title: Sex-biased genes in the primate brain are associated with human neurological disorders and facilitate rapid molecular evolution

status: Public on Jun 18 2024

city: Tempe

first: Kenneth

last: Chiou

state: AZ

address: 427 E Tyler Mall

department: Center for Evolution and Medicine

institute: Arizona State University

summary: Humans exhibit sex differences in the prevalence and presentation of many psychiatric and neurodevelopmental conditions, including Alzheimer’s disease, autism spectrum disorder (ASD), and schizophrenia; however, the ‘omic’, developmental, and environmental underpinnings of these conditions remain elusive. To illuminate these mechanisms and their interactions, and to identify potential therapies, we need large, sex-specific neurobiological data sets from model organisms whose brains exhibit similar characteristics to those of humans, including comparable sex differences. Among existing models, the rhesus macaque is likely to have the greatest translatability; however, comprehensive analyses of brain sex differences in this species are necessary to demonstrate their relevance to sex-biased human conditions. We present an in-depth investigation of sex differences in the rhesus macaque brain transcriptome (RNA-seq) across 527 samples of 15 regions from 36 free-ranging adult individuals (20F/16M), representing the largest collection of bulk brain gene expression data for this species. We identified hundreds of sex-biased genes throughout the rhesus macaque brain, most of which were shared across regions, suggesting convergent regulatory mechanisms. Similar to studies of human brains, these sex-biased genes are regulated by sex hormones and transcription factors that interact with these hormones, male-biased genes are associated with multiple sex-biased human neurological conditions (e.g., ASD, schizophrenia) and energy metabolism, and female-biased genes are associated with the immune response. We also accurately predicted sex from a relatively small number of genes per region and found that, among genes reported to escape X chromosome inactivation in humans, similar genes are the most predictive of sex both across human tissues and in this dataset. Finally, we demonstrated that sex-biased genes exhibit characteristics that facilitate rapid evolution, including a tendency to be located on the sex chromosomes, more tissue-specific expression, and higher genetic variance for expression. Overall, these findings suggest that the rhesus macaque may be an appropriate model for sex-biased human neurological conditions.

overall_design:
527 bulk tissue transcriptomes derived from a free-ranging population of rhesus macaques. The datataset includes 15 distinct brain regions sampled from 36 males and females spanning the natural adult rhesus macaque age distribution.

Please note that the current study represents re-analysis of GSE179328 raw data as following data processing steps:

Gene expression counts were quantified from RNA-seq reads using the pseudoalignment method implemented in kallisto.
Given that sequence homology across the sex chromosomes present in reference genomes/transcriptome (Mmul_10) can lead to technical mapping errors, we created two modified, sex-specific transcriptomes and separately mapped reads from males and females. Specifically, the Y chromosome was removed from the female-specific transcriptome, and CD99 on the Y chromosome (within the pseudoautosomal region; Hughes et al. 2012 [PMID: 22367542]) was removed from the male-specific transcriptome.
Estimated counts and transcripts-per-million (TPM) values were then imported into R v4.0.2 and summarized to genes using the tximport package.

and thus the complete raw data can be accesssed from GSE179328 records.

first: Alexandra

middle: R

last: DeCasien

first: Michael

last: Montague

last: Platt

first: Noah

last: Snyder-Mackler

first: James

middle: P

last: Higham


title: P300 Regulates Histone Crotonylation and Preimplantation Embryo Development (ChIP-Seq)

city: Shenzhen

first: Di

last: Gao

address: No. 1, Haiyuan 1st Road, Futian District

country: China

institute: the University of Hong Kong Shenzhen Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone lysine crotonylation is a non-acetyl histone lysine modification that is evolutionarily conserved. It plays an important role in regulating various biological processes, including gene transcriptional regulation, spermatogenesis, and cell cycle. However, the dynamic changes and functions of histone crotonylation in preimplantation embryonic development in mammals remain unclear. In this study, we have shown that the transcription coactivator P300 functions as a writer of histone crotonylation during embryonic development. Depletion of P300 resulted in significant developmental defects and dysregulation of the transcriptome of embryos. Importantly, we demonstrated that P300 catalyzes the crotonylation of histone, directly stimulating transcription and regulating gene expression, thereby ensuring successful embryo development to the blastocyst stage. Furthermore, it is showed that the histone H3 lysine 18 crotonylation (H3K18cr) modification is predominantly located in active promoter regions. It serves as an epigenetic hallmark of key transcriptional regulators and promotes the transcription activation of genes. Together, our results propose a model wherein P300-mediated histone crotonylation plays a crucial role in regulating the fate of embryonic development.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone H3 lyisne 18 sites crotonylation modifications (H3K18cr) in preimplantation embryos.

first: Chao

last: Li

first: Shao-Yuan

last: Liu

first: Teng-Teng

last: Xu

first: Xiao-Ting

last: Lin

first: Yong-Peng

last: Tan

first: Fu-Min

first: Li-Tao

last: Yi

first: Jian

middle: V

last: Zhang

first: Jun-Yu

last: Ma

first: Tie-Gang

last: Meng

first: William

middle: B

last: Yeung

first: Kui

first: Xiang-Hong

last: Ou

first: Rui-Bao

last: Su

first: Qing-Yuan

last: Sun


title: P300 Regulates Histone Crotonylation and Preimplantation Embryo Development (RNA-Seq)

type: Expression profiling by high throughput sequencing

overall_design: Comparative gene expression profiling analysis of RNA-seq data for preimplantation mouse embryos between the control group and the P300 knockdown group at three distinct developmental stages. Additionally, gene expression profiles comparative analysis of preimplantation mouse embryos from the control group, P300 knockdown group, and two rescue groups at the late 8-cell stage.


title: Wnt/Wingless signaling promotes lipid mobilization through signal-induced transcriptional repression

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

country: USA

institute: Tulane University

summary: The Wnt/Wingless signaling pathway plays critical roles in metazoan development and energy metabolism, but its involvement in lipid mobilization has remained unclear. Here, we report that canonical Wnt/Wg signaling reduces lipid accumulation in both larval and adult adipocytes, as well as cultured S2R+ cells, in Drosophila. This reduction occurs through promoting lipolysis while concurrently repressing lipogenesis and fatty acid β-oxidation. Leveraging RNA-sequencing and CUT&RUN assays, we have identified a set of Wnt target genes responsible for intracellular lipid homeostasis. Notably, active Wnt signaling directly represses the transcription of these genes, resulting in decreased triglyceride accumulation in lipid droplets, increased lipolysis, and reduced fatty acid β-oxidation. These changes lead to elevated free fatty acids and reduced triglyceride accumulation in adipocytes with active Wnt signaling. Conversely, downregulation of Wnt signaling in the fat body promotes triglyceride accumulation in both larval and adult stages. The attenuation of Wnt signaling also increases the expression of specific lipid metabolism-related genes in larval adipocytes, wing discs, and adult intestines. Collectively, our findings suggest that Wnt signaling-induced transcriptional repression plays an important role in regulating lipid homeostasis by enhancing lipolysis while simultaneously suppressing lipogenesis and fatty acid β-oxidation processes.

overall_design: To gain insights into the molecular mechanism underlying Wnt signaling-stimulated lipid catabolism and reduced lipogenesis, we conducted bulk RNA sequencing (RNA-seq) analyses on dissected larval fat body with specific depletions of Axn or slmb, and BTZ treated animals. To investigate potential direct targets of Wnt signaling, we performed CUT&Run on EGFP tagged Pan.

first: Mengmeng

first: Rajitha-Udakara-Sampath

last: Hemba-Waduge

first: Xiao

first: Xiahe

last: Huang

first: Tzu-Hao

first: Xianlin

last: Han

first: Yingchun

last: Wang

first: Jun-Yuan


title: P300 Regulates Histone Crotonylation and Preimplantation Embryo Development

first: Di

last: Gao

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

overall_design: Refer to individual Series


title: Mechanisms of resistance to oncogenic KRAS inhibition in pancreatic cancer

status: Public on Jun 17 2024

city: Boston

first: Julien

last: Dilly

state: MA

address: 450 Brookline avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: KRAS inhibitors demonstrate clinical efficacy in pancreatic ductal adenocarcinoma (PDAC); however, resistance is common. Among patients with KRASG12C-mutant PDAC treated with adagrasib or sotorasib, mutations in PIK3CA and KRAS, and amplifications of KRASG12C, MYC, MET, EGFR, and CDK6 emerged at acquired resistance. In PDAC cell lines and organoid models treated with the KRASG12D inhibitor MRTX1133, epithelial-to-mesenchymal transition and PI3K-AKT-mTOR signaling associate with resistance to therapy. MRTX1133 treatment of the KrasLSL-G12D/+;Trp53LSL-R172H/+;p48-Cre (KPC) mouse model yielded deep tumor regressions, but drug resistance ultimately emerged, accompanied by amplifications of Kras, Yap1, Myc, and Cdk6/Abcb1a/b, and co-evolution of drug-resistant transcriptional programs. Moreover, in KPC and PDX models, mesenchymal and basal-like cell states displayed increased response to KRAS inhibition compared to the classical state. Combination treatment with KRASG12D inhibition and chemotherapy significantly improved tumor control in PDAC mouse models. Collectively, these data elucidate co-evolving resistance mechanisms to KRAS inhibition and support multiple combination therapy strategies.

overall_design: Autochthonous KPC (KrasLSL-G12D/+;Trp53LSL-R172H/+;p48-Cre) genetically engineered mouse model (GEMM) of PDAC were treated with MRTX1133 (KRAS p.G12D inhibitor) or vehicle. Tumors were harvested after 3 days of continuous treatement ("Early vehicle" and “Early MRTX1133”) or after mice reached a humane endpoint ("Endpoint vehicle" or “MRTX1133 resistant”) based on criteria from the Institutional Animal Care & Use Committee (IACUC) at Dana-Farber Cancer Institute (DFCI).

first: Andrew

middle: J

last: Aguirre


sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq of MRTX1133-resistant human and murine cell lines were generated from parental cell lines by continuous dose escalation from as low as 1nM to 10μM. Once resistance to MRTX1133 was confirmed, resistant cell lines were routinely maintained in the corresponding medium with 1uM (10% of the maximum dose reached during the evolution of resistance) of MRTX1133.


title: The dynamic behavior of chromatophores marks the transition from bands to spots in leopard geckos

