title: Coordinated Regulation of Cortical Astrocyte Maturation by OLIG1 and OLIG2 through BMP7 Signaling Modulation

status: Public on Nov 30 2024

city: SHANGHAI

first: YU

last: TIAN

state: SHANGHAI

address: 131 DONGAN ROAD

country: China

institute: FUDAN UNIVERSITY

type: Expression profiling by high throughput sequencing

summary: Astrocyte maturation is crucial for brain function, yet the mechanisms regulating this process remain poorly understood. In this study, we identify the bHLH transcription factors Olig1 and Olig2 as essential coordinators of cortical astrocyte maturation. We demonstrate that Olig1 and Olig2 work synergistically to regulate cortical astrocyte maturation by modulating BMP7 expression. Genetic ablation of both Olig1 and Olig2 results in defective astrocyte morphology, including reduced process complexity, and an immature gene expression profile. Single-cell RNA sequencing reveals a shift towards a less mature astrocyte state, marked by elevated levels of HOPX and GFAP, resembling human astrocytes. Mechanistically, Olig1 and Olig2 bind directly to the Bmp7 enhancer, repressing its expression to promote astrocyte maturation. Overexpression of Bmp7 in vivo replicates the astrocyte defects seen in Olig1/2 double mutants, confirming the critical role of BMP7 signaling in this process. These findings provide new insights into the transcriptional and signaling pathways regulating astrocyte development and highlight Olig1 and Olig2 as key regulators of cortical astrocyte maturation, with potential implications for understanding glial dysfunction in neurological diseases.

overall_design: ScRNA-seq were performed on FACS sorted tdT+ cells from the P1 Olig2f/f;IS-reporter mice cortex which were electroporated of pCAG-Cre plasmid at E15.The cortex were immediately submerged in fresh ice-cold Hanks balanced salt solution and  was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit according to the manufacturer’s instructions.

first: Ziwu

last: Wang

first: Yu

last: Tian

first: Feihong

last: Yang

first: Jialin

last: Li

first: Wen

last: Zhang

first: Tongye

last: Fu

first: Wenhui

last: Zheng

first: Zhejun

last: Xu

first: Yan

last: You

first: Xiaosu

first: Dashi

last: Qi

first: Yunli

last: Xie

first: Zhengang

first: Zhuangzhi


title: Single cell RNA seq of mouse embryos from E7.0, E7.25 and E7.5

city: Westmead

first: V. Pragathi

last: Masamsetti

state: NSW

address: 214 Hawkesbury rd

department: Embryology Unit

country: Australia

institute: Children's Medical Research Institute

summary: During mouse gastrulation, the formation of germ layers proceeds concurrently with the transition pluripotency state and the allocation of the multipotent epiblast cells to the germ layer derivatives. Lineage analysis and fate-mapping studies have revealed that groups of cells in different regions of the epiblast and the primitive streak of the gastrulating embryo are allocated to separate progenitors of the ectoderm, mesoderm and endoderm lineages three germ layers with descendants of each progenitor contributing to specific types of germ layer derivatives. Spatiotemporal transcriptomic analysis of the epiblast cell population has inferred that besides the allocation of the epiblast cells to progenitors of germ layers, a population of putative mesendoderm progenitors may be present in the gastrulating embryos.

overall_design: Single cells were isolated from Mouse embryos at the gastrulation stages of E7.0, E7.25 and posterior region of E7.5 mouse embryo

first: V  Pragathi

first: Nazmus

last: Salehin

first: Hani Jieun

last: Kim

first: Nicole

last: Santucci

first: Megan

last: Weatherstone

first: Riley

last: McMahon

first: Lee

last: Marshal

first: Hilary

last: Knowles

first: Jane

last: Sun

first: Josh

middle: B

last: Studdert

first: Nader

last: Aryamanesh

first: Ran

first: Naihe

last: Jing

first: Pengyi

first: Pierre

last: Osteil

first: Patrick P L

last: Tam


title: Analysis of transcriptome and metabolome characteristics of blood in yaks at different reproductive stages

