to nonsmoking mice.
Conclusion
Altogether, the data from our mouse model indicate that cigarette smoke exposure prolongs innate immune responses against influenza. The results from this study help to explain the susceptibility of current smokers to severe influenza disease.

overall_design: Mice were exposed to cigarette smoke for 4 weeks. After three weeks, mice were exposed to influenza X31 virus. Either three or seven days after infection mice were sacrificed and lungs were isolated for total transcriptome analysis

first: J

middle: R

first: B

middle: N

last: Melgert

first: C

last: Brandsma

first: M

last: Nawijn

last: de Jager

first: T

last: Van der Veen


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUT&RUN]

status: Public on Jun 26 2024

first: Ly-sha

last: Ee

address: 413 E 69th Street

institute: Weill Cornell Medicine

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&RUN to map OTX2-bound genomic regions and identify OTX2-regulated genes during directed differentiation of EpiSCs to DE

overall_design: EpiSCs were converted to DE and live cells isolated by flow cytometry. OTX2 binding sites were mapped in mouse EpiSCs and definitive endoderm using CUT&RUN for HA in OTX2-HA tagged cell lines.

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano

first: Alexander

last: Polyzos


title: Evaluating TF-target gene interactions in the placenta using siRNA knockdowns

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

summary: Gene regulation is essential to placental function and fetal development. We built a genome-scale transcriptional regulatory network (TRN) of the human placenta using digital genomic footprinting and transcriptomic data. We integrated 475 transcriptomes and 12 DNase hypersensitivity datasets from placental samples to globally and quantitatively map transcription factor (TF)-target gene interactions. We performed siRNA knockdowns of 4 TFs and achieved concordance between the predicted gene targets in our TRN. This GEO dataset summarizes the results of the knockdowns for these 4 TFs: GCM1, CREB2L2, ESRRG, and GRHL2 compared to siRNA controls (SCR).

overall_design: We performed siRNA knock downs of selected transcription factors in primary villous trophoblast cells from placental samples collected through the OHSU placental biorepository.

first: Alison

last: Paquette

first: Samantha

last: Lapehn

first: Leslie

last: Myatt

first: Nathan

last: Price


title: Immunologic drivers of immune checkpoint inhibitor therapy myocarditis, fatality and anti-tumor response in cancer patients

status: Public on Jun 22 2024

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Immune checkpoint inhibitors (ICIs) can offer remarkable benefits to patients with cancer, but these agents can cause morbid and potentially fatal immune-related adverse events (irAEs), the most lethal of which is ICI-related myocarditis (irMyocarditis). The pathogenesis of irMyocarditis and its relationship to anti-tumor immunity remain poorly understood. We sought to define how immune cell trafficking between heart, tumor and blood contributes to irMyocarditis pathogenesis and fatality by leveraging single-cell (sc)RNA-seq coupled with T cell receptor (TCR) sequencing, microscopy, and proteomics analysis of 28 irMyocarditis patients and 23 controls. Our analysis of ~284,360 cells from the heart and blood specimens identified enrichment of cytotoxic T-cell subsets, inflammatory macrophage subsets, conventional dendritic cells (cDCs), and fibroblasts in the heart that accompany the upregulation of potentially targetable, pro-inflammatory transcriptional programs. Expanded TCR clones enriched in irMyocarditis are largely distinct from those in paired tumors, suggesting distinct mechanisms between anti-tumor immune response and irMyocarditis. We also identified circulating biomarkers of fatality, including decreased circulating CD4+ T cells, decreased cDCs, and the presence of cardiac-expanded TCRs in a circulating, cycling CD8+ T cell population. Collectively, these findings highlight critical biology driving disease pathogenesis and nominate putative biomarkers and tailored therapeutic interventions for patients with irMyocarditis.

overall_design:
Heart samples were taken through endomyocardial biopsies or autopsy from patients receiving an ICI for cancer.  Additionally, patients had PBMCs collected at multiple timepoints through their course of treatment.  Samples were then used for scRNA-seq.

>>>Submitter states: The raw data will be submitted via dbGaP as it needs to be under controlled access.<<<

first: Isabela

middle: J

last: Kernin

first: Steven

last: Blum

last: Zlotoff

first: Alexandra-Chloe

last: Villani


title: Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [RNA-seq]

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Thymine DNA Glycosylase (TDG) is a versatile protein involved in DNA mismatch repair, DNA demethylation, and transcriptional regulation. Here, we identify TDG as a synthetic essential effector in p53-deficient tumours. We found that deletion of TDG inhibits cell proliferation specifically in p53-deficient cancer cells. Using a genetically engineered mouse model of lung adenocarcinoma (LUAD), we demonstrate that depletion of TDG suppresses tumour growth in the p53-deficient context. Notably, A novel and selective inhibitor developed to disrupt the DNA binding activity of TDG exhibits therapeutic efficacy against p53-deficient tumours in both cellular and xenograft models. Mechanistically, TDG coordinates with p53 to orchestrate the transcription of RNA helicase DHX9, which functions to eliminate dsRNA. Depletion of TDG in p53-deficient cells results in the downregulation of DHX9 and aberrant cytoplasmic double-strand (dsRNA) accumulation derived from Alu elements, subsequently activating the RIG-I/MDA5-MAVS mediated antiviral response. Moreover, single-cell RNA-sequencing analysis revealed the depletion of TDG in p53-deficient tumours facilitates the recruitment of tumour-infiltrating lymphocytes. We observed that TDG inhibition combined with immune checkpoint blockade (ICB) achieved a strong synergistic anti-tumour effect in p53-deficient tumours. This study highlights the function of TDG in maintaining p53-deficient tumour growth and provides an alternative therapeutic target for p53-deficient cancers.

overall_design: Gene expression analysis of RNA-seq data for listed cells and tissues.

first: Jiaxin

last: Zhou


title: A comprehensive analysis of the effect of quorum-sensing molecule 3-oxo-C12-homoserine lactone on Candida auris and Candida albicans

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: Candida auris occupies similar niches in various infections as Pseudomonas aeruginosa; however, the details of their interspecies communication remain largely unknown. To gain deeper insights into this bacterial–fungal relationship, phenotypic and transcriptomic analyses were conducted in the presence of the primary P. aeruginosa quorum-sensing molecule, 3-oxo-C12-homoserine lactone (HSL), against C. auris, with the results compared to those of C. albicans. We demonstrated a significant HSL-induced reduction in adhesion of C. auris cells at 100- and 200-μM concentrations. Furthermore, HSL exposure reduced intracellular iron and zinc levels and modulated C. auris metabolism toward beta-oxidation, which may be associated with the observed reduction in in vivo virulence at lower HSL concentrations compared with C. albicans. RNA-sequencing transcriptome analysis revealed 67 and 306 upregulated genes, as well as 111 and 168 downregulated genes, in response to 100 and 200 μM HSL, respectively. We identified 45 overlapping upregulated and 25 overlapping downregulated genes between the two HSL concentrations. Our findings indicate that HSL-induced effects are not specific to C. albicans; additionally, several characteristics are present in C. auris but not in C. albicans following HSL exposure. Similar to other Candida-derived C12 compounds (e.g., farnesol), HSL reduces several C. auris survival strategies, which may significantly influence the nature of P. aeruginosa–C. auris co-habitation.

sample_organism:
Candida albicans
Candidozyma auris

platform_organism:
Candida albicans
Candidozyma auris

overall_design: Comparative gene expression profiling analysis of RNA-seq data of 3-oxo-C12-homoserine lactone treated and untreated Candida auris and Candida albicans cells.