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

summary: Reptilian skin coloration is spectacular and diverse, yet little is known about the ontogenetic processes that govern its establishment and the molecular signaling pathways that determine it. Here, we focus on the development of the banded pattern of leopard gecko hatchlings and the transition to black spots in the adult. With our histological analyses, we show that iridophores are present in the white and yellow bands of the hatchling and they gradually perish in the adult skin. Furthermore, we demonstrate that melanophores can autonomously form spots in the absence of the other chromatophores both on the regenerated skin of the tail and on the dorsal skin of the Mack Super Snow (MSS) leopard geckos. This color morph is characterized by uniform black coloration in hatchlings and black spots in adulthood; we establish that their skin is devoid of xanthophores and iridophores at both stages. Our genetic analyses identified a 13-nucleotide deletion in the PAX7 transcription factor of MSS geckos, affecting its protein coding sequence. With our single-cell transcriptomics analysis of embryonic skin, we confirm that PAX7 is expressed in iridophores and xanthophores, suggesting that it plays a key role in the differentiation of both chromatophores. Our in situ hybridizations on whole-mount embryos document the dynamics of the skin pattern formation and how it is impacted in the PAX7 mutants. We hypothesize that the melanophores–iridophores interactions give rise to the banded pattern of the hatchlings and black spot formation is an intrinsic capacity of melanophores in the postembryonic skin.

overall_design: single cell RNA-seq of a E35 wild-type leopard gecko embryo dorsal skin sample.

first: Athanasia

last: C Tzika


title: STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia

city: Regensburg

first: Alexander

last: Fischer

address: Franz-Josef-Strauß-Allee 11

country: Germany

institute: Leibniz Institute for Immunotherapy


title: A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma [ATAC-seq]

city: Songpa-Gu

first: Byung-Kwan

last: Jeong

state: Seoul

address: 88, Olympic-ro 43-gil

department: Pathology

country: South Korea

institute: Asan Medical Center

summary: The lack of an appropriate preclinical model of non-alcoholic fatty liver disease (NAFLD) that recapitulates the whole disease spectrum impedes exploration of disease pathophysiology and the development of effective treatment strategies. Therefore, we developed new mose model with Streptozotocin (STZ)and high-fat diet (HFD). In breif, male C57BL/6J mice were injected with low-dose streptozotocin (40 mg/kg) for 5 consecutive days beginning at 7 weeks of age and subsequently fed a high-fat diet from week 8 (STZ+HFD) onwards. Hepatic histopathology, transcriptomics, epigenetics, and metabolic phenotypes were evaluated at various time-points. The hepatic transcriptomes of STZ+HFD mice and NAFLD patients with similar liver histopathology were compared. In STZ+HFD mice, dietary changes from HFD to standard chow and administration of tirzepatide, a dual glucose-dependent insulinotropic polypeptide/glucagon-like peptide-1 receptor agonist, were introduced to assess the therapeutic efficacy of these interventions. STZ+HFD mice gradually developed fatty liver, non-alcoholic steatohepatitis (NASH), hepatic fibrosis, and hepatocellular carcinoma (HCC) in the context of metabolic dysfunction. In particular, from 32 weeks of age, NASH and advanced fibrosis were evident. At 38 weeks, a proportion of STZ+HFD mice developed HCC, which was subsequently observed in all mice up to 68 weeks of age. Furthermore, the hepatic transcriptomic features of STZ+HFD mice closely reflected those of patients with NASH and NAFLD-related HCC. Notably, dietary changes and tirzepatide administration alleviated NASH, hepatic fibrosis, and hepatic tumorigenesis in STZ+HFD mice. Put together, we established a murine model recapitulating the main histopathologic, transcriptomic, and metabolic alterations observed in NAFLD patients with metabolic dysfunction was successfully established.

overall_design: We performed  ATAC-seq profiling in the four groups of C57BL/6J mice clasffied by STZ treatment and dietary method (STZ+HFD, STZ+standard chow diet(SCD), HFD only, SCD only) at 20 weeks of age to examine how STZ+HFD mice rapidly progress to NASH.

first: Won-Il

last: Choi

first: Wonsuk

first: Hail

last: Kim

first: Jun-Yong

last: Park


title: Activity of DNA polymerase kappa across the genome in human fibroblasts

city: Hershey

first: Thomas

middle: E

last: Spratt

state: PA

address: 500 University Dr

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: DNA polymerase kappa (PolK) is a specialized polymerase that has multiple cellular roles such as translesion DNA synthesis, replicating repetitive sequences, and nucleotide excision repair. We have developed a method for capturing DNA synthesized by PolK utilizing a PolK - specific substrate, N2-(4-ethynylbenzyl)-2′-deoxyguanosine (EBndG). After shearing of the DNA into 200-500bp lengths, the EBndG-containing DNA was covalently bound to biotin using the Cu(I)-catalyzed alkyne–azide cycloaddition reaction, and isolated with streptavidin beads. Isolated DNA was then ligated to adaptors, followed by PCR amplification and next-generation sequencing (NGS) to generate genome-wide repair maps. We have termed this method polymerase k sequencing (polK-seq). Here we present the human genome maps for pol k activity in an undamaged cell line. We found that pol k activity was enhanced in euchromatin regions, the promoter of genes, and in DNA that is replicated early in S-phase

overall_design: Cells treated with EBndG for 4 h, harvested and genomic DNA isolated. EBndG was attached to biotin via Click reaction. DNAwas sheared, EBndG containing DNA isolated with streptavidin beads and NGS libraries prepared

first: Mariela

middle: C

last: Torres

first: Abbey

last: Rebok

first: Dongxiao


title: The impact of conditional Opa1 Knockout in neural stem cells on transcriptome changes

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary:
To investigate the function of Opa1 in the regulation of adult neurogenesis, we created a conditional Opa1-knockout mouse line by cross-breeding Nestin-CreERT2;ROSA26YFP mice with Opa1-Flox mice.
Using Tamoxifen, we induced Opa1 knockout on 8-weeks-old Nestin-CreERT2;ROSA26YFP;Opa1-Flox mice. We then sorted YFP-positive cells from the hippocampus using flow cytometry at 10 weeks. RNA was extracted from sorted cells and subjected to next generation sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Opa1-KO neural stem cells.

first: Mohamed

middle: A

last: Iqbal


title: A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma [RNA-seq]

summary: The lack of an appropriate preclinical model of metabolic dysfunction-associated steatotic liver disease (MASLD) that recapitulates the whole disease spectrum impedes exploration of disease pathophysiology and the development of effective treatment strategies. Considering the fact that MASLD patients accompanying type 2 diabetes mellitus (T2DM) have high risk of developing metabolic dysfunction-associated steatohepatitis (MASH), advanced fibrosis, and HCC, we treated low-dose streptozotocin (STZ; 40 mg/kg) for 5 consecutive days and subsequently fed a high-fat diet (HFD) to male C57BL/6J mice at 7 weeks of age (STZ+HFD). STZ+HFD mice gradually developed fatty liver, MASH, hepatic fibrosis, and hepatocellular carcinoma (HCC) in the context of metabolic dysfunction. In particular, from 20 weeks of age, MASH was evident, and from 32 weeks of age, advanced fibrosis was developed. At 38 weeks, a proportion of STZ+HFD mice developed HCC, which was subsequently observed in all mice up to 68 weeks of age. Furthermore, the hepatic transcriptomic features of STZ+HFD mice closely reflected those of obese patients with T2DM, MASH and MASLD-related HCC. Notably, dietary changes and tirzepatide administration alleviated MASH, hepatic fibrosis, and hepatic tumorigenesis in STZ+HFD mice. In conclusion, a murine model recapitulating the main histopathologic, transcriptomic, and metabolic alterations observed in MASLD patients with metabolic dysfunction was successfully established.

overall_design:
To investigate transcriptomic alterations during MASLD progression, we profiled hepatic transcriptome of the model mouse at different ages with RNA-seq (7 weeks, healthy control; 8 weeks, acute STZ-treated state; 14-20 weeks, MASL to MASH transition; 32 weeks, MASH with fibrosis; 44 weeks, MASH with advanced fibrosis; 50-56 weeks, MASLD-related dysplastic nodules and HCC.
Then we compared hepatic transcriptome of mice with that of human NAFLD patients with different MASLD acitivty score and fibrosis stage using RNA-seq profiling.
We also performed RNA-seq profiling in hepatic tumors developed in model mice at 44-56 weeks.
In addition, we performed RNA-seq profiling in the four groups of C57BL/6J mice clasffied by STZ treatment and dietary method (STZ+HFD, STZ+standard chow diet(SCD), HFD only, SCD only) at 20 and 32 weeks of age to examine how STZ+HFD mice rapidly progress to NASH.
And we performed RNA-seq profiling in the model mice with dietary change to chow for 6 or 18 weeks with control unchanged group, and the model mice treated with tirzepatide or vehicle for 10 to 11 weeks at different ages (21-32 weeks, 28-38 weeks, and 41-52 weeks).


title: The impact of conditional Opa1 Knockout


title: The impact of conditional Opa1 Knockout on gene expression profile at single cell level during adult neurogenesis in the hippocampus

summary: To investigate the function of Opa1 in the regulation of adult neurogenesis, we created a conditional Opa1-knockout mouse line by cross-breeding Nestin-CreERT2;ROSA26YFP mice with Opa1-Flox mice.

overall_design: Using Tamoxifen, we induced Opa1 knockout on 8-weeks-old Nestin-CreERT2;ROSA26YFP;Opa1-Flox mice. We then sorted YFP-positive cells from the hippocampus using flow cytometry at 12 weeks. Single cell transcriptome was performed on the 10XGenomics platform.


title: Therapeutic strategy for spinal muscular atrophy by combining gene supplementation and genome editing

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Defect in the SMN1 gene causes spinal muscular atrophy (SMA), which shows loss of motor nerve cells, muscle weakness and atrophy. While current treatment strategies including small molecules or viral vectors improved motor function and survival, an ultimate treatment is highly challenging to correct the endogenous mutations by genome-editing technologies. We have developed the CRISPR-Cas9 based homology-independent targeted integration (HITI) strategy, which allowed for DNA knock-in in both dividing and non-dividing cells in vivo. Here, we demonstrated a gene correction of mutant mSmn1 by using the HITI strategy to treat SMA model mice. To provide the long-term therapeutic benefits of gene correction, we established a unique approach to treat SMA by combination with gene cDNA supplementation and editing (Gene-DUET). As a proof of concept of therapeutic approach for SMA, we demonstrated the advantageous effects including motor function and survival improvement by Gene-DUET strategy in SMA model mice. The Gene-DUET represents a powerful strategy for treating inherited diseases especially for neurodegenerative disorders as well as neuromuscular diseases.