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: The reproductive physiology of yaks differs significantly from that of other cattle breeds due to late sexual maturity, low fecundity and short oestrus time. How to improve the reproductive efficiency of yaks has become the main research content and goal of yak reproduction technology. In this study, we collected blood samples from adult female yaks (4-8 years old) during different reproductive periods, including the period of anestrus (Y-A), estrus (Y-E) and pregnancy (Y-P), and investigated the changes of RNA expression and steroid hormone levels in yaks during different reproductive periods by using RNA-seq and target metabolomics, and screened for the genes and regulatory pathways that were differentially expressed. and related regulatory pathways. DEGs such as PDK4, ALAS2, GLP1R, SLC25A39, PGAP6, FOS, CD36, MMP9 and BCL-6 were identified to play key roles in ovarian function, follicular development, hormone homeostasis and energy metabolism. Functional annotation and enrichment analysis indicated that DEGs were involved in ovarian angiogenesis, hormone synthesis and follicular development. It was found that SLC25A39 may affect glucocorticoid homeostasis and physiological readiness by regulating energy metabolism during anestrus, MARCHF2 and DHEA may be closely related to reproductive hormone fluctuation and system activation during estrus, glucocorticoid down-regulation in pregnancy and maintenance of hormone homeostasis and regulation of immune tolerance by DHEA. The results of this study provide a theoretical basis for improving the reproductive performance of yaks and further analysing the reproductive characteristics of yaks.

overall_design: Comparative gene expression profile analysis of RNA-seq data of blood samples from adult female yaks ( 4-8 years old ) at different reproductive stages including anestrus ( Y-A ), estrus ( Y-E ) and pregnancy ( Y-P ).

first: Yandong

last: Kang

first: Jie

last: Pei

first: Xian

last: Guo


title: Molecular mechanism of IgE-mediated FcεRI activation

city: Hangzhou

first: Mengying

last: Chen

address: ShiLongShan

institute: Westlake University

summary: The high-affinity Fc receptor for IgE, mainly present on mast cells and basophils, plays a crucial role in the development of allergic diseases. Monomeric IgE binding to receptor regulates mast cell survival, differentiation, and maturation. However, the underlying molecular mechanism remains unclear. Here we demonstrate that, prior to IgE binding, IgE receptor mostly exists as a homo-dimer on human mast cell membrane. The structure of human IgE receptor confirms the dimeric organization.  Cholesterol-like molecules embedded within the transmembrane domain may stabilize the dimeric assembly. Upon IgE binding, the dimeric IgE receptor dissociates into two protomers, each binding to an IgE molecule. Importantly, this process elicits transcriptional activation of Egr1/3 and Ccl2 in rat basophils, which can be attenuated by inhibiting the IgE receptor dimer-to-monomer transition. Collectively, our study unveils the mechanism of antigen-independent, IgE-mediated receptor activation.

overall_design: To investigate the downstream events of IGE-mediated activation of rat basophils, we examined the effects of IgE treatment on RBL-2H3 cells by RNA-seq

first: Qiang

last: Su

first: Yigong

last: Shi


title: Macrophage-mimicking adipose-derived stem cells for atherosclerosis targeting and treatment through cell adhesion molecules VCAM-1 and ICAM-1

city: Shanghai

first: Zhaoxi

last: Peng

address: 639 Zhizaoju Rd

department: Vascular Surgery

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Background：Atherosclerosis is the major cause of cardiovascular disease. Endothelial injury is one of the initiating factors of atherosclerosis. Injured endothelial cells overexpress adhesion molecules such as vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1), facilitating the binding and accumulation of monocytes-macrophages into the vascular wall via the ligands. Adipose-derived stem cells (ADSCs) have been extensively researched for their anti-inflammatory properties and therapeutic potential in various diseases. Targeting atherosclerotic regions with ADSCs may offer a promising therapeutic strategy to alleviate local inflammation associated with atherosclerosis.Methods：The ligands of very late antigen-4 (VLA-4) and lymphocyte function-associated antigen-1 (LFA-1) were expressed in the ADSC to construct the Macrophage (Mφ)-mimicking ADSCs. Cell proliferation, adhesion, and migration assays were used to characterize the Mφ-mimicking ADSCs. An atherosclerosis model was established in ApoE-/- mice via partial carotid artery ligation. Mφ-mimicking ADSCs were administered through tail vein injection. Distribution of these cells was tracked by far-red fluorescent probe. Histological analyses, including H&E staining, Oil Red O staining, and immunofluorescence were conducted to assess the impact on plaque size, composition, and macrophage polarization.Results：Mφ-mimicking ADSCs were successfully constructed and characterized. These cells exhibited enhanced adhesion and migration capabilities. The culture medium from Mφ-mimicking ADSCs increased the proportion of M2 macrophages and decreased the lipid uptake capacity. In the atherosclerosis mouse model, fluorescently labeled Mφ-mimicking ADSCs specifically adhered to and accumulated in atherosclerotic regions, demonstrating targeted localization. Mφ-mimicking ADSC treatment resulted in a reduction in plaque size and a decrease in the number of M1 macrophages within the arterial wall.Conclusions：Mφ-mimicking ADSCs confirmed their preserved anti-inflammatory properties and enhanced adhesion and migration abilities. In vivo, Mφ-mimicking ADSCs exhibited targeted localization ability to regions of endothelial dysfunction in atherosclerosis and attenuate plaque progression. These findings suggest that Mφ-mimicking ADSCs may serve as a potential therapeutic strategy for alleviating atherosclerosis and reducing inflammation.