first: Fruzsina

last: Kovács

first: Ágnes

first: Noémi

last: Balla

first: Zoltán

last: Tóth

first: Dávid

last: Balázsi

first: Lajos

last: Forgács

first: Andrea

last: Harmath

first: Aliz

last: Bozó

first: Ágota

last: Ragyák

first: László

last: Majoros

first: Renátó


title: Loss of PTDSS1 in tumor cells improves immunogenicity and response to anti-PD-1 therapy [AmpSeq]

city: Houston

first: Jielin

last: Liu

address: 7455 Fannin St

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

summary: PTDSS1 (Phosphatidylserine synthase 1) encodes an enzyme that facilitates production of phosphatidylserine (PS), which mediates a global immunosuppressive signal. Here, based on in vivo CRISPR screen, we identified PTDSS1 as a target to improve anti-PD-1 therapy. Depletion of PTDSS1 in tumor cells increased expression of IFNγ-regulated genes, including B2m, Cxcl9, Cxcl10, and Stat1, even in the absence of IFNγ stimulation in vitro. Loss of PTDSS1 in tumor cells also led to increased expression of MHC-I, which was associated with enhanced cytotoxicity of CD8+ T cells and increased frequency of an iNOS+ myeloid subset. A gene signature derived from the iNOS+ myeloid cell subset correlated with clinical benefit in patients treated with anti-PD-1 therapy. Moreover, genetic and pharmacological inhibition of PTDSS1 in different tumor models improved anti-PD-1 therapy. Together, our results provide insights on a new therapeutic strategy for overcoming immunosuppression by inhibiting PTDSS1 and provide rationale for development of a combination immunotherapy strategy comprised of PTDSS1 inhibition plus PD-1 blockade.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: sgRNA composition in plasmids, cell pools, tumors treated with PBS or anti-PD-1 followed by Amplicon-seq to compare condition specific changes.


title: Single-cell RNA-sequencing of in vitro fertilized and nuclear transfer embryos

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

summary: Somatic cell nuclear transfer and transcription factor overexpression can induce reprogramming of somatic cells, whereby one cell fate is changed into another cell fate of choice. Yet the efficiency of this process for generating functional cells is low, limiting their therapeutic applications. The persistence of transcriptional memory from the cell's prior identity is thought to be a major hindrance to effective reprogramming and differentiation to functional cell types. To explore the effects of transcriptional memory on cell fate specification of reprogrammed cells, we analyzed epidermal tissue development in nuclear transfer embryos derived from endoderm nuclei. Our findings reveal variations in the success rate of differentiation to functional cells across cell types in cloned embryos. While some cell types, such as goblet cells, differentiated normally, a specific subset of cells resisted cell fate reprogramming, adopting a new endoderm-like state and disrupting normal body patterning. Furthermore, inefficient transcriptional reprogramming correlated with reduced basal stem cell populations, faulty differentiation of basal stem cell-derived fates, and increased cell death in the epidermis of cloned embryos. Crucially, we identified that the memory of active transcriptional states linked to key endoderm transcription factors plays a significant role in these issues. Mimicking active state transcriptional memory of these genes through the forced expression of Sox17b and Foxa4 in the epidermis of fertilized embryos produced the same defects. On the contrary, reducing transcriptional memory by interfering with the expression of Sox17b led to the rescue of observed epidermal defects. In summary, our study suggests that transcriptional memory tends to persist predominantly in specific reprogrammed cell types, hindering their differentiation into functional cells and embryonic structures. This underscores the critical need to assess and reduce transcriptional memory from the previous somatic identity during reprogramming, to efficiently generate functional cell types for therapeutic applications.

overall_design: Ectodermal explants from 5 In vitro fertilized (IVF) and 5 nuclear transfer (NT) Xenopus Laevis embryos at stage 12 from two independent experiments were subjected to single-cell RNA sequencing

first: Jonathan

last: Fiorentino

last: Hörmanseder

first: Tomas

last: Zikmund

first: Antonio

last: Scialdone

first: Marco

last: Stock


title: CDK12 prevents MYC-induced transcription-replication conflicts [EU-seq]

status: Public on Jun 19 2024

city: Milano

first: Stefano

last: Campaner

address: Via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

summary: In order to identify genes and pathways necessary to preserve genome integrity upon Myc over-expression, we conducted a large siRNA-based screen in isogenic lines. We discovered several genes that suppressed the Myc-induced DNA-damage response and that were essential for the cell survival upon Myc activation. We idntified CDK12, a cyclin dependent kinase involved in transcriptional control and genome stability. We uncovered a novel and unexpected role of CDK12 in controlling transcription at loci proximal to DNA damaged sites and dissected its upstream regulatory pathways and downstream effectors. Mechanistic studies and genome-wide mapping of replication dynamics and DSBs revealed how CDK12 is essential to suppress intrinsic transcription-replication conflicts, thus avoiding cytotoxic DNA damage in cancer cells. Overall, this study uncovers a novel role for CDK12 and a new liability of Myc-driven cancers, which could be exploited for therapeutic purposes.

overall_design: U2OS MycER cells (U20S cells expressing the MycER chimera) were infected with virus expressing non-targeting shRNAs (shNT) or shRNA targeting CDK12 (shCDK12). ShRNA expression was activated with 1 µg/mL doxycycline, while MycER was activated with 300 nM OHT for 40h. Cells were then treated with 100 ng/ml nocodazole (Sigma, Cat. No.  SML-1665) for 8h to induce mitotic arrest. G2/M arrested cells were isolated by shake-off, washed with PBS and released in warm medium for 12 hours. 0.5 mM EU (5-ethynyl-uridine, Jena Biosciences, Cat. No. CLK-N002-10) was added to the cells 2h before cells collection.

first: Laura

last: Curti

first: Ottavio

last: Croci

first: Nicola

last: Bianchi


title: CDK12 prevents MYC-induced transcription-replication conflicts [BLISS]

overall_design: U2OS MycER cells (U20S cells expressing the MycER chimera) were infected with virus expressing non-targeting shRNAs (shNT) or shRNA targeting CDK12 (shCDK12). ShRNA expression was activated with 1 µg/mL doxycycline, while MycER was activated with 300 nM OHT for 40h. Cells were then treated with 100 ng/ml nocodazole (Sigma, Cat. No.  SML-1665) for 8h to induce mitotic arrest. G2/M arrested cells were isolated by shake-off, washed with PBS and released in warm medium for 18 hours.

last: Crosetto

first: Roberto

last: Ballarino


title: Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer

first: Zhenyu

last: Shao

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: CDK12 prevents MYC-induced transcription-replication conflicts


title: CDK12 prevents MYC-induced transcription-replication conflicts [ChIP-seq]

overall_design: U2OS cells were transfected with either non-targeting siRNAs (siLuc) or siRNAs targeting CDK12 (siCDK12). 48 hours post transfection cells were collected and processed for ChIP-seq analysis.

first: Sara

last: Rohban


title: Dual targeting of EZH2 and Histone Deacetylases in hematological malignancies promotes transcriptional and metabolic deregulation leading to ferroptosis. [ChIP-Seq]

first: Sofie

last: Demeyer

overall_design: ChIP-sequencing on the RPMI-8402 cell line with a H3K27ac antibody, after treatment with DMSO, romidepsin, MS1943 or a combination of romidepsin and MS1943

first: Marlies

last: Vanden Bempt

first: Alexandra

last: Veloso

first: Daan

last: Dierckx

first: Jan

last: Cools


title: CDK12 prevents MYC-induced transcription-replication conflicts [EdU-seq]

overall_design: U2OS MycER cells (U20S cells expressing the MycER chimera) were infected with virus expressing non-targeting shRNAs (shNT) or shRNA targeting CDK12 (shCDK12). ShRNA expression was activated with 1 µg/mL doxycycline, while MycER was activated with 300 nM OHT for 40h. Cells were then treated with 100 ng/ml nocodazole (Sigma, Cat. No.  SML-1665) for 8h to induce mitotic arrest. G2/M arrested cells were isolated by shake-off, washed with PBS and released in warm medium containing 25 μM EdU (Invitrogen, Cat. No. A10044) and 2 mM hydroxyurea (Sigma, Cat. No. H8627-5G). After 24 h, cells were collected and fixed in 90% methanol.


title: The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality

status: Public on Jun 17 2024

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

institute: University of Exeter

summary: We used scRNA-seq to profile 199113 single cell transcriptomes of Hydractinia symbiolongicarpus, a highly regenerative colonial cnidarian. We characterized all major cell types, their transcription factors and gene networks, and analysed the basic mechanisms of coloniality in cnidarians.