overall_design: To investigate the global transcriptional alterations by HITI, cDNA and DUET treatments in SMA mice compared to untreated SMA mice and heterozygous mice.

first: Fumiyuki

last: Hatanaka

first: Keiichiro

last: Suzuki

first: Kensaku

last: Shojima

first: Yuta

last: Takahashi

first: Akihisa

last: Sakamoto

first: Javier

last: Prieto

first: Maxim

middle: N

last: Shokhirev

first: Concepcion

last: Esteban

first: Estrella

last: Delicado

first: Juan

middle: I

last: Belmonte


title: Traditional Chinese Medicine JianPiHuaTan Formula Improving Quality of Life and Survival in Patients with Colorectal Cancer through RAS/RAF Downstream Signaling Pathways

status: Public on Jun 15 2024

city: Beijing, China

first: Guojun

last: Li

address: 88 Kechuang Sixth Street, Beijing

institute: Chinese Academy of Sciences

summary: Abstract     Objective: JianPiHuaTan Formula (JPHTF), a traditional Chinese medicine (TCM), has been utilized as an adjunctive therapy for colorectal cancer (CRC). The study aims to evaluate the potential clinical benefits of JPHTF and its effectiveness in inhibiting tumor growth.  Methods: 300 stage II/III CRC patients and 412 advanced CRC patients were enrolled to verify the clinical value of JPHTF in CRC treatment. Furthermore, CRC patient-derived xenograft (PDX) mice were utilized to investigate the regulatory mechanisms of JPHTF.  Results: JPHTF significantly improved abdominal distension, shortness of breath, drowsiness, loss of appetite, sleep, and tiredness in stage II/III CRC patients, thereby improving their quality of life. Simultaneously, JPHTF served as a supportive therapy in extending the overall survival (OS) of stage IV CRC patients with RAS/RAF mutations undergoing chemotherapy. Additionally, JPHTF effectively impeded tumor progression in CRC PDX models with RAS mutation, accompanied by a reduction in tumor cell content in the JPHTF group. Transcriptomic analysis revealed the involvement of the Hippo and Hedgehog signaling pathways in JPHTF-mediated CRC inhibition. Furthermore, mice in the JPHTF group exhibited increased immune cell infiltration.  Conclusions: These findings suggested that JPHTF may inhibits tumor growth in CRC with RAS mutation by modulating RAS/RAF downstream signaling pathways, specifically the Hippo and Hedgehog signaling, leading to increased immune cell infiltration.

overall_design: To verify the inhibitory effect of JPHTF on the growth of CRC tumors carrying RAS mutations, we injected a human colorectal cancer cell carrying NRAS mutations into two groups of mice(Untreated control group (G1) vs JPHTF treatment group G2).RNA-sequencing was performed on tumor tissues from mice, treated with or without JPHTF.DEGs then were identified.

first: Linlin

last: Cai

first: Mingjiang

last: Yao

first: Qian

last: Chen


title: N2-heptynyl-dG sequencing

city: Riverside

first: feng

last: tang

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

summary: N2-heptynyl-dG sequencing in HEK293T cells

overall_design: HEK293T cells were treated with N2-heptynyl-dG for 3-h at a final concentration of 10 μM. The cells were then harvested immediately for N2-heptynyl-dG sequencing. The genomic DNA were extracted using Monarch® Genomic DNA Purification Kit (New England Biolabs) and reacted with biotin-azide at room temperature for 6 h. The biotinylated genomic DNA was sheared using a Covaris S220 sonicator. The N2-heptynyl-dG DNA were enriched with Dynabeads™ MyOne™ Streptavidin C1 (Thermo). Purified DNA was quantified and verified on an Agilent 2100 Bioanalyzer. The library was then constructed using NEBNext Ultra DNA Library Prep Kit (NEB, E7103S) following the manufacturer’s instructions. Subsequently, the purified DNA libraries were assessed using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on a DNBSEQ-G400 (BGI Genomics) .

first: Feng

last: Tang

first: Yinsheng

last: Wang


title: In vivo effects of Bay 11-7082 on fibroid growth and gene expression: a preclinical study

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

summary: The objective of this study was to elucidate the effects of the anti-inflammatory inhibitor, Bay 11-7082 on fibroid growth and gene expression in an in vivo model

overall_design: Comparative gene expression profiling analysis of RNA-seq data after being treated with Bay 11-7082 for two months in an in vivo model

first: Tsai-Der

last: Chuang

first: Nhu

last: Ton

first: Shawn

last: Rysling


title: A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma

status: Public on Jun 16 2024

first: Byung-Kwan

last: Jeong

first: Won-Il

last: Choi

first: Wonsuk

first: Won Hee

last: Lee

first: Jun Yong

last: Park

first: Hail

last: Kim


title: Unveiling Systemic Responses in Kidney Transplantation: Interplay between the Allograft Transcriptome and Serum Proteins

status: Public on Jun 14 2024

city: Muenster

first: Konrad

last: Buscher

address: Albert Schweitzer Campus A1

institute: University Hospital Muenster

summary: We explored a direct association between the kidney allograft phenotype and serum protein signatures. Time-matched samples of graft biopsies and blood serum were collected in a heterogenous cohort of kidney transplanted patients (n=15) for bulk RNA sequencing and proteomics, respectively.

overall_design: Human kidney allograft biopsies (n=15, healthy and rejecting) were digested and processed for RNA sequencing. A matched blood sample was used for proteomics, so that changes in the graft RNA landscape could be correlated with blood serum proteins.

first: Rebecca

last: Rixen

first: Paula

last: Schuetz

first: Veerle

last: Van Marck

first: Barbara

last: Heitplatz

first: Daniela

last: Braun

first: Gert

last: Gabriels

first: Ulrich

last: Jehn

first: Hermann

last: Pavenstaedt

first: Stefan

last: Reuter


title: Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Understanding prostate response to castration and androgen receptor signaling inhibitors (ARSI) is critical to improving long-term prostate cancer (PCa) patient survival. We use a multi-omics approach on 229,794 single cells to create a mouse single-cell reference atlas better suited to interpreting mouse prostate biology and castration response. Our reference atlas refines single-cell annotations and provides chromatin context, which, when coupled with mouse lineage tracing demonstrates that the castration-resistant luminal cells are distinct from the pre-existent urethra- proximal stem/progenitor cells.

overall_design: Bulk RNA sequencing analysis of lineage traced Nkx / Clu positive prostate epithelial cells was used to identify cell type specific transcriptomes and confirm lineage tracing relationship to single-cell transcriptomic cluster designations.

first: Jason

last: Kirk

first: Dean

last: Tang


title: The type Ⅲ effector NopL interacts with GmREM1a and GmNFR5 to promote symbiosis in soybean

status: Public on Jun 13 2024

city: Harbin

first: Chao

last: Ma

state: Hei Longjiang

address: 中国 哈尔滨 香坊区 长江路600号

department: College of Agriculture

institute: Northeast Agriculutral University

summary: The establishment of symbiotic interactions between leguminous plants and rhizobia requires complex cellular programming activated by Rhizobium Nod factors (NFs) as well as type III effector (T3E)-mediated symbiotic signaling. However, the mechanisms by which different signals jointly affect symbiosis are still unclear. Here we describe the mechanisms mediating the cross talk between the Sinorhizobium fredii T3E Nodulation Outer Protein L (NopL) effector and NF signaling in soybean. NopL physically interacts with the Glycine max Remorin 1a (GmREM1a) and the NFs receptor NFR5 (GmNFR5) and promotes GmNFR5 recruitment by GmREM1a. Furthermore, NopL and NF influence the expression of GmRINRK1, a receptor-like kinase (LRR-RLK) ortholog of the Lotus RINRK1, that mediates NF signaling. Taken together, our work indicates that S. fredii NopL can interact with the NF signaling cascade components to promote the symbiotic interaction in soybean.

overall_design:
For the RNA-seq experiment, two types of soybean plants were used: the DN50 (wild type) and derived Gmrem1 mutant. These plants were inoculated with different strains of rhizobia, including the wild type HH103, derived mutants HH103ΩnopL and HH103ΩnodA and a mock control using 10mM MgSO4. The plants were inoculated with these rhizobia strains, and the roots were sampled, and total RNA was isolated at 1 dpi.
The RNA-seq analysis was performed on the isolated total RNA from the roots of the different soybean plants under the various treatments. Rhizobia inoculation and sample collection were performed as described above. Three roots from different plants were collected as one replicate, and three biological replicates were collected for each treatment.
Three individual samples were sequenced using Illumina NovaSeq 6000. To identify differential expression genes (DEGs) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2. DEGs with |log2FC|≧1 and FDR≤ 0.05 were considered to be significantly different expressed genes.

first: Dawei

last: Xin

first: Qingshan

last: Chen

first: Xulun

last: Dong


title: Effect of Gilteritinib, Metformin and Combination treatments on gene expression in MOLM13-RES cells

city: Monrovia

first: Jianjun

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: Here, we report that Metformin shows a striking synergistic effect with Gilteritinib in suppressing cell proliferation and promoting apoptosis and cell cycle arrest in multiple FLT3-ITD AML cell lines, including FLT3 TKI-resistant MOLM13 cells. Mechanistically, the combinational treatment synergistically suppresses Polo-like kinase 1 (PLK1) expression and phosphorylation of FLT3/STAT5/ERK/mTOR in MOLM13-RES cells. Intriguingly, our retrospective clinical analysis has unveiled a significant correlation between Metformin intake and improved survival rates among FLT3-ITD AML patients. Collectively, the cotreatment of Metformin and Gilteritinib shows robustly enhanced therapeutic efficacy in treating FLT3-mutated AML by synergistically suppressing PLK1 expression and phosphorylation of FLT3/STAT5/ERK/mTOR.

overall_design: MOLM13-RES cells were cultured under standard conditions and were treated with DMSO, Gilteritinib, Metformin and Combination, respectively. Collect the four group cells after 24 hours treatment and extract total RNA. Use 10ug for next library preparation and sequencing.