overall_design: To investigate the effects of VLA-4 and LFA-1 expression in ADSCs, we analyzed transcriptomic changes in ADSCs overexpressing both VLA-4 and LFA-1 compared to unmodified ADSCs.

first: Xing

last: Zhang

first: Zhijue

last: Xu

first: Xinwu

last: Lu


title: Gene expression changes in triple-negative breast cancer by glucose restriction and cariporide treatment

city: Seoul

first: So Won

last: Kim

address: 88, OLYMPIC-RO 43-GIL

department: Pharmacology

country: South Korea

institute: University of Ulsan College of Medicine

summary: The cells were treated with a combination of media containing 10 or 5 mM glucose and 0 or 25 μM cariporide for 48 hours. A total of four groups were established: NG (normal glucose), CAR (cariporide), LG (low glucose), and LGCAR (low glucose and cariporide).

overall_design: Media containing 10 or 5 mM glucose and 0 or 25 uM cariporide treatment were combined. A total of four groups were established: NG (normal glucose), CAR (cariporide), LG (low glucose), and LGCAR (low glucose and cariporide).


title: INDETERMINATE DOMAIN-DELLA protein interactions orchestrate gibberellin-mediated cell elongation in wheat and barley

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

summary: DELLA proteins are members of the GRAS-domain family of transcriptional regulators and modulate transcriptional activity through protein-protein interactions with at least 15 different classes of transcription factor. The plant hormone gibberellin (GA) regulates a range of growth and development responses including promoting cell elongation, by triggering the degradation of DELLA proteins. More than 70% of modern wheat (Triticum aestivum L.) varieties carry alleles encoding DELLA proteins that are resistant to GA-mediated degradation. These alleles result in constitutive growth repression in stem tissues and confer a semi-dwarf growth habit associated with improved lodging resistance. However, these alleles also have negative pleiotropic effects such as reduced nitrogen use efficiency and weak early vigour that restrict their utility in some environments. A detailed understanding of the mechanisms by which DELLA proteins regulate growth and development will be necessary to dissect these responses and develop targeted strategies to breed improved crop varieties. We identified the orthologous C2H2 Zinc-finger transcription factors INDETERMINATE DOMAIN 5 (IDD5) in wheat and SEMI-DWARF3 (SDW3) in barley (Hordeum vulgare) as positive regulators of stem and leaf expansion. Both IDD5 and SDW3 physically interact with DELLA proteins and are epistatic to these genes. We propose a mechanism by which IDD proteins integrate GA signals to modulate downstream gene transcriptional activity through a protein complex dual activation and repression activities. Changes in GA biosynthesis gene expression levels suggest that part of this response involves GA homeostasis. Plants carrying null mutations in IDD5 and SDW3 exhibit a GA-insensitive semi-dwarf growth habit comparable to the Rht-D1b ‘Green Revolution’ allele and have potential as novel dwarfing alleles in cereal breeding programmes.

overall_design: RNA-seq was conducted on Cadenza, idd5 and Rht-D1b genotypes. Seven days after sowing, half of the plants were treated with 100 µM GA3 and the other half with water. Eight hours after the treatment leaf sheath tissue between the grain and the top of the coleoptile was harvested and flash-frozen in liquid nitrogen. Four biological replicates for each genotype and treatment were used. The trimmed paired-end reads were mapped to wheat IWGSC RefSeq v2.1 genome assembly. The raw mapped reads were counted and converted to TPM's (transcripts per million). The raw data (.fastq) and TPM values for all expressed genes are included in this submission.