overall_design: Tissue (polyps or stolons) were isolated from a whole colony of male clone 291-10 by cutting. Samples were simultaneously fixed and dissociated using ACME. Colony parts are identified based on library and Round 1 barcode.

first: David

last: Salamanca-Díaz

first: Helen

last: Horkan

first: Helena

last: García-Castro

first: Elena

last: Emili

first: Miguel

last: Salinas-Saavedra

first: Eleonora

last: Rossi

first: Marta

last: Álvarez-Presas

first: Rowan

last: Mac Gabhann

first: Febri

last: marsa

first: Alberto

last: Pérez-Posada

first: Nathan

last: Kenny

last: Paps

first: Uri

last: Frank


title: CDK12 prevents MYC-induced transcription-replication conflicts [RNA-seq]

first: Stefano

last: Campaner

overall_design: U2OS cells were transfected with either non-targeting siRNAs (siLuc) or siRNAs targeting CDK12 (siCDK12). 48 hours post transfection and MycER activation by 300nM OHT cells were collected and processed.

first: Sara

last: Rohban

first: Ottavio

last: Croci


title: Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites

status: Public on Jun 15 2024

city: Leicester

first: Shaun

last: Cowley

address: Henry Wellcome Building, Lancaster Road

department: Molecular and Cell Biology

institute: University of Leicester


title: Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ChIP-seq]

summary: Histone Deacetylase 1 (HDAC1) removes acetyl groups from lysine residues on the core histones, balancing histone acetyltransferase (HAT) activity. Despite this apparent repressive function, suppression of HDAC activity causes both up and downregulation of gene expression. Here we exploit the degradation tag (dTAG) system to rapidly degrade HDAC1 in embryonic stem cells (ESCs) lacking the paralog, HDAC2. Unlike HDAC inhibitors that lack isoform specificity the dTAG system allowed specific HDAC1 targeting and completely removed HDAC1 100x faster than genetic knockouts. HDAC1 degradation caused rapid increases in histone acetylation, with H2BK5 and H2BK11 most sensitive. The majority of differentially expressed genes following 2 hours of HDAC1 degradation were upregulated (275 genes up vs 15 down) with increased proportions of downregulated genes at 6 (1153 up vs 443 down) and 24 hours (1146 up vs 967 down). Upregulated genes showed increased H2BK5ac and H3K27ac around their transcriptional start site (TSS). In contrast, decreased acetylation of super-enhancers (SEs) was linked to the most strongly downregulated genes, leading to a collapse of the core pluripotency-associated gene network. These findings suggest that HDAC1 plays a crucial role in regulating the ESC gene expression network by maintaining the correct acetylation levels at key genomic sites.

overall_design: To investigate the consequences of HDAC1 removal in mouse embryonic stem cells we stably expressed a HDAC1-FKBP12F36V-Flag construct in conditional Hdac1/2 double knockout ESCs so that we could degrade the HDAC1-FKBP12F36V-Flag protein in the absence of endogenous HDAC1/2 and assay the consequences. We performed  ChIP-seq following 6 hours of HDAC1-FKBP12F36V-Flag degradation against a control treated with DMSO. Analysis allowed determination of which sites across the mouse genome show changes in acetylation following HDAC1 degradation.

last: English

first: Khadija

last: Sabat

first: Samuel

last: Lee

first: India

last: Baker

first: Trong

last: Khoa Pham

first: Mark

middle: O

last: Collins


title: Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [RNA-seq]

overall_design: To investigate the consequences of HDAC1 removal in mouse embryonic stem cells we stably expressed a HDAC1-FKBP12F36V-Flag construct in conditional Hdac1/2 double knockout ESCs so that we could degrade the HDAC1-FKBP12F36V-Flag protein in the absence of endogenous HDAC1/2 and assay the consequences. We performed bulk RNA-seq following 2, 6 or 24 hours of HDAC1-FKBP12F36V-Flag degradation against a control treated with DMSO for 24 hours. Analysis allowed determination of which genes becomes differentially expressed due to HDAC1 degradation at the above time points.

first: David

middle: M


title: Zaxinone Synthase Overexpression Modulates Rice Physiology and Metabolism, Enhancing Nutrient Uptake, Growth, and Productivity

status: Public on Jun 18 2024

city: Thuwal

first: Abdugaffor

last: Ablazov

address: Bld. 2 L3

department: BESE

country: Saudi Arabia

institute: KAUST

summary: The rice Zaxinone Synthase (ZAS) gene encodes a carotenoid cleavage dioxygenase (CCD) that forms the apocarotenoid growth regulator zaxinone in vitro. Here, we generated and characterized constitutive ZAS-overexpressing rice lines, to better understand ZAS role in determining zaxinone content and regulating growth and architecture. ZAS overexpression enhanced endogenous zaxinone level, promoted root growth and increased the number of productive tillers, leading to about 30% higher grain yield per plant. Hormone analysis revealed a decrease in strigolactone (SL) content, which we confirmed by rescuing the high-tillering phenotype through application of a SL analog. Metabolomics analysis revealed that ZAS overexpressing plants accumulate higher amounts of monosaccharide sugars, in line with transcriptome analysis. Moreover, transgenic plants showed higher carbon (C) assimilation rate and elevated root phosphate, nitrate and sulfate level, enhancing the tolerance towards low phosphate (Pi). Our study confirms ZAS as an important determinant of rice growth and architecture and shows that ZAS regulates hormone homeostasis and a combination of physiological processes to promote growth and grain yield, which makes this gene an excellent candidate for sustainable crop improvement.

overall_design: The research aimed to examine how the overexpression of Zaxinone Synthase (ZAS) affects the transcriptome of rice. To achieve this, an RNA sequencing experiment was conducted on the roots and shoots of 21-day-old plants from the ZAS-overexpressing line (OX6) and the wild-type (Nipponbare, NB) that were grown in a hydroponic system.

first: Salim

last: Al-Babili


title: Deep learning of enhancer codes highlights similarities between mammalian and avian telencephalon cell types [multiome]

status: Public on Jun 14 2024

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

institute: VIB

summary: Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We utilized deep learning to characterize these enhancer codes and devised three novel metrics to compare cell types in the telencephalon between mammals and birds. To this end, we generated single-cell multiome and spatially-resolved transcriptomics data of the chicken telencephalon. Enhancer codes of orthologous non-neuronal and GABAergic cell types show a high degree of similarity across vertebrates, while excitatory neurons of the mammalian neocortex and avian pallium exhibit varying degrees of similarity. Enhancer codes of avian mesopallial neurons are most similar to those of mammalian deep layer neurons. With this study, we present generally applicable deep learning approaches to characterize and compare cell types solely based on genomic sequences.

overall_design: 15 days old domestic chicken (broiler) were used for the experiments. The telencephalon was dissected from the brains and two samples were prepared: a sample covering the whole telencephalon and a coronal section. Both samples were analyzed with 10X Single Cell Multiome ATAC + Gene expression.

first: Nikolai

last: Hecker

first: Niklas

last: Kempynck

last: Mauduit

first: Darina

last: Abaffyova

first: Ioannis

last: Sarropoulus

first: Sam

last: Dieltens

first: Carmen

last: Bravo Gonzalez-Blas

first: Roel

last: Vandepoel

first: Elke

last: Leysen

first: Lynette

last: Lim

first: Joris

last: De Wit

first: Valerie

last: Christiaens

first: Suresh

last: Poovathingal

first: Aerts

last: Stein


title: Transcriptional response of NGN3 J2 enteroids.

first: Sara

middle: Chloe

last: Di Rienzi

address: 1 Baylor Plaza Room 743E

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary: Enteroendocrine cells are hormonal secreting cells in the gut. However, as they comprise <1% of the total epithelial cell population, studies on their response to stimuli have been limited. Chang-Graham, Danhof, Engevik, and Tomaro-Duchesneau et al (PMID 31029854) developed a model enteroid system to overcome this limitation. By driving expression of NGN3 in human jejunal enteroids, their system allows for analysis of hormonal secretion and transcriptional analysis in response to a stimulus. To further characterize these NGN3 enteroids, we performed RNASeq on these enteroids in the induced or uninduced state, treated with a media control or Limosilactobacillus reuteri conditioned media. .

overall_design:
A total of 30 samples were sequenced. In the uninduced state (NGN3 not induced, low number of enteroendocrine cells), 2 batches of enteroids, triplicate enteroids for each treatment: media alone (LDM4), or LDM4 + Lactobacillus reuteri 6475 = 12 samples. In the induced state (NGN3 induced, high number of enteroendocrine cells), 2 batches of enteroids, triplicate enteroids for each treatment: media alone (LDM4), LDM4 + Lactobacillus reuteri 6475, LDM4 + Lactobacillus reuteri 1793, and LDM4 = 18 samples.