first: Meiling

first: Keren

last: Zhou


title: Bioprinted spatially defined breast tumor microenvironment models of intratumoral heterogeneity and drug resistance

city: Guangzhou

first: xihong

last: Fu

state: Guangdong Province

address: 58 Zhongshan Second Rd, Guangzhou

institute: Sun Yat-sen University

summary: Cellular extracellular matrix (ECM) and spatial heterogeneity of tumor microenvironments (TME) regulate disease progression and treatment efficacy. Developing in vitro models that recapitulate the TME promises to accelerate studies of tumor biology and identify new targets for therapy. Here, we employed extrusion-based, multi-nozzle three-dimensional (3D) bioprinting to spatially pattern triple-negative MDA-MB-231 breast cancer cells, endothelial cells, and human mammary cancer-associated fibroblasts with biomimetic ECM inks. Bioprinted models captured key features of the spatial architecture of human breast tumors, including varying-sized dense regions of cancer cells and surrounding microvessel-rich stroma. Angiogenesis and ECM stiffening occurred in the stromal area but not the cancer cell rich regions, mimicking pathological changes in patient samples. Transcriptomic analyses revealed upregulation of angiogenesis-related and ECM remodeling-related signatures in the stroma region and identified potential ligand-receptor mediators of these processes. Breast cancer cells in distinct parts of the bioprinted TME showed differing sensitivities to chemotherapy, highlighting environmentally mediated drug resistance. In summary, our 3D bioprinted tumor model will act as a platform to discover integrated functions of the TME in cancer biology and therapy.

overall_design: we employed extrusion-based, multi-nozzle three-dimensional (3D) bioprinting to spatially pattern triple-negative MDA-MB-231 breast cancer cells, endothelial cells, and human mammary cancer-associated fibroblasts with biomimetic ECM inks.We identified spatial patterns based on morphology and staining of blood vessels. We mapped tumors into spatially distinct regions, including cancer cell rich (CCR) regions and adjacent stroma rich (SR) regions: (1) CCR regions were dominantly occupied by varying-sized cancer cell clusters with the occurrence of blood vessels and fibroblasts; (2) SR regions showed enrichment for blood vessels and fibroblasts. Based on the above spatial characteristics, we established vascularized breast cancer models with heterogeneous patterns of CCR and SR regions using an extrusion-based multi-nozzle 3D bioprinter. As a control, we fabricated unpatterned models with a generally uniform distribution of three cell types throughout the construct

first: Tianying

last: Yuan

first: Xihong


title: Apelin 13 breaks the immune cell route from lung to brain [scRNA-Seq]

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: To investigate the effect of Apelin 13 on lung in experimental autoimmune encephalomyelitis(EAE) at peak, we perform single cell RNA sequencing of the whole lung of Control, EAECont and EAE with Apelin 13 treatment(EAEA13)

overall_design: 3 lungs of each group(Cont, EAECont, EAEA13) were pooled together and dissociated using papain and liberase solution and single cell RNA isolation was performed utilizing BD rhapsody.

first: Hongryeol

last: Park

first: Ralf

middle: H

last: Adams


title: Apelin 13 breaks the immune cell route from lung to brain [RNA-Seq]

summary: We treated HUVEC with Apelin 13 or siRNA of Aplnr to investigate the impact of Apelin 13 and APLNR knockdown. We then performed gene expression profiling analysis using data obtained from RNA-seq of 7 different conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Static vs flow, flowCont vs flow with Apelin 13, siCont vs siAPLNR in both static and flow conditions.


title: Apelin 13 breaks the immune cell route from lung to brain

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

overall_design: Refer to individual Series


title: Diagnostic Utility of DNA Methylation Analysis in Genetically Unsolved Pediatric Epilepsies and CHD2 Episignature Refinement

city: Memphis

first: Heather

last: Mefford

state: FL

address: 262 Danny Thomas Pl

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

summary: Sequence-based genetic testing identifies causative variants in ~50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.

overall_design: We performed Illumina DNA Methylation Array (EPIC 850K V1) on peripheral blood-derived DNA samples for individuals with genetically unresolved Developmental and Epileptic Encephalopathies (DEEs) in order to determine potential causal etiologies. We also investigated a subset of individuals with pathogenic variants in CHD2. All samples in GSE269416 are derived from peripheral blood DNA, except for 207179240107_R06C01 (saliva), 207179240107_R08C01 (saliva), and 205707890075_R05C01 (fibroblast).

first: Christy

last: LaFlamme


title: Stress-induced nuclear translocation of transcription factor ONAC023 improves drought and heat tolerance through integrated regulation of multiple processes in rice

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Although hundreds of stress-related genes have been identified in the past two decades, very few genes have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, identified through NAC-centered gene regulatory network and genetic association analyses, is a hub stress-regulator that integrates the regulations of both drought and heat tolerance in rice. The loss-of-function mutant of ONAC023 showed significantly increased sensitivity to drought and heat stresses, whereas the overexpression of ONAC023 confers drought and heat tolerance at both seedling and reproductive stages. Notably, drought and heat stresses activated the function of ONAC023 not only by the induction of ONAC023 transcript but also by the nuclear accumulation of ONAC023 protein through a remorin-importin-α-assisted translocation. Under drought or heat stress, ONAC023 can directly target and promote the expression of functionally diverse downstream genes, such as OsPIP2;7, PGL3, OsFKBP20-1b, and OsSF3B1, which are involved in various stress-responsive processes including water transport, reactive oxygen species homeostasis, and alternative splicing (AS). Furthermore, genome-wide AS profiling revealed that the loss of ONAC023 function led to alternation of the encoding outcomes of thousands of AS transcripts under drought and heat stresses. These results manifested that ONAC023 is fine tuned to positively regulate drought and heat tolerance through the integration of multiple stress-responsive processes. Our findings provide not only an underlying connection between drought and heat responses, but also a promising candidate for engineering multi-stress-resilient rice.

overall_design: Drought or heat treated 4-leaf stage onac023 T-DNA insertion mutants and the derived wild type seedlings (DJ)  were harvested for RNA-seq and ChIP-seq, in triplicate (two replicates for ChIP-Seq under the drought treatment), using Illumina Hiseq X Ten.

first: Yujie

last: Fang

first: Lizhong

last: Xiong


title: UBXN3B Is Crucial for B Lymphopoiesis

status: Public on Jun 12 2024

city: Farmington

first: Tingting

last: Geng

state: CT

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

summary: Hematopoiesis is finely regulated to enable timely production of the right numbers and types of immune cells. Herein, we report the crucial function of UBXN3B in B lymphopoiesis. In the inducible global knockout and B cell-specific Ubxn3b knockout model, the terminal B cell number is reduced by > 90% in both Ubxn3b-/- mouse models. Transfer of wildtype bone marrows to irradiated global Ubxn3b-/- restores the B population, while reverse transplantation fails to do so. The deficiency begins from the precursor stage. The B population drops rapidly with significant apoptosis, presents a much higher level of pro-caspase-3 protein following induction of Ubxn3b knockout. RNA-sequencing reveals significantly suppressed cell cycle genes while upregulated TP53 signaling in Ubxn3b-/- B cells. Ubxn3b-/- mice are highly vulnerable to respiratory viruses, with increased lung viral loads and immunopathology, reduced B population and virus-specific IgM/IgG. This study reveals a cell-intrinsic essential role of UBXN3B in B cell survival and UBXN3B as a potential therapeutic target for B-cell related diseases.

overall_design: To investigate the function of UBXN3b in B lymphopoiesis, we established an inducible global knockout mouse model. In this model, tamoxifen administration induces the knockout of Ubxn3b.  Bone marrows from tamoxifen or oil treated mice were sorted for B subsets. Subsequent comparartive gene expression profilling analysis was conduted using RNA-seq data from mature B subset.

first: Penghua

last: Wang


title: Kdm4a is an activity downregulated barrier to generate engrams for memory separation

city: Shanghai

first: xiuxian

last: guo

state: Shanghai

address: 393 Middle Huaxia Road, Pudong

institute: ShanghaiTech University

summary: Memory engrams are a subset of learning activated neurons critical for memory recall, consolidation, extinction and separation. While the transcriptional profile of engrams after learning suggests profound neural changes underlying plasticity and memory formation, little is known about how memory engrams are selected and allocated. As epigenetic factors suppress memory formation, we developed a CRISPR screening in the hippocampus to search for factors controlling engram formation. We identified histone lysine-specific demethylase 4a (Kdm4a) as a novel regulator for engram formation. Kdm4a is downregulated after neural activation and controls the volume of mossy fiber boutons. Mechanistically, Kdm4a anchors to the exonic region of Trpm7 gene loci, causing the stalling of nascent RNAs and allowing burst transcription of Trpm7 upon the dismissal of Kdm4a. Furthermore, the YTH domain containing protein 2 (Ythdc2) recruits Kdm4a to the Trpm7 gene and stabilizes nascent RNAs. Reducing the expression of Kdm4a in the hippocampus via genetic manipulation or artificial neural activation facilitated the ability of pattern separation in rodents. Our work indicates that Kdm4a is a negative regulator of engram formation and suggests a priming state to generate a separate memory.

overall_design: To dissect the molecular mechanisms underlying Kdm4a-mediated memory allocation, we examined Kdm4a knockdown-induced transcriptional changes via through RNA sequencing (RNA-seq) by comparing the neurons with Kdm4a shRNA to the neurons with control shRNA in dentate gyrus of naïve mice

first: Xiuxian

last: Guo

first: Pengfei

last: Hong

first: Songhai

first: Yuze

last: Yan

first: Hong

last: Xie

first: Ji-Song

last: Guan


title: Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs [RNA-seq]

city: Los Angeles

first: Song

last: Li

state: California

address: 404 Westwood Plaza, Eng VI

institute: UCLA

summary: Synthetic Notch (synNotch) receptors are modular synthetic components that are genetically engineered into mammalian cells to detect signals presented by neighboring cells and respond by activating prescribed transcriptional programs. To date, synNotch has been used to program therapeutic cells and pattern morphogenesis in multicellular systems. However, cell-presented ligands have limited versatility for applications that require spatial precision, such as tissue engineering. To address this, we developed a suite of materials to activate synNotch receptors and serve as generalizable platforms for generating user-defined material-to-cell signaling pathways. First, we demonstrate that synNotch ligands, such as GFP, can be conjugated to cell- generated ECM proteins via genetic engineering of fibronectin produced by fibroblasts. We then used enzymatic or click chemistry to covalently link synNotch ligands to gelatin polymers to activate synNotch receptors in cells grown on or within a hydrogel. To achieve microscale control over synNotch activation in cell monolayers, we microcontact printed synNotch ligands onto a surface. We also patterned tissues comprising cells with up to three distinct phenotypes by engineering cells with two distinct synthetic pathways and culturing them on surfaces microfluidically patterned with two synNotch ligands.  We showcase this technology by co-transdifferentiating fibroblasts into skeletal muscle or endothelial cell precursors in user-defined spatial patterns towards the engineering of muscle tissue with prescribed vascular networks. Collectively, this suite of approaches extends the synNotch toolkit and provides novel avenues for spatially controlling cellular phenotypes in mammalian multicellular systems, with many broad applications in developmental biology, synthetic morphogenesis, human tissue modeling, and regenerative medicine.