first: Peter

last: Hedden

last: Thomas


title: Genomic characterization of normal and aberrant human milk production [bulkRNA-seq]

city: San Francisco

first: Nadav

last: Ahituv

state: CA

department: Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics

country: USA

institute: University of California San Francisco

summary: Breastfeeding is vital for reducing morbidity and mortality, yet exclusive breastfeeding rates are low, with insufficient milk supply being a major weaning factor whose molecular causes remain largely unknown. In this study, we collected fresh milk samples from 30 lactating individuals, classified as low, normal, or high milk producers at multiple postpartum stages, and conducted extensive genomic and microbiome analysis. Using bulk RNA sequencing on human milk fat globules (MFG), milk cells, and breast tissue, we found that MFG-derived RNA closely resembles RNA from milk luminal cells. Furthermore, bulk and single-cell RNA-seq revealed changes in the transcriptome and cellular content linked to milk production. We identified specific genes and cell-type proportions differing in low and high milk production. Infant microbiome diversity was affected by feeding type, but not by maternal milk supply. This study provides a comprehensive human milk transcriptomic catalog, identifies genes associated with milk production, and highlights MFG as a useful biomarker for milk transcriptome analysis.

overall_design: Human milk samples from donors with low, normal, and high milk production were collected fresh and centrifuged at 800g for 20 minutes in 4°C to pellet the cells and separate the fat layer. Fat layer was removed using a sterile spoon and mixed with RLT lysis buffer for RNA extraction using the RNeasy kit (Qiagen) then sequenced with RNA-seq. For select samples, pelleted cells were lysed and sequenced as well.

first: Yarden

last: Golan

first: Sarah

middle: K

last: Nyquist

first: Zhe

last: Liu

first: Dena

last: Ennis

first: Jingjing

last: Zhao

first: Emily

last: Blair

first: Abdur

middle: R

last: Kahn

first: Mary

last: Prahl

first: Stephanie

middle: L

last: Gaw

first: Moran

last: Yassour

first: Barbara

middle: E

last: Engelhardt

first: Valerie

middle: J

last: Flaherman


title: Single cell RNA seq of micropatterns derived from Human ESC Micropatterns

first: V. Pragathi

last: Masamsetti

overall_design: Differentiation of the cells on micropatterned coverslips was a protocol adapted from Warmflash et al. 2014 (Warmflash, Sorre et al. 2014).  HES3 Mixl1:GFP cells were passaged as single cells with StemPro Accutase Cell Dissociation Reagent (ThermoFisher Scientific) and seeded on micropatterned coverslips at a density of 2.5x105 cells/cm2 with 10μM Y-27632 dihydrochloride Rock inhibitor (TOCRIS) in mTeSR Plus (StemCell Technologies) into a total volume of  0.5 mL per well of a 24-well plate. Cells were incubated at 37 °C with 5% CO2. After 24 hours, micropatterns were incubated with either 50 ng/mL recombinant human BMP-4 (R&D Systems), 6µM CHIR99021 (StemCell Technologies) alone or 3 µM CHIR99021 and 100 ng/ml recombinant h/m/rActivin A (R&D Systems) in mTeSR Plus and incubated for a further 48 hours at 37 °C with 5% CO2.  The micropatterned cells were lifted off the gelled coverslips by first washing with PBS to remove debris, followed by incubating in PBS at 37°C for 5 min and then by vigorous tapping of the plate. Whole micropatterned cells floating in PBS were visualized under a microscope and approximately 10 micropatterns for each treatment were picked up with a 200µl-capacity pipette tip. Cells were dissociated with StemPro Accutase Cell Dissociation Reagent (ThermoFisher Scientific) at 37°C for 5 min. Cells were assessed for viability and concentration, before loading into a 10X Chromium Chip G (10X Genomics) for an output of 10,000 cells using single cell droplet capture performed on the Chromium Controller (10X Genomics).

first: V  Pragathi

first: Nazmus

last: Salehin

first: Hani Jieun

last: Kim

first: Nicole

last: Santucci

first: Megan

last: Weatherstone

first: Riley

last: McMahon

first: Lee

last: Marshal

first: Hilary

last: Knowles

first: Jane

last: Sun

first: Josh

last: Studdert

first: Nader

last: Aryamanesh

first: Ran

last: Wang

first: Naihe

last: Jing

first: Pengyi

last: Yang

first: Pierre

last: Osteil

first: Patrick P L

last: Tam


title: Genomic characterization of normal and aberrant human milk production [scRNA-seq]

first: Nadav

last: Ahituv

overall_design: Cells from human milk donors with low, normal, and high milk production were isolated by centrifugation at 800g for 20 min, washed, then cryopreserved before scRNA-sequencing with Chromium Next GEM Single Cell 3' Kit v3.1.