This Series reuses the 12 samples of Series GSE138350.

first: Heather

last: Danhof

first: Robert

last: Britton


title: Neoadjuvant-induced Complement Upregulation in Tumor Microenvironment is Associated with Immunomodulation and Improved Survival in Pancreatic Ductal Adenocarcinoma: Insights from Spatially Resolved Transcriptomics

status: Public on Jun 05 2024

city: New Orleans

first: Ruoxin

last: Lan

state: LA

address: 204 S Saratoga St, Apt 316

institute: Tulane University

summary: Recently neoadjuvant therapy (NAT) is being increasingly used in the treatment of pancreatic ductal adenocarcinoma (PDAC). However, how NAT differentially impacts the tumor and the tumor microenvironment (TME) is still poorly defined. Therefore, we compared the spatial transcriptomics profiles in tumor and the TME of PDACs resected from patients with versus without NAT. We found that NAT can significantly upregulate multiple key complement genes (C3, C1S, C1R, C4B and C7) in TME but not in tumor, making the complement pathway the most significantly modified pathways by NAT. In addition, the NAT-treated patients s with higher TME complement show significantly higher expression of gene signatures for immunomodulatory and neurotropic fibroblast, mast cells, CD4+ T cells and monocytes, significantly lower expression of immune exhaustion gene signature, and improved overall survival. Our results suggested that NAT may have immunostimulatory effect for PDAC through upregulating TME complement signaling.

overall_design:
A total of 116 regions of interest (ROIs) with the most representative tumor morphology for each case were selected from the 36 patients in our cohort. Using immunofluorescence images, each ROI was further segmented into the tumor area (CK+, SMA-) and the TME area (CK-, SMA+). 223 (96.1%) of these 232 samples passed the quality control and were used for spatial transcriptomics analysis, including 42 TME samples and 43 tumor samples from the naïve group; and 72 TME samples and 66 tumor samples from the NAT group.

*** FASTQ raw data files have been requested. ***

first: Xiaofei

last: Zhang

first: Yao-Zhong

last: Liu

first: Yongjun


title: Spatial transcriptomics analysis identifies a unique tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease.

status: Public on Jun 03 2024

city: St. Petersburg

first: Oscar

middle: E

last: Ospina

state: FL

address: 600 5th Street South

department: Health Informatics

institute: Johns Hopkins All Children's Hospital

summary: Leptomeningeal disease (LMD) remains a rapidly lethal complication for late-stage melanoma patients. The inaccessible nature of the disease site and lack of understanding of the biology of this unique metastatic site are major barriers to developing efficacious therapies for patients with melanoma LMD. This study aims to characterize the tumor microenvironment of the leptomeningeal tissues and patient-matched extra-cranial metastatic sites using spatial transcriptomic analyses.

overall_design: This study presents five LMD samples and four extracranial metastases from two patients (denoted A and B within the sample names, included in the sample description field) profiled with Visium.

first: Inna

last: Smalley


title: Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms

status: Public on Jun 01 2024

city: Beijing

first: Yifan

last: Su

address: Haidian District

department: School of Environment

institute: Tsinghua University

summary: Cellulose is the most abundant component of plant litter, which is critical for terrestrial carbon cycling. Nonetheless, it remains unknown how climate changes affect cellulose-decomposing microorganisms. Here, we carried out a multi-year litterbag experiment to examine cellulose decomposition undergoing +3°C warming in an Oklahoma tallgrass prairie, USA. GeoChip 5.0M was employed to detect microbial functional genes.

sample_organism:
soil metagenome
decomposition metagenome

overall_design: Samples were collected under control and warming treatment from 2016 to 2018 in an Oklahoma tallgrass prairie, USA, each treatment has 4 replicates.

first: Yunfeng

last: Yang

first: Jizhong

last: Zhou


title: Effect of terahertz irradiation on HUVEC cells (ATAC-Seq)

first: Jichang

last: Li

address: No. 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

summary: Terahertz (THz) is an electromagnetic wave with a spectrum between microwave and infrared. Due to its unique characteristics, THZ has great application prospects in both medical imaging and biomedicine. however, its effects on the angiogenesis capacity of human umbilical vein endothelial cells (HUVECs) are still unclear. The assay for transposase-accessible chromatin (ATAC) sequencing indicated that the expression of genes related to cytoskeletal increased significantly after THz irradiation.

overall_design: In order to explore the effect of terahertz irradiation on angiogenesis, we used 2.52 THz (100 mW/cm2) to irradiate human umbilical vein endothelial cells(HUVECs)  for 10 min and then continued to culture for 12 h, and then ATAC sequencing to detect the changes in gene expression

first: Hongjie

last: Guo

first: Lin

middle: X

last: Tan

first: Meng

last: Chen

first: Xin

last: Wang

first: Shanwen

first: Yingxin

first: Hao

last: Yu

first: Pengyuan


title: Stromal expression profiling reveals immune-driven adaption to malignancy in canine melanoma subtypes

status: Public on May 31 2024

city: Zurich

first: Enni

last: Markkanen

address: Winterthurerstr. 260

country: Switzerland

institute: University of Zurich

summary: Canine mucosal melanoma (CMM) is the most common oral malignancy in dogs and exhibits significantly higher aggressiveness than its cutaneous counterpart (CCM), yet the reasons for this disparity remain unclear. The influence of cancer-associated stroma (CAS) on tumour progression is well-recognized, but a detailed understanding of CAS in canine melanoma is missing. To comprehensively assess stromal reprogramming in canine melanoma, we analysed CAS from 21 CMM, 14 CCM and normal stroma from 10 skin and 9 oral mucosa samples by laser-capture microdissection followed by RNA sequencing. Results were assessed in relation to subtypes, prognostic factors including mitotic count (MC), ulceration, necrosis, pigmentation, and immune cell infiltration (CD3, CD20 and CD68), scored using immunohistochemistry. While stromal reprogramming was evident in both subtypes, it was significantly more pronounced in CMM. Furthermore, MC strongly correlated with stromal gene expression in both subtypes, suggesting CAS reprogramming to depend on tumour malignancy. Comparison of subtypes revealed specific downregulation of key regulators of leukocyte activation and proliferation in mucosal CAS, supporting a role for impaired immune control in CMM aggressiveness. CMM presented with significantly more CD20 infiltrated (excluded or hot) cases than CCM. In CMM, CD20 infiltration was significantly associated with MC, with excluded cases displaying highest MC. Finally, we identify an immune-suppressive stromal signature in a subset of CMM that influences tumour aggressiveness and predicts overall survival in human melanoma patients. Together, these findings provide a solid foundation for understanding the role of CAS in canine melanoma, with relevance for the human disease.

overall_design: Clinical FFPE specimen of canine mucosal and cutaneous melanoma. Comparison of gene expression in cancer-associated stroma compared to non-matched cutaneous or mucosal normal stroma.

first: Erin

last: Beebe

first: Christiane

last: Krudewig

first: Zahra

last: Motamed

first: Alexandra

last: Malbon


title: Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid [ChIP-seq]

city: Cordova

first: YINWEN

last: ZHANG

state: TN

address: 2189 Purple Leaf Ln

institute: stjude research hospital

summary: Retinoic acid (RA) is a standard-of-care neuroblastoma drug thought to act primarily via differentiation. However, this has never been conclusively demonstrated in vivo. Curiously, RA has little effect shrinking primary human tumors when applied in upfront treatment but can eliminate neuroblastoma cells from the bone marrow during consolidation therapy—a discrepancy that has never been explained. To investigate this, we treated a large cohort of neuroblastoma cell lines with RA and observed that the most RA-sensitive cells tended to undergo apoptosis or senescence, rather than differentiation. We conducted genome-wide CRISPR knockout screens under RA treatment, which identified BMP signaling as controlling the apoptosis/senescence vs differentiation cell fate decision and RA’s overall potency. We then conducted integrative analysis of high throughput ChIP-seq and RNA-seq data, which indicates that downstream BMP and RA transcription factors cooperate to determine cell fate, following exposure to RA.