overall_design: C3h/10t1/2 fibroblasts were engineered with 1) anti-GFP SynNotch activating mCherry or 2) anti-GFP SynNotch activating myoD and mCherry or 3)  anti-mCherry SynNotch activating ETV2 and BFP. These cells were then cultured/activated by their respective ligands (GFP or mCherry) and cultured for 2 days before RNA extraction and sequencing. Negative controls include the parental C3H cell line as well as these same synNotch cell lines cultured without the presence of their respective ligands. Positive controls include C2C12 skeletal muscle cell line and BEnd.3 endothelial cell line.

first: Megan

last: McCain

first: Leonardo

last: Morsut

first: Tyler

last: Hoffman

first: Mher

last: Garibyan

first: Yifan

last: Wu

first: Brian

last: Williams


title: Single-cell analysis of human PBMCs in healthy and type 2 diabetes populations: Dysregulated immune networks in type 2 diabetes unveiled through single-cell profiling

city: Seoul

first: Do-eon

last: GU

state: Korea

address: 81 Irwon-Ro, Gangnam-gu

institute: Sungkyunkwan University

summary: Abnormalities in glucose metabolism that precede the onset of type 2 diabetes (T2D) activate immune cells, leading to elevated inflammatory factors and chronic inflammation. However, no single-cell RNA sequencing (scRNA-seq) studies have characterized the properties and networks of individual immune cells in T2D. Here, we analyzed peripheral blood mononuclear cells (PBMCs) from healthy controls and T2D patients by scRNA-seq. We found that CD14 monocytes in T2D patients were in a pro-inflammatory state and intermediate monocytes expressed more MHC class II genes. In T2D patients, cytotoxic CD4 T cells, effector memory CD8 T cells, and γδ T cells have increased cytotoxicity and clonal expansion. B cells were characterized by increased differentiation into intermediate B cells, plasma cells, and isotype class switching with increased expression of soluble antibody genes. These results suggest that monocytes, T cells, and B cells could interact to induce chronic inflammation in T2D patients with pro-inflammatory characteristics.

overall_design: PBMCs from Type 2 diabietes patients were subjected to scRNA-seq, scBCR-seq and scTCR-seq with 10x Genomics.

first: Doeon

last: Gu

first: Jinyeong

last: Lim

first: Kyung

middle: Y

last: Han

first: In-Ho

last: Seo

first: Dong-Hyuk

last: Jung

first: Woong-Yang

last: Park


title: Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs [snRNA-seq]

overall_design: C3h/10t1/2 fibroblasts were engineered with 1) anti-GFP SynNotch activating myoD and miRFP AND anti-mCherry SynNotch activating ETV2 and BFP. These cells were then cultured/activated on patterned ibidi wells with No ligand, GFP rows, mcherry rows, or both GFP and mCherry interdigiting rows and cultured for 3 days before single nuclei RNA extraction and sequencing.


title: Mitochondrial respiration in microglia is essential for response to demyelinating injury but not proliferation

status: Public on Jun 10 2024

city: Chicago

first: Rogan

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

summary: Microglia are necessary for CNS function during development and play roles in aging, Alzheimer’s Disease (AD) and the response to demyelinating injury. Mitochondrial respiratory chain (RC) is necessary for conventional T cell proliferation6 and macrophage-dependent immune responses. However, whether mitochondrial RC is essential for microglia proliferation or function is not known. We conditionally deleted the mitochondrial complex III subunit Rieske Iron-Sulfur Protein (RISP) in the microglia of adult mice to assess the requirement of microglial RC for survival, proliferation, and adult CNS function in vivo. Surprisingly, mitochondrial RC function was not required for survival or proliferation of microglia in vivo. RNA-seq analysis showed that loss of RC function in microglia caused changes in gene expression distinct from aged or disease-associated microglia (DAM). Microglia-specific loss of mitochondrial RC function is not sufficient to induce cognitive decline. Amyloid-β plaque coverage decreased and microglial interaction with Amyloid-β plaques increased in the hippocampus of 5xFAD mice with mitochondrial RC-deficient microglia. Microglia-specific loss of mitochondrial RC function did impair remyelination following an acute, reversible demyelinating event. Thus, mitochondrial respiration in microglia is dispensable for proliferation but is essential to maintain a proper response to CNS demyelinating injury.

overall_design: For FACS of microglia for RNAseq and microglial enumeration, single cell suspension from whole brain were initially incubated in 1:50 Anti-mouse CD16/32 (biolegend 101302, clone 93) and, subsequently, stained with the following antibodies: 1:100 Anti-Mouse CD45.2-PacBlue (ebioscience 48-0454-82, clone 104) and 1:200 Anti-mouse CD11b(Mac-1)-APC (ebioscience, 50-0112-80, clone M1/70) in 200µL final volume of FACS Buffer. Viability was assessed with addition of DAPI 3 minutes before collection on flow cytometer (Fisher, D1306 0.1µg/mL final concentration). RNA quality and quantity were assessed using TapeStation 4200 High Sensitivity RNA tapes (Agilent), and RNA-seq libraries were prepared from 5-10ng of total RNA using the SMARTer Stranded Total RNA-seq Kit v2 (Takara Bio). For analysis of allele status, libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB E7370L). Library QC was then performed using TapeStation 4200 High Sensitivity DNA tapes (Agilent). Dual-indexed libraries were pooled and sequenced on a NextSeq 500 instrument (Illumina) for untreated RISP-/- and wild-type, age-matched animals, or a NextSeq2000 instrument for all other samples (Illumina) 75 or 100 cycles, respectively, single-end, to an average sequencing depth of 27.5 million reads per sample.

first: Stoolman

middle: S

last: Joshua

first: Grant

last: Rogan

first: Chandel

last: Navdeep


title: CD56-mediated activation of human natural killer cells is triggered by Aspergillus fumigatus galactosaminogalactan

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

overall_design:
Bulk RNA sequencing was performed to identify genes that are differentially regulated in NK cells upon exposure to periodate-treated versus untreated A. fumigatus germ tubes.
A. fumigatus germ tubes were treated with periodate in RPMI for 60 min, or were left untreated.

first: Linda

last: Heilig

first: Fariha

last: Natasha

first: Nora

last: Trinks

first: Vishukumar

last: Aimanianda

first: Sarah

last: Wong

first: Thierry

last: Fontaine

first: Ulrich

last: Terpitz

first: Lea

last: Strobel

first: François

last: Le Mauff

first: Donald

last: Sheppard

first: Oliver

last: Kurzai

first: Kerstin

last: Hünniger

first: Esther

last: Weiss

first: Mario

last: Vargas

first: P

middle: L

last: Howell

first: Gianni

last: Panagiotou

first: Sebastian

last: Wurster

first: Hermann

last: Einsele

first: Jürgen

last: Löffler


title: Maternal high fat diet induces circadian clock-independent endocrine alterations impacting metabolism of the offspring

status: Public on Jun 09 2024

city: St Lucia

first: Benjamin

last: Weger

state: QLD

address: 306 Carmody Road

department: IMB

country: Australia

institute: University of Queensland

summary: Maternal obesity has long-term effects on offspring metabolic health. Among the potential mechanisms, prior research has indicated potential disruptions in circadian rhythms and gut microbiota in the offspring. To challenge this hypothesis, we implemented a maternal high fat diet regimen before and during pregnancy, followed by a standard diet after birth. Our findings confirm that maternal obesity impacts offspring birth weight and glucose and lipid metabolisms. However, we found minimal impact on circadian rhythms and microbiota that are predominantly driven by the feeding/fasting cycle. Notably, maternal obesity altered rhythmic liver gene expression, affecting mitochondrial function and inflammatory response without disrupting the hepatic circadian clock. These changes could be explained by a masculinisation of liver gene expression similar to the changes observed in polycystic ovarian syndrome. Intriguingly, such alterations seem to provide the first-generation offspring with a degree of protection against obesity when exposed to a high fat diet.

overall_design: RNA-Seq from mouse liver mRNA of 4-week and 16-week offspring from maternal control diet mice and maternal high-fat diet mice

first: Lu

last: Ding

first: Jieying

last: Liu

first: Liyuan

last: Zhou

first: Yenkai

last: Lim

first: Dongmei

last: Wang

first: Ziyan

last: Xie

first: Jing

last: Ren

first: Jia

last: Zheng

first: Qian

last: Zhang

first: Miao

last: Yu

first: Meltem

first: Mark

last: Morrison

first: Xinhua

last: Xiao

first: Frédéric

last: Gachon


title: Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers

status: Public on Jun 06 2024

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary: Submerged cultivation using low-value agro-industrial side streams allows large-scale and efficient production of fungal mycelia, which has a high nutritional value. As the dietary properties of fungal mycelia in poultry are largely unknown, the present study aimed to investigate the effect of feeding a Pleurotus sapidus (PSA) mycelium as a feed supplement on growth performance, composition of the cecal microbiota and several physiological traits including gut integrity, nutrient digestibility, liver lipids, liver transcriptome and plasma metabolome in broilers. 72 male, 1-day-old Cobb 500 broilers were randomly assigned to three different groups and fed three different adequate diets containing either 0% (PSA-0), 2.5% (PSA-2.5) and 5% (PSA-5.0) P. sapidus mycelium in a three-phase feeding system for 35 days. Each group consisted of 6 cages (replicates) with 4 broilers/cage. Body weight gain, feed intake and feed:gain ratio and apparent ileal digestibility of crude protein, ether extract and amino acids were not different between groups. Metagenomic analysis of the cecal microbiota revealed no differences between groups, except that one α-diversity metric (Shannon index) and the abundance of two low-abundance bacterial taxa (Clostridia UCG 014, Eubacteriales) differed between groups (P < 0.05). Concentrations of total and individual short-chain fatty acids in the cecal digesta and concentrations of plasma lipopolysaccharide and mRNA levels of proinflammatory genes, tight-junction proteins, and mucins in the cecum mucosa did not differ between groups. None of the plasma metabolites analyzed using targeted-metabolomics differed across the groups. Hepatic transcript profiling revealed a total of 144 transcripts to be differentially expressed between group PSA-5.0 and group PSA-0 but none of these genes was regulated greater 2-fold. Considering either the lack of effects or the very weak effects of feeding the P. sapidus mycelium in the broilers it can be concluded that inclusion of a sustainably produced fungal mycelium in broiler diets at the expense of other feed components has no negative consequences on broilers´ performance and metabolism.