first: Yarden

last: Golan

first: Sarah

last: Nyquist

first: Zhe

last: Liu

first: Dena

last: Ennis

first: Jingjing

last: Zhao

first: Emily

last: Blair

first: Abdur

last: Kahn

first: Mary

last: Prahl

first: Stephanie

last: Gaw

first: Moran

last: Yassour

first: Barbara

last: Engelhardt

first: Valerie

last: Flaherman


title: Colonization of tomato seedlings by Fusarium incarnatum strain K23 establishes a different host response to salt stress

city: Bengaluru

first: Nataraja

last: Karaba

state: Karnataka

address: GKVK

department: Plant Physiology

country: India

institute: University of Agricultural Sciences, GKVK,

summary: The Fusarium incarnatum strain K23, originally isolated from a habit-adapted wild plant Thapsia species, colonized the roots and shoots of tomato seedlings and protected them against salt stress. Comparison of expression and metabolite profile changes uncovered that the fungus completely reprogramed the tomato response to salt stress. Barely any overlap was observed among the genes and metabolites which are regulated by salt stress in uncolonized and colonized tomato seedlings. In colonized seedlings exposed to salt stress, less stress- related genes are activated than in un-colonized seedlings. Furthermore, K23 produced gibberellin and gibberellin-responsive genes were detected in all RNA samples. Our analysis demonstrates that K23 colonisation completely alters the salt-responsive gene and metabolite profiles in tomato seedlings.

overall_design: To investigate the effect of Fusarium incarnatum strain K23 fungus on tomato seedlings under salt stress conditions, RNA sequencing was conducted. There were four conditions: (1) Fungus with salt, (2) Fungus without salt, (3) Control with salt, and (4) Control without salt. Each condition had three replicates.

first: Priya

middle: Y

last: Reddy

first: N

last: Pallavi

first: Geetha

last: Govind

first: Michael

last: Reichelt

first: Clabe

last: Wekesa

first: Uma

last: Shaanker

first: Ralf

last: Oelmüller

first: Karaba

middle: N

last: Nataraja


title: BDNF augmentation reverses cranial radiation therapy-induced cognitive decline and neurodegenerative consequences

city: Irvine

first: Mingyu

last: Du

address: 419 Physical Sciences Quad

institute: UC Irvine

summary: Spatial transcriptomic profiling was conducted on hippocampal brain sections from mice across four experimental combinations: cranial radiation therapy(RT) with Riluzole (label as Ir-Rz), cranial radiation therapy with vehicle (label as Ir-Veh), control with Riluzole (label as Ctl-Rz), and control with vehicle (label as Ctl-Veh).

overall_design: We used a commercial spatial transcriptomics Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH) platform (MERSCOPE, Vizgen, Cambridge, MA), and cell boundary segmentation was completed with custom Cellpose pipeline.


title: Single cell RNA seq of mouse epiblast stem cells and embryoid bodies

first: V. Pragathi

last: Masamsetti

overall_design: Single cells were isolated from Mouse epiblast stem cell  and  Day 2 of embryoid bodies  derived from mouse epiblast stem cells.

first: V  Pragathi

first: Nazmus

last: Salehin

first: Hani Jieun

last: Kim

first: Nicole

last: Santucci

first: Megan

last: Weatherstone

first: Riley

last: McMahon

first: Lee

last: Marshal

first: Hilary

last: Knowles

first: Jane

last: Sun

first: Josh

last: Studdert

first: Nader

last: Aryamanesh

first: Ran

last: Wang

first: Naihe

last: Jing

first: Pengyi

last: Yang

first: Pierre

last: Osteil

first: Patrick P L

last: Tam


title: Spatiotemporal single-cell RNA sequencing reveals that CD4+T subpopulation with high metabolic flux plays pivotal roles under in hyperthermia treatment warts

city: Shenyang

first: Xueli

last: Niu

address: No.77 Puhe Road, Shenyang North New Area

institute: China Medical University

summary: Cutaneous wart, regarded as a benign tumor, is a proliferative disease caused by human papillomavirus (HPV) infection. Local hyperthermia at 44°C can clear multiple HPV-infected skin lesions (warts) by targeting a single lesion, which suggested that the clearance of HPV was related to the activation of T cells immunity. To identify potential inflence on T cells  for anti-HPV immunity after in response to hyperthermia treatment, single-cell RNA sequencing (scRNA-seq) was performed on CA tissue samples (A type of viral warts).