overall_design: ChIP-seq for transcription factor RARA, SMAD4 and SMAD9 in the three neuroblastoma cell lines of CHP-134, TGW and BE2.

first: Min

last: Pan

first: Yinwen

last: Zhang

first: Paul

last: Geeleher


title: Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid [RNA-seq]

overall_design:
RNA-seq was performed on CHP-134 cell lines treated with DMSO (control) and ATRA for durations of 1 day, 3 days, and 6 days.
We first implanted our hypersensitive CHP-134 cells in mice, then treated them with a pharmacologically relevant dosage of 13-cis RA. Then we performed RNA-seq on our untreated-control and RA-treated xenograft tumors.


title: The Swi/Snf chromatin remodeling complex regulates pancreatic endocrine cell expansion and differentiation in vivo

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

summary: Strategies to augment functional β-cell mass include directed differentiation of  stem cells towards a β-cell fate, which requires extensive knowledge of transcriptional programs governing endocrine progenitor cell differentiation in vivo. Here we describe the contributions of the Brg1 and Brm ATPase subunits of the Swi/Snf chromatin remodeling complex on endocrine cell development. Through the use of transgenic knockout animal models we reveal that conditional knockout of Brg1 in endocrine progenitors results in blood glucose dysregulation, reduced islet mass and function, while loss of all Swi/Snf activity (Brg1 and Brm) results in early postnatal death, resulting from severe hyperglycemia and reduced β-cell mass. Single-cell RNA Sequencing of embryonic day 15.5 lineage-labeled cells revealed reduced expression of maturation markers, proliferation genes, and hormones in endocrine-committed, β- and α-cell clusters, highlighting a critical role for Swi/Snf in governing gene-expression programs essential for endocrine cell development.

overall_design: Florescence-activated cell sorting of tomato+ cells from E15.5 Control, Brg1Δendo;Brm+/-, and DKOΔendo mutants were subsequently analyzes by droplet-based single-cell RNA-Sequencing (scRNA-Seq)


title: Effect of terahertz irradiation on HUVEC cells

first: Jichang

summary: Terahertz (THz) is an electromagnetic wave with a spectrum between microwave and infrared. Due to its unique characteristics, THZ has great application prospects in both medical imaging and biomedicine. However, its effects on the angiogenesis capacity of human umbilical vein endothelial cells (HUVECs) are still unclear. RNA sequencing indicated that the expression of genes related to cytoskeleton increased significantly after THz irradiation.

overall_design: In order to explore the effect of terahertz irradiation on angiogenesis, we used 2.52 THz (100 mW/cm2) to irradiate human umbilical vein endothelial cells(HUVECs)  for 10 min and then continued to culture for 12 h, and then transcriptome sequencing to detect the changes in gene expression

first: Hongjie

first: Lin


title: The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells [RNA-Seq]

status: Public on May 28 2024

city: Mexico city

first: Hober

last: Nuñez

state: CDMX

address: Cto. Exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

summary: Master hematopoietic transcription factors (TFs) and long non-coding RNAs (lncRNAs) coordinate shaping lineage-specific gene expression programs during hematopoietic differentiation. The architectural protein CCCTC-binding factor (CTCF) has emerged as a pivotal regulator of gene expression in cell differentiation. However, the relationship and its regulatory effect of CTCF on lncRNA genes in hematopoiesis remains elusive. We demonstrated that CTCF constrains DUBR transcription throughout erythroid differentiation. DUBR is highly expressed in human hematopoietic stem and progenitor cells (HSPC) but depleted in erythroblasts. DUBR perturbation dysregulates the expression of hematopoietic-erythroid cell differentiation genes and facilitates genome-wide activation of regulatory elements. A genomic map of RNA occupancy revealed that DUBR directly regulates a set of TFs involved in regulating hematopoietic differentiation, including the erythroid repressor HES1, which in turn targets a subset of regulatory elements of DUBR-dysregulated genes. Our results support the role of DUBR as a regulator of a hematopoietic differentiation gene program, by coordinating the expression of TFs and influencing the chromatin regulatory landscape.

overall_design: To analyze the contribution of lncRNA DUBR in erythroid gene expression, we targeted DUBR by CRISPR-Cas9-mediated gene editing in K562 cells and performed differential gene expression analysis.

last: Núñez Martínez

first: Gustavo

last: Tapia Úrzua

first: Ángel

last: Cerecedo Castillo

first: Carlos

last: Peralta Álvarez

first: Georgina

last: Guerrero

first: Maite

last: Huarte

first: Félix

last: Recillas Targa


title: Atlas of metastatic gastric cancer links ferroptosis to disease progression and immunotherapy response

status: Public on May 23 2024

first: Linghua

last: Wang

address: 1881 East Road,

summary: Gastric adenocarcinoma (GAC) remains a significant cause of cancer-related deaths worldwide, with the majority of mortality resulting from metastatic spread. To elucidate the evolution of cancer cells and their interactions with the tumour microenvironment (TME), we conducted a comprehensive single-cell transcriptome and immune repertoire profiling of primary tumours (PRIs), matched liver metastases (LMs) or peritoneal carcinomatosis (PC), adjacent normal tissues, and blood samples from 20 treatment-naïve patients. We found that the TME within metastases varied substantially from PRIs and differed between LMs and PC samples. Indicative of immune evasion, we observed diminished T cell clonal expansion, a marked reduction in the fraction of tumour-reactive CD8 T cells, and an enrichment of naïve T cells, M2-like, and proliferative macrophages in PC samples compared to PRIs. LMs displayed significantly reduced B cells, with increased fractions of exhausted CD8 T cells and NK/NKT cells. Both LMs and PC showed nearly depleted plasma cells. Malignant cells largely exhibited diminished gastric lineage identity, predominantly adopting intestinal-like and mixed cell states, with the acquired expression of gastrointestinal stem-cell markers. LM cancer cells showed increased epithelial-to-mesenchymal signalling, while PC cancer cells had increased levels of aneuploidy. We observed differentially expressed cancer meta-programs and gene modules (GMs) between LMs and PC, with high GM2 expression in the PRI predicting an increased risk of distant metastases. Further analysis of GM signature genes revealed ferroptosis evasion through GPX4 upregulation during malignant progression. Functional validation via patient-derived xenografts and a novel autochthonous mouse model of GAC confirmed that genetic or pharmacological inhibition of ferroptosis resistance attenuates tumor growth and metastatic progression. Together, our mapping of malignant progression provides a rationale for targeting ferroptosis defense in combination with next-generation CAR T-cell immunotherapy as a potential avenue to overcome T cell dysfunction in advanced metastatic GAC therapy.

overall_design:
A total of 20 patients with stage-IV gastric adenocarcinoma (GAC) treated at Zhejiang Cancer Hospital were enrolled in this study. All patients were at stage IV and treatment-naïve prior to sample collection. This cohort included nine patients with liver metastases (LM), six patients with peritoneal carcinomatoses (PC), one patient with both LM and PC, and four patients with both PC and ovarian metastases. Based on the Lauren classification, 13 primary GACs were defined as intestinal type, six as diffuse type, and one as mixed type. Three patients had signet-ring cell carcinoma and seven patients had Heliobacter pylori (H. Pylori) infection. The primary GAC diagnosis of all patients was confirmed through endoscopic biopsies. LMs were shown as hypoechoic nodules on B-scan ultrasonography. The diagnosis of PC was confirmed by cytologic examination or laparoscopic exploration, which was also used to verify whether the patient had ovarian metastases. The pathology results were confirmed by two experienced gastrointestinal pathologists independently. In addition, computed tomography (CT) images of all patients were verified by two experienced radiologists. Except for patient 17 (Pt-17) who underwent radical extremital partial gastrectomy in 2006, none of the patients had a past medical history of gastrointestinal tumours.
**Raw data not provided due to patient privacy concerns**

first: Dai

last: Enyu

first: Qin

last: Jiangjiang

first: Cheng

last: Xiangdong

first: Wang

last: Linghua


title: The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells [ChIRP-Seq]

overall_design: To analyze the contribution of lncRNA DUBR in erythroid gene expression, we targeted DUBR by antisense biotin-tagged probes and analyzed its associated genomic regions.