first: Lea

last: Schäfer

first: Klaus

last: Eder


title: Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs

first: Song

last: Li


title: Unraveling the molecular architecture of autoimmune thyroid diseases at spatial resolution

city: Madrid

first: Rebeca

last: Martinez

address: C/Diego de Leon 62

department: Endocrinology

institute: IIS la Princesa

summary: Autoimmune thyroid diseases (AITD) such as Graves' disease (GD) or Hashimoto's thyroiditis (HT) are organ-specific diseases related to complex interactions between distinct components of the thyroid ecosystem. We applied spatial transcriptomics (ST) to explore the molecular architecture and heterogeneity of different cells present in the thyroid tissue, including thyroid follicular cells (TFCs) and stromal cells such as fibroblasts and endothelial cells. We identified damaged antigen-presenting TFCs that had an upregulated CD74/MIF axis in thyroids from AITD patients. Furthermore, we discerned two main fibroblast subpopulations in the connective tissue including ADIRF+ myofibroblasts, mainly upregulated in GD, and inflammatory-associated fibroblasts (IAFs), mainly overexpressed in HT patients. We also demonstrated an increase of fenestrated PLVAP+ vessels in AITD, especially in GD. Our data unveil novel stromal and thyroid epithelial cell subpopulations that could play an essential role in the pathogenesis of AITD.

overall_design: We used thyroid tissue samples from AITD lesions and histologically normal parenchyma adjacent to other thyroid lesions from patients who underwent thyroidectomy at the Surgical Department of the Hospital Universitario la Princesa. Thyroid tissue samples were immediately snap-frozen in liquid nitrogen cooled in isopentane and transferred to a −80 °C freezer. RNA was isolated from 40 fresh-frozen thyroid tissues (21 controls, 11 HT and 8 GD samples). Total RNA was isolated using miRNeasy Mini Kit (Qiagen). The quality and quantity of RNA was assessed in a 2100 Bioanalyzer using a RNA 6000 Nano kit (Agilent Technologies). Eight samples with RIN>7 were selected for Spatial Transcriptomics using the Visium spatial Gene expression Kits from 10X Genomics. Briefly, the Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics) was used to optimize permeabilization conditions for thyroid tissue. Then, they were cryosectioned at 10μm onto 6.5 × 6.5 mm capture areas from Visium spatial slides and processed according to the manufacturer’s instructions (10x Genomics).

last: Martínez-Hernández

first: Nuria

last: Sánchez de la Blanca

first: Pablo

last: Sacristán-Gómez

first: Ana

last: Serrano-Somavilla

first: Miguel

last: Sampedro-Núñez

first: José

last: Muñoz De Nova

first: Fátima

last: Sánchez Cabo

first: Holger

last: Heyn

first: Mónica

last: Marazuela


title: Expression data of enterohemorrhagic E. coli (EHEC) fimbrial mutants

status: Public on Jun 07 2024

city: Charlottesville

first: Melissa

last: Kendall

state: VA

address: 1340 Jefferson Park Ave.

department: Microbiology

institute: University of Virginia

summary:
Fimbriae are important virulence traits that promote bacterial adhernece to surfaces. Here, we assessed whether fimbriae modulate gene expression using microarrays.
We used microarrays to compare gene expression in wild-type of fimbrial deletion strains of EHEC

overall_design: EHEC strains were grown planktonically in tissue culture medium, RNA was extracted, and Affymeetrix E. coli 2.0 arrays to assess global differences in gene expression.


title: Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair

status: Public on Jun 11 2024

city: St. Louis

first: Mayssa

last: Mokalled

state: MO

address: 4523 Clayton Ave, CB 8103

department: Developmental Biology

institute: Washington University in St. Louis

summary: Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, a transient population of injury-responsive neurons (iNeurons) show elevated plasticity between 1 and 3 weeks post-injury. We found iNeurons are injury-surviving neurons that acquire a neuroblast-like gene expression signature after injury. CRISPR/Cas9 mutagenesis showed iNeurons are required for functional recovery and employ vesicular trafficking as an essential mechanism that underlies neuronal plasticity. This study provides a comprehensive resource of the cells and mechanisms that direct spinal cord regeneration and establishes zebrafish as a model of plasticity-driven neural repair.

overall_design: we performed complete SC transections on adult zebrafish and dissected 3 mm sections of SC tissues surrounding the lesion site at 1, 3, and 6 weeks post-injury (wpi) for nuclear isolation. Corresponding tissue sections were collected from uninjured controls. SC tissues were pooled from 50 animals per time point, and 2 pools of independent biological replicates were analyzed for each time point. Our dataset spans key regenerative windows including early injury-induced signals at 1 wpi, neuronal and glial regeneration at 3 wpi, and cellular remodeling at late stages of regeneration at 6 wpi (Mokalled et al., 2016). Isolated nuclei were sequenced using 10x genomics platform (3’ v3.1 chemistry) and aligned to zebrafish genome GRCz11 with improved zebrafish transcriptome annotation (Lawson et al., 2020; Matson et al., 2018). Nuclei were subsequently filtered using the Decontx and DoubletFinder packages to exclude droplets that include doublet nuclei or a high proportion of ambient mRNA, respectively (McGinnis et al., 2019; Yang et al., 2020). A second round of filtering is performed by thresholding the covariates such as number of counts, genes and fraction of counts from mitochondrial genes per barcode. A total of 58,973 nuclei was obtained for downstream analysis using the Seurat package .

first: Vishnu

last: Muraleedharan Saraswathy

first: Lili

last: Zhou


title: Time-course analysis and transcriptomic identification of a groupⅢ ERF CmTINY2 involved in waterlogging tolerance in chrysanthemums

city: Hangzhou

first: xueting

last: gu

address: yuhangtang road 866

institute: Zhejiang university

summary: ‘Hangju’ is a variety of Chrysanthemum morifolium Ramat with both aesthetic and medicinal value, cultivated as traditional Chinese medicine for four centuries. The cultivation of ‘Hangju’ faces a significant challenge due to waterlogging stress, resulting in a considerable decrease in crop yield. Nevertheless, there is a scarcity of studies exploring the underlying mechanisms of waterlogging tolerance in ‘Hangju’. This investigation focused on comparing the characteristics of the waterlogging-tolerant variety EWT and the waterlogging-sensitive variety CK of ‘Hangju’. The study revealed that EWT exhibited a more advanced aeration tissue structure and demonstrated rapid development of adventitious roots following waterlogging. Through a time-course transcriptome analysis, it was observed that EWT could swiftly adjust the expression of genes involved in energy metabolism signaling pathways to acclimate to the waterlogged environment. WGCNA analysis identified INTEGRASE-TYPE DNA-BINDING PROTEIN (CmTINY2) as a key factor in regulating waterlogging tolerance in EWT. CmTINY2, a transcription factor belonging to the ethylene responsive factor (ERF) subfamily III, operated within the nucleus and activated downstream gene expression. Its role in enhancing waterlogging tolerance might be linked to the control of stomatal aperture. In summary, this research has elucidated that the waterlogging tolerance exhibited by EWT chrysanthemum is a result of a combination of morphological structure and molecular regulatory mechanisms. Furthermore, the discovery of a waterlogging-tolerant gene from the ERF subfamily III has broadened our understanding of the role of ERF genes in waterlogging signaling pathways.

overall_design: Root samples of EWT and CK were collected immediately at 0, 3, 12, 24 h after waterlogging and 24 h after waterlogging with 3 h of reoxygenation (24_3h). Each sample contained four biological replicates. Total RNA was extracted using the Tiangen RNA Extraction Kit with the RNase-Free DNase Set (Tiangen Biotech, Beijing, China), according to the manufacturer’s instructions. Libraries for mRNA-seq were constructed and sequenced by Novogene (Beijing). Briefly, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). mRNAs were isolated from total RNAs by poly(A) selection, fragmented into short fragments, and converted to cDNAs. cDNAs were ligated to adapters and the suitable fragments were selected for PCR amplification as templates. All the RNA-seq libraries were pair-end sequenced on an Illumina Novaseq platform.

first: Xueting

last: Gu

first: Xinyi

last: Liu

first: Haodong

last: Sha

first: Bizeng

last: Mao


title: A niche-derived non-ribosomal peptide triggers planarian sexual development.

city: Madison

first: Melanie

last: Issigonis

state: WI

address: 330 N. Orchard Street, Newmark Lab

institute: Morgridge Institute for Research

summary: Germ cells are regulated by local microenvironments (niches), which secrete instructive cues. Conserved developmental signaling molecules act as niche-derived regulatory factors, yet other types of niche signals remain to be identified. Single-cell RNA-sequencing of sexual planarians revealed niche cells expressing a non-ribosomal peptide synthetase (nrps). Inhibiting nrps led to loss of female reproductive organs and testis hyperplasia. Mass spectrometry detected the dipeptide β-alanyl-tryptamine (BATT), which is associated with reproductive system development and requires nrps and a monoamine-transmitter-synthetic enzyme (AADC) for its production. Exogenous BATT rescued the reproductive defects after nrps or aadc inhibition, restoring fertility. Thus, a non-ribosomal, monoamine-derived peptide provided by niche cells acts as a critical signal to trigger planarian reproductive development. These findings reveal an unexpected function for monoamines in niche-germ cell signaling. Furthermore, given the recently reported role for BATT as a male-derived factor required for reproductive maturation of female schistosomes, these results have important implications for the evolution of parasitic flatworms and suggest a potential role for non-ribosomal peptides as signaling molecules in other organisms.

overall_design: Single cells isolated from tissues enriched for reproductive organs from sexually mature S. mediterranea.

first: Katherine

last: Browder

first: Phillip

last: Newmark


title: A combination treatment based on drug repurposing demonstrates mutation agnostic efficacy in pre-clinical retinopathy models. [RNA-seq: Rd10]

city: Koupio

first: Henri

last: Leinonen

address: Yliopistonranta 1

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

summary: To determine the gene expression changes in the retina of two separate groups (experimental groups: vehicle and TMB) of vivarium-reared 5-week-old Rd10 mice (strong disease), as well as one group of 4-week-old dark-reared Rd10 mice (mild disease) and one group of wild-type mice (healthy). TMB group received dietary administration of tamsulosin, metoprolol and bromocriptine drug cocktail between 4-5-weeks of age, for 9 days prior to sample collection. All other groups received base/vehicle diet.