overall_design: Sample collection:Condyloma acuminatum (CA) tissues were obtained from two patients requiring surgical treatment for CA in the outpatient clinic of the Department of Dermatology. No patient received treatment for the lesions prior to the surgery, including drug treatment, freezing or electrocautery and photodynamic therapy, to avoid confounding.  Each patient's sample was split in two and half was treated with a 37℃ water bath for 30 minutes to serve as a control group. The other half were treated with a 44℃ water bath for 30 minutes as the hyperthermia treatment group.

first: Zhe

last: Long

first: Tao

last: Zhang

first: Ruiqun

last: Qi


title: Bulk RNA seq of mouse epiblast stem cells with Mixl1 differential timing expression

first: V. Pragathi

last: Masamsetti

overall_design: We converted  ESCs to EpiSCs (Mixl1DOX) in vitro, in which induction by DOX enhanced the expression of Mixl1 .   Mixl1DOX EpiSC expressed FLAG-Mixl1 transcript in response to Doxycycline (Dox) treatment, and generated FLAG-MIXL1 protein (30KDa) in embryoid bodies Embryoid bodies (EB) were collected on respective days aftertreating with /without  Doxycycline. Doxycycline induction, where appropriate, was achieved by adding 1 μg/mL Doxycycline (Sigma) to the culture.

first: V  Pragathi

first: Nazmus

last: Salehin

first: Hani Jieun

last: Kim

first: Nicole

last: Santucci


title: NAT10-ac4C axis promote renal fibrosis

city: Guangzhou

first: Ning

address: 600 Tianhe road

institute: Sun Yat-sen University

summary: RNA modification play vital roles in renal fibrosis. However, whether ac4C modification functions in renal fibrogenesis remains unknown. Here, we found that NAT10-ac4C axis plays pro—fibrotic role in kidney. ac4C RIP sequencing demonstrated NAT10-ac4C axis functions via regulating multiple master genes of exosome secretion in tubular epithelial cells. In summary, targeting NAT10-ac4C axis is a promising strategy for renal fibrosis.

overall_design: Wild-type HK-2 cells and NAT10 KD HK-2 cells were used for ac4C-RIP-seq.

first: Tong

last: Zheng

first: Yuqing

last: Tan

first: Ruojiao


title: Synthetic biomolecular condensates enhance translation from a target mRNA in living cells

city: Durham

first: Daniel

middle: Mark

last: Shapiro

state: NC

address: 101 Science Dr

institute: PhD Candidate at Chilkoti Lab at Duke University

summary: Biomolecular condensates composed of proteins and RNA are one approach by which cells regulate post-transcriptional gene expression. Their formation typically involves the phase separation of intrinsically disordered proteins with a target mRNA, sequestering the mRNA into a liquid condensate. This sequestration regulates gene expression by modulating translation or facilitating RNA processing. Here, we engineer synthetic condensates using a fusion of an RNA-binding protein, the human Pumilio2 homology domain, and a synthetic intrinsically disordered protein, an elastin-like polypeptide, that can bind and sequester a target mRNA transcript. In protocells, sequestration of a target mRNA largely limits its translation. Conversely, in E. Coli, sequestration of the same target mRNA increases its translation. We characterize the Pum2-ELP condensate system using microscopy, biophysical and biochemical assays, and RNA-seq. This approach enables modulation of cell function via the formation of synthetic biomolecular condensates that upregulate the expression of a target protein.

overall_design: We expressed synthetic biomolecular condensates containing the Pum2-ELP-GFP protein and mCherry mRNA with and without the Pum2 recognition sequence (PRS) in E. coli cells. We isolated the condensates and compared the RNA  identified in condensates and in cell lysate between cells expressing Pum2-ELP-GFP (PEG) and mCherry (M) or mCherry-PRS (MP).