title: Single-cell Analysis of Subcutaneous Fat Reveals Pro-fibrotic Cells that Correlate with Visceral Adiposity in HIV

status: Public on May 22 2024

city: Nashville

first: Samuel

last: Bailin

address: 1161 21st Avenue South, MCN A-2200

institute: Vanderbilt Universit Medical Center

summary: Cardiometabolic diseases are common in persons with HIV (PWH) on antiretroviral therapy (ART), which has been attributed to preferential lipid storage in visceral adipose tissue (VAT) compared with subcutaneous adipose tissue (SAT). However, the relationship of SAT-specific cellular and molecular programs with VAT volume is poorly understood in PWH. We characterized SAT cell-type specific composition and transcriptional programs that are associated with greater VAT volume in PWH on contemporary ART. We enrolled PWH on long-term ART with a spectrum of metabolic health.We enrolled PWH on long-term ART with a spectrum of metabolic health. Ninety-two participants underwent SAT biopsy for bulk RNA sequencing and 43 had single-cell RNA sequencing. Computed tomography quantified VAT volume and insulin resistance was calculated using HOMA2-IR. VAT volume was associated with HOMA2-IR (p<0.001). Higher proportions of SAT intermediate macrophages (IMs), myofibroblasts, and MYOC+ fibroblasts were associated with greater VAT volume using partial Spearman’s correlation adjusting for age, sex, and body mass index (r =0.34-0.49, p<0.05 for all). Whole SAT transcriptomics showed PWH with greater VAT volume have increased expression of extracellular matrix (ECM)- and inflammation-associated genes, and reduced expression of lipolysis- and fatty acid metabolism-associated genes. In PWH, greater VAT volume is associated with higher proportion of SAT IMs and fibroblasts, and a SAT ECM and inflammatory transcriptome, which is similar to findings in HIV-negative persons with obesity. These data identify SAT cell-type specific changes associated with VAT volume in PWH that could underlie the high rates of cardiometabolic diseases in PWH, though additional longitudinal studies are needed to define directionality and mechanisms.

overall_design:
To investigate the relationship of subcutaneous adipose tissue gene expression and visceral adipose tissue volume in persons with HIV, we performed subcutaneous adipose tissue biopsy and bulk RNA-sequencing.
We then performed differential gene expression between individuals with high visceral adipose tissue volume compared with individuals with low visceral adipose tissue volume using DESeq2.

first: Bailin

last: Samuel

first: Gabriel

last: Curtis

first: Gangula

last: Rama

first: Hannah

last: LaToya

first: Nair

last: Sangeeta

first: Carr

last: Jeffrey

first: Terry

last: James

first: Silver

last: Heidi

first: Simmons

last: Joshua

first: Mahsayekhi

last: Mona

first: Kalams

last: Spyros

first: Mallal

last: Simon

first: Kropski

last: Jonathan

first: Wanjalla

last: Celestine

first: Koethe

last: Johhn


title: High-Resolution Spatial Transcriptomics Reveals Stroma Damage in Human Ovarian Tissue Response to Cryopreservation

status: Public on May 18 2024

city: HK

first: Kun

last: MA

state: Hong Kong

address: No 12 Kam Ling Court Whitty Street Sai Wan HK Island

country: Hong Kong

institute: The University of Hong Kong

summary: Ovarian tissue cryopreservation is an important technique for preserving fertility potential, albeit the associated tissue damage may severely impact post-thaw tissue viability. We collected human ovarian tissues from multiple samples and performed Stereo-Seq high-resolution spatial transcriptomics to comprehensively profile and compare the molecular impacts of two cryopreservation methods - slow freezing and vitrification. We identified 8 major spatial clusters and revealed their functional heterogeneity by subclustering. We then detailed cryopreservation response at both the global and subcluster levels to illustrate overall and niche specific effects. Compared to fresh samples, we observed a decrease in major metabolic pathways in frozen samples with both techniques, whereas vitrified samples have severer decrease than slow-frozen samples. The affected metabolic pathways included those related to proteins, such as ribosomal processes and proteasomal degradation; lipids, specifically sterol and cholesterol metabolism; and overall energy production, which encompassed cellular respiration and mitochondrial processes. On the other hand, slow freezing elicited a strong but balanced inflammatory and tissue remodeling state compared to vitrification. We also reported upregulated cell-cell signaling related to angiogenesis, cellular adhesion and extracellular matrix remodeling in slow-frozen tissue. These pathways were responsible for enhancing tissue repair by coordinating with certain stromal and endothelial subclusters. In summary, our study offered insights on ovarian cell response to cryopreservation, which may guide optimization of ovarian tissue cryopreservation protocols for clinical applications.

overall_design: Human ovarian tissues were donated from one patient aged 35 years who underwent oophorectomy due to cervical cancer. We conducted Stereo-seq profilling of transcriptomic data on three tissue pieces stored under different conditions. According to the Stereo-Seq protocol, one piece of fresh group tissues was fixed in O.C.T. compound (Tissue Tek) for subsequent sequencing, tissues of the two cryopreservation groups were processed after freezing and thawing.

first: Peikun

last: Zhao

last: Ma

first: Yuan

last: Li

first: Chenxi

last: Guo

first: Huijia

last: Du

first: Huayan

last: Wu

first: Xian

first: Kui

last: Liu

first: Yaokai

last: Wang


title: An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast

status: Public on May 17 2024

city: London

first: Ashley

middle: RG

last: Libby

address: 1 Midland Rd

institute: The Francis Crick Insitute

summary: Developing tissues rely on the coordinated differentiation of stem cell populations in dynamically changing environments. The formation of the vertebrate neural tube is a well characterized example, where stem cells in the caudal epiblast differentiate to neural tissue while transitioning through a changing landscape of signals: rostro-caudally from Retinoic Acid (RA) to Wnt/FGF and dorsal-ventrally from sonic hedgehog to BMP. Despite an understanding of the signaling pathways involved in neural specification, the precise signal interpretation and gene regulatory mechanisms within an embryonic context remain poorly defined. To address this, we first developed an in vivo CRISPR screening approach in chick embryos. We then performed a multiplexed in vivo single-cell perturbation screen of transition genes from caudal epiblast to the neural tube. Our screen revealed a role for MLLT3, a component of the super elongation complex, in the specification of neural identity. MLLT3 is expressed in the epiblast and not the neural tube. Perturbation of MLLT3 disrupted caudal epiblast morphology, reduced neural tube identities, and resulted in the misregulation of genes involved in WNT and RA signaling. Neural specification was also disrupted by expressing mutant forms of Retinoic Acid Receptor A (RARα) lacking the MLLT3 binding domain or consisting only the MLLT3 binding region. Together, these findings validate an in vivo CRISPR screen in chick embryos for the first time and identify a previously unreported role for MLLT3 in caudal neural cell specification, mediated through an interaction with RARα.

overall_design: HH8 chicken embryos were electroporated ex ovo with CRISPR system marked by Citrine fluorescence, allowed to develop for 24 hours, and subsequently enriched for successful electroporation via disociation and FACS for Citrine expression. Finally cells were profiled by single cell RNA sequencing on the 10x platform.

first: Tiago

last: Rito

first: Arthur

last: Radley

first: James

last: Briscoe


title: Clinical and molecular characterization of the cisplatin-vinorelbine chemotherapeutic regimen in HER2(-) metastatic breast cancer

status: Public on May 16 2024

city: taipei

first: Jiun-I

last: Lai

state: State...