overall_design: Experimental Rd10 mice were dark reared between P0-P28. Dietary tamsulosin, metoprolol and bromocriptine (TMB) administration was started at P28. Another group remained on a base/vehicle diet. One day later at P29, the vehicle- and TBM-treated Rd10 mice were transferred to normal vivarium conditions which induced faster progressing retinal degeneration. At P37, the mice were euthanized under ketamine & xylazine anesthesia, and the eyes were enucleated, retinas dissected, and RNA was extracted from the one retina per mouse. One group of C57BL/6J mice (healthy control) experienced the same housing conditions and were euthanized for sample collection at P37 under ketamine & xylazine anesthesia. One group of Rd10 mice was reared under darkness throughout their life and euthanized without experience to light at P28 under ketamine & xylazine anesthesia. The dark reared Rd10 mice carry the disease, but the phenotype is milder due to protective effect of dark rearing in this retinal degeneration model.

first: Umair

last: Seemab


title: A combination treatment based on drug repurposing demonstrates mutation agnostic efficacy in pre-clinical retinopathy models. [RNA-seq: RPE65-KO]

summary: To determine the gene expression changes in the retina of two separate groups (experimental groups: vehicle and TMB) of Rpe65-/- mice at P64, as well as one group of age-matched wild-type mice (healthy). Mice in the TMB group received dietary administration of tamsulosin, metoprolol and bromocriptine drug cocktail between P22-P64. All other mice received base/vehicle diet.

overall_design: Mice were housed in normal laboratory conditions with ad libitum feeding. Dietary tamsulosin, metoprolol and bromocriptine (TMB) administration were started in Rpe65-/- mice (n=5) at P22. Another group of Rpe65-/- mice (n=4) remained on a base diet (vehicle). At P64, the mice were euthanized under ketamine & xylazine anesthesia, and the eyes were enucleated, retinas dissected, and RNA was extracted from the one retina per mouse. One group of 2-month-old C57BL/6J mice (healthy control, n=3) experienced the same housing conditions and were euthanized for sample collection under ketamine & xylazine anesthesia.


title: Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma suppress CD8+ T cell activation and inhibit response to immune checkpoint therapy [hPDAC]

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

summary: Senescent cells appear within tumors and their stroma, exerting complex pro- and anti-tumorigenic functions. The effects of senescent tumor stromal cells are mostly unknown, as is the potential for targeting such senescent cells for improved therapy. Here we uncover the presence of a senescent subset of cancer-associated fibroblasts (CAFs) within pancreatic adenocarcinomas and in premalignant pancreatic lesions. Senescent CAFs show reduced proliferation, and are often associated with the inflammatory CAF (iCAF) subtype. We isolated and characterized senescent CAFs from mouse models and directly from human patients, and found that they express elevated levels of immune-regulatory genes. In a panel of mouse PDACs, high levels of senescent CAFs correlated with low T cell infiltration. Removal of senescent CAFs from PDAC stroma, either genetically or through treatment with the senolytic drug ABT-199 (venetoclax), a Bcl2 inhibitor, increased rates of activated cytotoxic CD8+ T cells within tumors. Conversely, activation of CAF senescence within PDACs led to reduced CD8+ T cell numbers. Media from senescent PDAC CAFs inhibited T cell proliferation and activation. We show that implanted PDAC tumors show improved response to immune checkpoint therapy when co-treated with the senolytic drug. These results reveal that the presence of senescent CAFs in PDAC stroma acts to repress cytotoxic T cell activity, and suggest that their targeted elimination through senolytic treatment may enhance immunotherapy.

overall_design: Senescent and non-senescent CAFs were sorted from human PDAC tumors, and their transcriptome was analyzed.

first: Benjamin

last: Assouline

first: Jonathan

last: Monin


title: Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma suppress CD8+ T cell activation and inhibit response to immune checkpoint therapy [Kras_p53]

overall_design: Senescent and non-senescent CAFs were sorted from mouse PDAC models, and their transcriptome was analyzed.


title: PD-1 expression contributes to the functional impairment of NK cells in patients with B-CLL

status: Public on Jun 05 2024

city: Birmingham

first: Paul

last: Moss

address: University of Birmingham

department: Imunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

summary: Chronic lymphocytic leukaemia (B-CLL) is associated with immune suppression and functional impairment of NK cells, due partly to the reduced expression of activating receptors. We studied the profile of inhibitory checkpoint receptor expression on NK cells from patients with B-CLL. Single, dual and triple expression of the checkpoint receptors PD-1, CTLA-4, LAG-3 and CD96 was increased in patients compared to age-matched healthy controls. PD-1pos cells were present within the late differentiated CD56dim NK pool and showed strong downregulation of all activatory receptors whilst transcriptional profiles revealed a profile of strong receptor signalling. PD-1pos NK cells demonstrated impaired cytokine production and degranulation following target engagement and transfection of PD-1 into NK cell lines directed suppressed cytotoxic function. Importantly, blockade of PD-1:PD-L1 engagement acted to partially reverse these functional defects. These results reveal expression of inhibitory checkpoint receptors to be a new mechanism of NK cell dysfunction in patients with cancer and indicate a potential therapeutic role for single or combinatorial checkpoint blockade to boost immune function in patients with B-CLL.

overall_design: Single Cell RNA profiles of NK cells, positve for PD-1 and Negative for PD-1

first: Mustafa

last: Farhat

first: Wayne

last: Croft

first: Helen

middle: M

last: Parry

first: Kriti

last: Verma

first: Francesca

last: Kinsella

first: David

last: Bone

first: Tina

last: McSkeane

first: Shankara

last: Paneesha

first: Guy

last: Pratt

first: Jianmin

last: Zuo


title: Antibody Fc-receptor common gamma chain FcεR1γ stabilizes cell surface receptors in group 3 innate lymphoid cells and promotes anti-infection immunity

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

summary: Group 3 innate lymphoid cells (ILC3s) are crucial for maintaining mucosal homeostasis and regulating inflammatory diseases, but the molecular mechanisms governing their phenotype and function are not fully understood. Here, we showed that ILC3s highly expressed Fcer1g gene, which encodes the antibody Fc-receptor common gamma chain (FcεR1γ). Genetic perturbation of FcεR1γ led to the absence of critical cell membrane receptors NKp46 and CD16 in ILC3s. Alanine scanning mutagenesis identified two residues in FcεR1γ that stabilize its binding partners. FcεR1γ expression in ILC3s was essential for effective protective immunity against bacterial and fungal infections. Mechanistically, FcεR1γ influenced the transcriptional state and proinflammatory cytokine production of ILC3s, relying on the CD16-FcεR1γ signaling pathway. Overall, our findings highlight the significance of FcεR1γ as an adaptor protein that stabilizes cell membrane partners in ILC3s and promotes anti-infection immunity.

overall_design: For bulk RNA-seq experiments, CCR6+ ILC3s were flow-sorted from the lamina propria (LPs) of Rorc-cre+Fcer1g f/f (CKO) mice and  Fcer1g f/f (control) mice on day 5 after the intravenously (i.v.) injection of Candida albicans (C.A.) or vehicle (PBS). Freshly sorted CCR6+ ILC3s from each group were then lysed for library construction using SMART-Seq2 prptocol. For the single cell (sc)RNA-seq experiment, immune cells were isolated from the small intestinal lamina propria (siLPs) and colonic lamina propria (cLPs) of control and CKO mice at steady state, labeled with hashtag and fluorescent antibodies prior to fluorescence-activated cell sorting (FACS). Then the flow-sorted cells were pooled for gene expression library and Feature Barcode library construction via using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10×Genomics).

first: Chao

last: Huang

first: Shaorui

last: Liu


title: Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma suppress CD8+ T cell activation and inhibit response to immune checkpoint therapy [Cultured_Human_Mouse]

first: Ittai

last: Ben-Porath

overall_design: Senescence was induced in cultured primary mouse and human PDAC CAFs using a CRE-ER inducible system, and transcriptomes were analyzed.


title: Identification of Evolutionarily Conserved VSX2 Enhancers in Retinal Development

status: Public on Jun 04 2024

city: Memphis

first: Asha Jacob

last: Jannu

state: TN

address: Inspiration4 Advanced Research Center

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

summary: Super-enhancers (SEs) are expansive regions of genomic DNA that regulate the expression of genes involved in cell identity and cell fate. Recently, we found that distinct modules within a murine SE regulate gene expression of transcription factor Vsx2 in a developmental stage- and cell-type specific manner. In the present study, we examine the ability of these modules to drive retinal development between species. By inserting the human build of one Vsx2 SE module into a mouse with microphthalmia, eye size was rescued. To understand the implications of these SE modules in a model of human development, we generated human retinal organoids. Deleting one module results in small organoids, recapitulating the small-eyed phenotype of mice with microphthalmia, while deletion of the other module leads to a complete loss of ON cone bipolar neurons. This prototypical SE serves as a model for uncoupling developmental stage- and cell-type specific effects of neurogenic transcription factors with complex expression patterns. Moreover, by elucidating the gene regulatory mechanisms, we can begin to examine how dysregulation of these mechanisms contributes to phenotypic diversity and disease.

overall_design: Retinal organoids derived from hESC line H9 VSX2-GFP/CRX-TdTomato were generated using an established protocol from the Laboratory of Dr David Gamm. Each organoid was placed in one well of a 24-well plate (1 organoid/ 1 well) with 1mL of 3D Retinal Differentiation Media containing 1:1000 EC23 (3D RDM) and incubated at 37C. Media changes occurred weekly and Mycoplasma testing occurred every 2 months. After 100 days, 3D RDM media changes did not include EC23.

first: Victoria

last: Honnel

first: Jackie

last: Norrie

first: Asha

last: Jacob Jannu

first: Cody

last: Ramirez

first: Michael

last: Dyer


title: A combination treatment based on drug repurposing demonstrates mutation agnostic efficacy in pre-clinical retinopathy models.

first: Henri

last: Leinonen

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

overall_design: Refer to individual Series


title: Adiponectin pathway activation dampens inflammation and enhances alveolar macrophage fungal killing via LC3-associated phagocytosis

city: Terre Haute

first: Steven

last: Templeton

state: Indiana

address: 620 Chestnut St HH135 HH135

institute: Indiana University School of Medicine - Terre Haute

summary: Although innate immunity is critical for antifungal host defense against the human opportunistic fungal pathogen Aspergillus fumigatus, potentially damaging inflammation must be controlled. Adiponectin (APN) is an anti-inflammatory adipokine, and we observed 100% mortality and increased fungal burden and inflammation in neutropenic mice with invasive aspergillosis (IA) that lack APN or the APN receptors AdipoR1 or AdipoR2. Alveolar macrophages (AMs), early immune sentinels that detect and respond to lung infection, express both receptors, and APN-/- AMs exhibited an inflammatory/M1 phenotype that was associated with decreased fungal killing and decreased activation of LC3-associated phagocytosis (LAP). Furthermore, AM treatment with the AdipoR agonist AdipoRon partially rescued deficient killing in APN-/- AMs that was dependent on both receptors. Our study identifies a novel role for APN in LC3-mediated killing of A.fumigatus.