first: Shapiro

last: Daniel

first: Deshpande

last: Sonal

first: Eghtesadi

last: Seyed Ali

first: Zhong

last: Miranda

first: Mendes Fontes

last: Cassio

first: Fiflis

last: David

first: Rohm

last: Dahlia

first: Min

last: Junseon

first: Kaur

last: Taranpreet

first: Peng

last: Joanna

first: Ney

last: Max

first: Su

last: Jonathan

first: Dai

last: Yifan

first: Asokan

last: Aravind

first: Gersbach

last: Charles

first: Chilkoti

last: Ashutosh


title: Restoration of PKM1 improves functional maturation of stem-cell derived-b by regulating PEP metabolism

city: Guanggzhou

first: Haopeng

last: Lin

state: Guangdong Province

address: No. 9 XingDaoHuanBei Road

institute: Guangzhou national lab

summary: In stem cell-derived β (SC-β) cells, metabolic abnormalities persist as obstacles to glucose responsiveness and functional maturation, with the primary metabolic bottlenecks yet to be identified. This study demonstrated that restoring pyruvate kinase 1 (PKM1) re-established pyruvate kinase activity, effectively reversing the SC-β-cell identity loss and functional impairment associated with phosphoenolpyruvate (PEP) accumulation. 13C-glucose labeling metabolomics revealed a disruption in glucose-stimulated metabolite production beginning at the glycolytic PEP stage in stem cell-derived islets (SC-islets). Uniquely, elevated PEP prevented glycolytic metabolite-dependent increase of exocytosis and significantly increased intracellular calcium levels through a KATP channel-independent pathway, even under basal glucose condition. Furthermore, exposure to PEP led to downregulated expression of genes involved in the TCA cycle and respiratory electron transport. This PEP accumulation in SC-islets was associated with markedly reduced pyruvate kinase activity. Overexpression of PKM1 rescued the transcriptional changes induced by PEP accumulation and improved both glucose-stimulated calcium responses and insulin secretion. These findings suggest that PKM1 plays a pivotal role in promoting SC-β cell differentiation and functional maturation by regulating PEP metabolism, offering potential improvements for SC-β cell replacement in diabetes treatment.

overall_design: H1 ES cells were differentiated into β cell-containing islet organoids. The Islet organoids  were collected at S7D1 and S7D14 analysed by scRNA-seq.

first: Huisheng

last: Liu


title: Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization - ATAC-seq

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identified conserved cis-regultaory elements based on their dynamic chromatin accessibility over the gastrula-larva stages

sample_organism:
Strongylocentrotus purpuratus
Patiria miniata

overall_design: ATAC-seq assays in wild-type sea urchin whole embryos

first: Marta Silvia

first: Danila

last: Voronov

first: Jovana

last: Ranđelović

first: Maria Ina

last: Arnone

first: Ignacio

last: Maeso

first: José

last: Gómez-Skarmeta


title: Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by a poor prognosis, and resistance to gemcitabine, a frontline chemotherapeutic agent, poses a significant challenge to effective treatment. Unraveling the molecular underpinnings of gemcitabine resistance is essential for devising novel therapeutic strategies. Here we derived gemcitabine-resistant and parental pancreatic cancer cell lines from KPC mouse models of PDAC. Employing a multi-omics approach, we integrated RNA-seq, ATAC-seq, and ChIP-seq analyses to characterize the genome-wide alterations in gene transcription, chromatin accessibility, histone modifications, and transcription factor (TF) binding in resistant cells. High-throughput chromatin conformation capture (Hi-C) was used to explore 3D chromatin remodeling. Our analyses identified differentially expressed genes (DEGs) critical for gemcitabine metabolism and resistance, notably Rrm1 and Cdadc1. We observed the upregulation of NF-kB, p53, and MAPK pathways, and the downregulation of mTORC1, MYC targets, and reactive oxygen species pathways. Differentially accessible regions (DARs) showed a significant positive correlation with the expression patterns of DEGs and histone mark H3K27 acetylation. Motif enrichment analyses revealed that TFs from the AP-1, Fox, and Hox families were significantly enriched at DARs, underscoring Foxa1 as a pivotal regulator of resistance-associated genes. We discovered that 3D chromatin reorganization, particularly the enhancement of enhancer-promoter interactions involving super-enhancer (SE) reprogramming mediated by Foxa1 and Ctcf/Smc3, drives the expression of critical resistance genes. Targeting Foxa1 or disrupting SE-associated transcription using JQ1, a bromodomain inhibitor, effectively inhibited resistant cell proliferation and enhanced gemcitabine sensitivity. In summary, this study elucidates the role of TF-mediated chromatin remodeling in gemcitabine resistance and suggests that targeting super-enhancers could be a promising therapeutic strategy to overcome resistance in PDAC, potentially revolutionizing drug therapy for this disease.