address: no 155, linong street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming Chiao-Tung University

summary: Despite rapid advances in treatment options, challenges still persist in advanced breast cancer. Bevacizumab is a VEGF-neutralizing antibody with proven efficacy in combination with chemotherapy for treatment of HER2 negative metastatic breast cancer (mBC). Vinorelbine, a semisynthetic vinca alkaloid, is a well-established and well tolerated chemotherapeutic in breast cancer. The combination of vinorelbine with platinum and addition of bevacizumab is relatively underreported in the literature. We propose this combination regimen as safe, well tolerated and efficacious in HER2 negative mBC patients.

overall_design: To model the molecular perturbations by cisplatin-vinorelbine combination, we treated the triple negative breast cancer MDA-MB-231 cell line with a combination of 7μM cisplatin + 14μM vinorelbine, in comparison to vehicle treatment. Total RNA extracted from treated cells underwent RNA-sequencing for transcriptional profiling.

first: I-Wei

last: Ho

first: Yi-Ru

last: Tseng

first: Chun-Yu

first: Yi-Fang

last: Tsai

first: Chi-Cheng

last: Huang

first: Ling-Ming

first: Ta-Chung

last: Chao


title: Humanized CXCL12 Antibody Delays Onset and Modulates Immune Response in Alopecia Areata  Mice

status: Public on Jun 09 2024

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: It has been demonstrated that CXCL12 inhibits hair growth via CXCR4, and its neutralizing antibody (Ab) increases hair growth in alopecia areata (AA). However, the molecular mechanisms have not been fully elucidated. In the present study, we further prepared humanized CXCL12 Ab for AA treatment and investigated underlying molecular mechanisms using single-cell RNA sequencing. Subcutaneous injection of humanized CXCL12 Ab significantly delayed AA onset in mice, and dorsal skin was analyzed. T cells and dendritic cells/macrophages were increased in the AA model, but decreased after CXCL12 Ab treatment. Pseudobulk RNA sequencing identified 153 differentially expressed genes that were upregulated in AA model and downregulated after Ab treatment. Gene ontology analysis revealed that immune cell chemotaxis and cellular response to type II interferon were upregulated in AA model but downregulated after Ab treatment. We further identified key immune cell-related genes such as Ifng, Cd8a, Ccr5, Ccl4, Ccl5, and Il21r, which were colocalized with Cxcr4 in T cells and regulated by CXCL12 Ab treatment. Notably, CD8+ T cells were significantly increased and activated via Jak/Stat pathway in the AA model but inactivated after CXCL12 Ab treatment. Collectively, these results indicate that humanized CXCL12 Ab is promising for AA treatment via immune modulatory effects.

overall_design: Skin samples were collected from unaffected C3H/HeN mice (negative control, Neg), AA model mice, and AA model mice treated with CXCL12-neutralizing antibody (AA + Ab).

first: Jong-Hyuk

last: Sung

first: Minsoo

last: Noh

first: Seungchan

last: An

first: Mei

last: Zheng

first: InGuk

last: Park


title: The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells [ChIP-Seq]

first: Hober

last: Nuñez

overall_design: To analyze the contribution of lncRNA DUBR in hematopoietic gene expression, we targeted DUBR by CRISPR-Cas9-mediated gene editing in K562 cells and analyzed histone marks associated with regulatory elements.

last: Núñez Martínez

first: Gustavo

last: Tapia Úrzua

first: Ángel

last: Cerecedo Castillo

first: Carlos

last: Peralta Álvarez

first: Georgina

last: Guerrero

first: Maite

last: Huarte

first: Félix

last: Recillas Targa


title: Exploiting a metabolic vulnerability in brain tumour stem cells using a brain-penetrant drug with safe profile

status: Public on May 15 2024

city: Pessac

first: Ahmad

last: Sharanek

address: Allée Geoffroy St Hilaire

country: France

institute: BRIC INSERM U1312

summary: Glioblastoma (GB) remains one of the most treatment refractory and fatal tumour in humans. GB contains a population of self-renewing stem cells, the brain tumour stem cells (BTSC) that are highly resistant to therapy and are at the origin of tumour relapse. Here, we report, for the first time, that mubritinib potently impairs stemness and growth of patient-derived BTSCs harboring different oncogenic mutations. Mechanistically, by employing bioenergetic assays and rescue experiments, we provide compelling evidence that mubritinib acts on complex I of the electron transport chain to impair BTSC stemness pathways, self-renewal and proliferation. Global gene expression profiling revealed that mubritinib alters the proliferative, neural-progenitor-like, and the cell-cycling state signatures. We employed in vivo pharmacokinetic assays to establish that mubritinib crosses the blood-brain barrier. Using preclinical models of patient-derived and syngeneic murine orthotopic xenografts, we demonstrated that mubritinib delays GB tumourigenesis, and expands lifespan of animals. Interestingly, its combination with radiotherapy offers survival advantage to animals. Strikingly, thorough toxicological and behavioral studies revealed that mubritinib does not induce any damage to normal cells and has a well-tolerated and safe profile. Our work warrants further exploration of this drug in in-human clinical trials for better management of GB tumours.

overall_design: To investigate the effect in vitro of Mubritinib treatment on brain tumor stem cells. Three biological replicates by condition (Control, Mubritinib) were obtained.

first: Audrey

last: Burban

last: Charanek

first: Nathalie

last: Nicot

first: Barbara

last: Klink

first: Johanna

last: Galvis

first: Benjamin

last: Dartigues

first: Macha

last: Nikolski

first: Thomas

last: Daubon


title: Knockout mice with pituitary malformations help identify human cases of hypopituitarism

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

country: USA

institute: University of Michigan

summary: Congenital hypopituitarism (CH) and its associated syndromes, septo-optic dysplasia (SOD) and holoprosencephaly (HPE), are midline defects that cause significant morbidity for affected people. Variants in 67 genes are associated with CH, but a vast majority of CH cases lack a genetic diagnosis. Whole exome and whole genome sequencing of CH patients identifies sequence variants in genes known to cause CH, and in new candidate genes, but many of these are variants of uncertain significance (VUS). The International Mouse Phenotyping Consortium (IMPC) is an effort to establish gene function by knocking-out all genes in the mouse genome and generating corresponding phenotype data. We used mouse embryonic imaging data generated by the Deciphering Mechanisms of Developmental Disorders (DMDD) project and identified 51 genes that cause recessive, embryonic pituitary malformations in embryonic lethal or subviable knockout mice. These genes not only represent new candidates for CH, but also reveal new molecular pathways not previously associated with pituitary organogenesis. We used this list of candidate genes to mine whole exome sequencing data of a cohort of patients with CH, and we identified variants in two unrelated cases for two genes, MORC2A and MKS1, not previously associated with CH.  This provides proof-of-principle that recessive lethal mouse mutants are an excellent source of candidate genes for congenital hypopituitarism in children

overall_design: Embryonic pituitary glands were dissected at e12.5 and e14.5 and used for transcript analysis by scRNAseq

first: Julian

last: Martinez-Mayer

first: Michelle

last: Brinkmeier

first: Sean

middle: P

last: O’Connell

first: Arnold

last: Ukagwu

first: M

last: Marti

last: Miras

first: Maria

middle: V

last: Forclaz

middle: G

last: Benzrihen

first: Leonard

middle: Y

last: Cheung

first: Sally

last: Camper

first: Buffy

middle: S

last: Ellsworth

first: Lori

last: Raetzman

middle: I

last: Pérez Millán

first: Shannon

middle: W

last: Davis


title: Gene expression profiles at single-cell level of human post-mortem brain tissue from the orbitofrontal cortex

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: The human cortex consists of a variety of different cell types. We used single-nuclei RNA sequencing to characterize cell-type specific gene-expression profiles in a cohort of psychiatrically healthy controls and individuals diagnosed with psychiatric disease.

overall_design: Fresh-frozen post mortem orbitofrontal cortex tissues of Brodmann area 11 (BA 11) was obtained from the NSW Brain Tissue Resource Centre in Sydney, Australia. Single-nucleus RNA sequencing from tissue samples from 35 psychiatrically healthy donors and 57 donors diagnosed with a psychiatric disease was performed.