overall_design: Alveolar macrophages were isolated from adiponectin-deficient mice, cultured for ten days, treated with 20um AdipoRon or vehicle (containg DMSO) for 24 hours, then infected with swollen/fixed A. fumigatus for 12 hours at 1:1 ratio, or left uninfected. Cells were harvested and RNA isolated for bulk RNAseq.

first: Sri

last: Goli


title: Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity [Xenium]

city: Toronto

first: Amy

last: Wong

state: Ontario

address: 686 Bay Street, Toronto

department: Developmental & Stem Cell Biology

institute: The Hospital for Sick Children

summary: While animal models have provided key insights into conserved mechanisms of how the lung forms during development, human-specific developmental mechanisms are not always captured. To fully appreciate how developmental defects and disease states alter the function of the lungs, studies in human lung models are important. Here, we sequenced >150,000 single single-cells from 19 healthy human fetal lung tissues from gestational weeks 10-19 and identified at least 58 unique cell types/states contributing to the developing lung. We captured novel dynamic developmental trajectories from various progenitor cells that give rise to ciliated, pulmonary neuroendocrine cells, and other specialized cell types. We also identified four CFTR-expressing progenitor cell types and pinpointed the temporal emergence and spatial localization of these cell types. These developmental dynamics reveal broader epithelial cell plasticity and novel lineage hierarchies that were not previously reported. Combined with spatial transcriptomics, we identified both cell autonomous and non-cell autonomous signalling pathways that may dictate the temporal and spatial emergence of cell lineages. Finally, we showed that human pluripotent stem cell (hPSC)-derived fetal lung models capture similar cell lineage trajectories specifically through progenitor cells that express abundant levels of the CFTR gene. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from hPSC differentiations to similar developmental window.

overall_design: Two archived FFPE fetal lung tissues (GW 15 and 18) were freshly sectioned and analyzed through 10X Xenium.

first: Henry

last: Quach

first: Spencer

last: Farrell

first: Ming

last: Wu

first: Kayshani

last: Kanagarajah

first: Joseph

middle: W

last: Leung

first: Xiaoqiao

first: Prajkta

last: Kallurkar

first: Andrei

last: Turinsky

first: Christine

last: Bear

first: Felix

last: Ratjen

first: Brian

last: Kalish

first: Sidhartha

last: Goyal

first: Theo

last: Moreas


title: Cell fate decision by a morphogen-transcription factor-chromatin modifier axis

city: zhejiang, china

first: jin

last: ming

address: 西湖大学

institute: Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.

summary:
Bulk RNA-sequences show the differences upon primitive endoderm cell related gene expression between JGES induced somatic cell reprogramming with or without BMP4 treatment, and between WT-SALL4 or delN12-SALL4 induced transdifferentiation from E13.5 mouse embryonic fibroblasts, primitive endoderm cell related gene are from our single cell RNA sequence data
So as to estimate the chromatin remodeling differences between SALL4-WT and SALL4-delN12 during single factor induced PrE formation, we performed Tn5 dependent ATAC-sequence to compare the open and close chromatin of the two group.
In order to identify the bingding differences of SALL4 and H3K27ac level  diversity between SALL4-WT and SALL4-delN12 on PrE related genes, wo performed CUTandTAG experiments.
Single cell analysis provides clarity unattainable with bulk approaches. Here we apply single cell RNA-seq to a newly established mouse somatic cell reprogramming system with or without BMP4 treatment at Day 7, this reprogramming system are induced by four transcriptional factors Jdp2-Glis1-Esrrb-Sall4 or JGES and cultured in iCD3. We first show that cells could be clustered into four group, primitive endoderm cell like cells, pluripotent cells, endothelial cells, and intermediate state cells which are hard to be clarified, after BMP4 treatment, a placenta-like state arise, the percentage of endothelial cells and primitive endoderm cell like cells increase and pluripotent cells decrease sharply. Our results not only show the ability of JGES and BMP4 in different cell lineage induction but also provide a model to explore mechanisms of first and second cell lineage decision during early embryogenesis.

overall_design:
We analyzed the transcriptome expression of mixture cells generated during mouse somatic cell reprogramming and transdifferentiation
We analyzed the transcriptome expression of mixture cells generated during mouse somatic cell reprogramming with or without BMP4 treatment
ATAC-seq data shows the chromatin accessibility differences between SALL4-WT and SALL4-delN12 single factor indeuced PrE formation, four time points were checked, Day1, Day5, Day9 and Day11
CUT&Tag analysis was performed in PrE formation at day 6 to map SALL4 and H3K27ac  binding sites.

first: Jin

last: Ming

first: Chengchen

last: Zhao

first: Duanqing

last: Pei


title: Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma impair CD8+ T cell activation and responsiveness to immunotherapy in mice

first: Ittai

last: Ben-Porath


title: Differential expression between WT and AhRR fetal liver macrophages

city: Bonn

first: Joachim

last: Schultze

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: We analyzed the gene expression differences in RNA-seq data of murine WT and AhRR fetal liver macrophages. RNA of 6 samples isolated and cultured for 5 weeks in vitro using GM-CSF.

overall_design: Examination of differential gene expression in RNA-seq data of  WT and AhRR-deficient fetal liver macrophages

first: Fabian

last: Godorf

first: Laia

last: Reverte Salisa

first: Thomas

last: Ulas

first: Irmgard

last: Förster


title: Tumor cell intrinsic type I interferon signaling dictates CD47-SIRPα blockade immunotherapy via metabolic reprograming.

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences


title: Tumor cell intrinsic type I interferon signaling dictates CD47-SIRPα blockade immunotherapy via metabolic reprograming [dataset 2]

summary: Type I interferons (IFN-Is) have been well recognized for their roles in immune cells in tumor immunotherapy. However, their direct effects on tumor cells are less understood. Oxidative phosphorylation (OXPHOS) is typically latent in tumor cells. However, whether OXPHOS can be targeted for immunotherapy remains unclear. Here, we found that tumor cell responsiveness to IFN-Is is essential for CD47-SIRPα blockade immunotherapy. Interestingly, IFN-Is directly reprogram tumor cell metabolism by activating OXPHOS for ATP production via ISG15. ATP extracellular release is also enhanced by IFN-Is via autophagy. Tumor cells with a genetic deficiency in OXPHOS or autophagy were resistant to CD47-SIRPα blockade. ATP released upon CD47-SIRPα blockade primes the anti-tumor T cell response via ATP-P2X7 receptor-mediated dendritic cell activation. Further combination with inhibitors of ATP-degrading ectoenzymes, CD39 and CD73, showed synergistic anti-tumor effects. Together, these data reveal the unrecognized mechanisms of IFN-Is on tumor cell metabolic reprograming in tumor immunotherapy and provide novel strategies harnessing this pathway for enhanced efficacy of CD47-SIRPα blockade.

overall_design: MC38 cells were seeded into 6-well plates and inoculated with or without 1 µg/mL recombinant IFN-α. After 6, 24, and 48 h, the cells were harvested for the generation of RNA-seq. libraries.

first: Hang

last: Zhou

first: Wenjun

last: Wang

first: Jiyu

last: Ding


title: IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer

first: Sven

last: Wehner

address: Venusberg-Campus 1

department: Department of Surgery

institute: University Clinics Bonn

summary: To investigate the effect of transcriptomic changes in colorectal cancer, we performed 3' bulk mRNA sequencing of naive and AOM/DSS treated mice. Mice were subjected to the AOM/DSS mouse model for colorectal cancer or kept under naive conditions. Samples of the most distal 0.5 cm of the colon were taken on day 70 of the model and processed for 3' bulk mRNA sequencing.

overall_design: Comparative gene expression analysis of naive and AOM/DSS-treated mice.

first: Linda

last: Schneider


title: Nuclear actin assembly is needed for decidualization of human endometrial stromal cells

city: Ube

first: Yuichiro

last: Shirafuta

state: Yamaguchi

address: 1-1-1, minami-kogushi

country: Japan

institute: Yamaguchi university

summary: To know the role of nuclear F-actin in the change of mRNA expression during desidualization, we compared the mRNA expression profiles between cAMP-stimulation and cAMP-stimulation with the overexpression of R62D (actin mutant ActinR62D).

overall_design: hESC were overexpressed with mCherry (as a mock control) or R62D, and were treated with or without cAMP for 96 h. RNA extraction was performed by using NucleoSpin® RNA (TaKaRa) and were moved into 1×Reaction buffer from SMART-seq v4 Ultra Low Input RNA Kit (24888N, Takara). SMART-seq library preparation was performed using SMART-seq v4 Ultra Low Input RNA Kit and Nextera DNA Sample Preparation Kit (FC-131-1024, illumine, San Diego, CA) according to the vendor’s instruction. Paired-end sequencing (50 bp + 25 bp) was done by using the NextSeq platform (Illumina). Raw reads were first filtered to get rid of low quality reads using Trimmomatic). Reads of less than 20 bases and unpaired reads were also removed. Furthermore, removal of adaptor, polyA, polyT and polyG sequences were performed using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). For mapping of reads, trimmed reads were first aligned to the human genome hg19 using STAR aligner. Gene counts in triplicate were used to identify differentially expressed genes (DEGs, fulfilling the following criteria: padj<0.05) using DESeq2.

first: I

last: Tamura

first: K

last: Miyamoto


title: Pigment epithelium-derived factor (PEDF) on gene expression of mouse empbryonic fibroblasts (MEF)

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

institute: National Center for Geriatrics and Gerontology

summary: Exercise training has been reported to induce changes in cellular homeostasis in various tissues, but the exact mechanisms remain unclear. Our findings demonstrate that in a mouse model, muscle-derived PEDFs have the capacity to intricately regulate cellular function at distal sites after training. The aim of this study was to investigate the effects of PEDF on gene expression in cultured MEFs and to elucidate the complex mechanisms involved.

overall_design: To investigate the effects of PEDF on gene expression, wild-type MEF at passage 2 were treated or untreated with PEDF (100 ng/mL) for 24h, and RNA expression was analyzed by RNA-seq. Two independent experiments were conducted. In each experiment, MEFs were prepared from different embryos.

first: Hiromichi

last: Tsushima