first: Anna

last: Fröhlich

first: Nathalie

last: Gerstner

first: Miriam

last: Gagliardi

first: Maik

last: Ködel

first: Natalie

last: Matosin

first: Simone

last: Roeh

first: Vanessa

last: Murek

first: Janine

last: Knauer-Arloth

first: Michael

last: Ziller

middle: B


title: RNA Post-transcriptional Modifications of an Early-Stage Large Subunit Ribosomal Intermediate

city: El Paso

first: Eda

last: Kocui

state: TX

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

summary: Protein production by the ribosomes is fundamental to life and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all the ribosome assembly intermediates and on each pathway. There are 26 RNA post-transcriptional modifications in 23S RNA of the mature Escherichia coli (E.coli) large ribosomal subunit. The levels of these modifications have been investigated extensively only for a small number of large subunit intermediates and under a limited number of cellular and environmental conditions. In this study we determine the level of incorporations of 2-methyl adenosine, 3-methyl pseudouridine, 5-hydroxycytosine and eight pseudouridines in an early-stage E.coli  large subunit assembly intermediate with a sedimentation coefficient of 27S. The 27S intermediate is one of three large subunit intermediates accumulated in E.coli  cells lacking the DEAD-box RNA helicase DbpA and expressing the helicase inactive R331A DbpA construct. The majority of the investigated modifications are incorporated into the 27S large subunit intermediate to similar levels as in the mature 50S large subunit, indicating that these early modifications or the enzymes that incorporate them have important roles in the initial events of large subunit ribosome assembly.

overall_design: 27S ribosomal particles were treated with CMCT and NaHCO3 (2 replicates), or NaHCO3 alone (1 replicate).

last: Koculi


title: Single-cell sequencing analysis of PD-L1 immune escape signal axis in lung adenocarcinoma

city: Zhongshan

first: Xiuqiong

last: Xia

address: No. 2 Sunwen East Road, Zhongshan City, Guangdong Province

country: China

institute: Zhongshan People's Hospital

summary: Lung cancer is the most common malignant tumor of lung and bronchus, with the highest mortality rate, and its immunotherapy is easy to cause drug resistance. In order to understand the molecular mechanism of immune escape in patients and develop prediction and therapeutic targets, this study carried out analytical experiments by single-cell sequencing.

overall_design: In this study, 8 tumor tissue samples from 8 lung adenocarcinoma patients were collected, grouped according to the level of PD-L1 positive reaction, and the single-cell landscape was detected. We showed the proportion of immune cells and endothelial cells by UMAP and proportion map of cell types. The cells were subdivided by molecular markers, and the cell subpopulations were divided into different groups according to the proportion of PD-L1 positive reaction and tumor marker positive reaction. The correlation between the occurrence of PD-L1 reaction and the response time of immune cells was explored by quasi-time series analysis. The expression of important differential genes between different groups as shown by heat map, volcano map and bubble map


title: Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes

city: Davis

first: Stefan

middle: Matthias

last: Keller

state: California

address: One Shields Avenue

department: Pathology, Immunology, Microbiology

institute: University of California, Davis

summary: Introduction: The domestic cat (Felis catus) is a valued companion animal and the second most popular pet (over 46.5 million US households). They are also an important model system for virally-induced cancers (feline leukemia virus) and virally-mediated immunodeficiency (feline immunodeficiency virus). However, species specific research limitations such as a lack of reagents and immune cell markers limit our ability to utilize these models to their full capacity. The goal of this study is to characterize the transcriptomic landscape of circulating feline T cells and other captured leukocytes utilizing CD5 (only available selective feline T cell marker) flow cytometry enriched single cell RNA-sequencing and V(D)J repertoire analysis in clinically healthy domestic shorthair cats between the ages of 6 months and 9 years  as well as contextualize them with the leukocytes of other species. Methods: 5 mL of peripheral whole blood was collected from 4 healthy cats (6 months, 1 year, 4 years, 9 years) and were housed at the UC Davis Nutrition and Pet Care Center. Samples were enriched for T cells by flow cytometry using a mouse anti-feline CD5 monoclonal antibody. The GEX library was constructed using the Chromium Next GEM Single Cell 5’ Kit v2 (10x Genomics). The V(D)J library for all 4 T cell receptor loci was prepared using the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. Sequencing was done via Illumina NovaSeq S4 and pre-processed using the Cell Ranger for alignment to the feline genome (felis_catus_9.0). Processing and downstream analyses were conducted via Seurat v5. Additional annotated datasets for cross species T cell integration were acquired from peer-reviewed literature. Results: Unsupervised clustering of GEX data revealed 7 major populations – T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved different populations of naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and γδ T cells for the first time. Cross species analysis revealed relatively high conservation of T cell subtypes along an effector gradient with equitable representation of veterinary species (horse, dog, pig) and humans with the cat. Our V(D)J repertoire analysis demonstrated marked differences in CD8+ cytotoxic T cells from other alpha/beta T cell subsets including productive TRG transcript expression. Among the myeloid cells, we resolved 3 clusters of classical monocytes with polarization into pro- and anti-inflammatory phenotypes in addition to a cluster of conventional dendritic cells. Lastly, our neutrophil sub clustering revealed a larger mature neutrophil cluster and a smaller exhausted/activated cluster.  Discussion: Our study is the first to characterize the subtypes of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species integration. Additionally, we also characterize subtypes in the myeloid cells expanding our understanding of the feline immune system. We have also demonstrated species immune cell relatedness which can provide an important foundation for further translational immunology, pathogenesis, translational treatments, and species-tropism of pathogens in veterinary medicine and research.

overall_design: Flow sort of PBMCs with CD5+ enrichment from 4 healthy domestic shorthair cats followed by 5' scRNAseq with V(D)J analysis (ab TCR & gd TCR)

first: Raneesh

last: Ramarapu

first: Judit

last: Wulcan

first: Haiyang

last: Chang

first: Peter

middle: F

last: Moore

first: William

last: Vernau


title: The asymmetric expression of HSPA2 in blastomeres governs the first embryonic cell-fate decision

status: Public on May 14 2024

city: Jinan

first: jiayin

last: Gao

state: --- Select One ---

address: Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, C

institute: shandong university

summary: The first cell fate decision is the process by which cells of an embryo take on distinct lineage identities for the first time, thus representing the beginning of developmental patterning. Here, we demonstrate that the molecular chaperone heat shock protein A2 (HSPA2), a member of the 70 kDa heat shock protein (HSP70) family, is asymmetrically expressed in the late 2-cell stage of mouse embryos. The knockdown of Hspa2 in one of the two-cell blastomeres prevented its progeny predominantly toward the inner cell mass (ICM) fate, thus indicating that the differential distribution of HSPA2 in the blastomeres of two-cell embryos can influence the selection of embryonic cell lineages. In contrast, the overexpression of Hspa2 in one of the two-cell blastomeres did not induce blastomeres to differentiate towards the ICM fate. Furthermore, we demonstrated that HSPA2 forms a complex with CARM1 and activates ICM-specific gene expression. Collectively, our data identify HSPA2 as a critical regulator of the first cell fate decision which specifies the ICM via the execution of commitment and differentiation phases.

overall_design: To test the heterogeneous distribution of HSPA2 in late 2-cell plays a direct or indirect role in the early stages of lineage commitment., we knocked down the expression of Hspa2 by injecting Hspa2-specific small interfering RNA (siRNA) which targeted the gene in the coding region into the cytoplasm of zygote; NC-FAM (negative control with FAM label) siRNA-injected embryos served as the control

last: gao


title: Single-cell or nucleus RNAseq of neuroblastoma patient-derived xenografts

city: Memphis

last: Dyer

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Gene expression profile at single cell level of 17 orthotopic-patient derived xenografts from neuroblastoma samples. All xenografts were obtained through the St. Jude Childhood Solid Tumor Network (https://cstn.stjude.cloud/)

overall_design: 15 samples underwent single-nucleus RNA-sequencing, and 2 samples underwent single-cell RNA-sequencing. Fastq files were aligned to a combined human and mouse reference (GRCh38-and-mm10).

first: Anand

last: Patel

middle: A

first: Richard

middle: H

last: Chapple

first: Paul

last: Geeleher