overall_design:
1. Cell Culture and Resistance Induction. Maintain parental cancer cells in culture. Induce resistance by exposing cells to increasing concentrations of gemcitabine over several passages. Monitor cell viability and drug sensitivity to confirm resistance. 2. RNA-seq. Extract total RNA from both parental and resistant cells. Prepare sequencing libraries using an RNA-seq kit. Sequence libraries on a high-throughput sequencing platform to obtain transcriptome data. 3. ATAC-seq. Isolate nuclei from both cell types. Perform ATAC-seq to profile accessible chromatin regions. Prepare and sequence ATAC-seq libraries to obtain chromatin accessibility data. 4. ChIP-seq. Crosslink proteins to DNA in both cell types. Sonicate chromatin to shear DNA. Perform ChIP using antibodies against histone modifications and TFs. Prepare and sequence ChIP-seq libraries to obtain binding data. 5. Data Analysis. Process raw sequencing data to remove low-quality reads. Align RNA-seq reads to the reference genome. Align ATAC-seq and ChIP-seq reads to the reference genome. Identify differentially expressed genes, accessible chromatin regions, and differential ChIP-seq peaks between parental and resistant cells. Integrate multi-omics data to identify co-regulated genes and regulatory elements associated with gemcitabine resistance.
Genome-wide landscaps of 3D chromatin architecture in parental and doxorubicin-resistant pancreatic cancer cells. In total, 6 samples were analyzed. Hi-C_Pa_1, Hi-C_Pa_2 and Hi-C_Pa_3 were three biological replicates and served as the control group. Hi-C_GR_1, Hi-C_GR_2 and Hi-C_GR_3 were three biological replicates and served as the treatment group.


title: CRLF1 involves in intervertebral disc degeneration via exacerbating extracellular matrix degradation and nucleus pulposus cells senescence

first: Jian

last: Zhu

address: No.58, Zhongshan 2nd Road, Yuexiu District

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

summary: Low back pain (LBP) is one of the most common musculoskeletal disorders with a huge global impact. Intervertebral disc degeneration (IVDD) is an important cause of low back pain. Therefore, it is crucial to identify and elucidate the key factors affecting IVDD. We identified CRLF1, a key molecule in the process of IVDD, by Gene Expression Omnibus dataset, and determined the high expression of CRLF1 within the degenerated discs and in senescent NPCs by IHC, WB. To further explore the effect of CRLF1 on NPCs, we applied RNA-seq to explore the phenotypic changes of NPCs treated with CRLF1.

overall_design: Normal rat nucleus pulposus cells (NPCs) were treated with vehicle or recombinant CRLF1 (r-CRLF1, Cloud-Clone Corp, China) for 3 days.

first: Yumin

last: Huang

first: Linchuan

last: Lei

first: Zhaomin

last: Zheng


title: Effect of overexpression of oilseed rapetrehalose-6-phosphate synthesis gene BnaC02.TPS8 in Arabidopsis

city: Wuhan

first: Shi

address: No.1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvemen

summary: Trehalose-6-phosphate (T6P) serves as a pivotal signaling molecule, sensing sucrose availability and carbon metabolism. However, the mechanisms governing the regulation of T6P synthase (TPS) genes responsible for anthocyanin accumulation under conditions of low N and high sucrose remain elusive. In a previous study, we demonstrated the positive impact of a cytoplasm-localized class II TPS protein ‘BnaC02.TPS8’ on photosynthesis and seed yield improvement in Brassica napus. Ectopic overexpression of BnaC02.TPS8 in Arabidopsis seedlings resulted in elevated shoot T6P levels under N-sufficient conditions, as well as an increased carbon-to-nitrogen (C/N) ratio, sucrose accumulation, and starch storage under low N conditions. Overexpression of BnaC02.TPS8 in Arabidopsis heightened sensitivity to low N stress and high sucrose levels, accompanied by increased anthocyanin accumulation and upregulation of genes involved in flavonoid biosynthesis and regulation.

overall_design: To identify the pathways regulated by TPS8, we conducted transcriptome analysis of the 35S: BnaC02.TPS8-O2 lines and WT plants under N sufficient conditions using RNA-Seq.

first: Pan

last: Yuan

first: Mingzhu

last: Yu

first: John

middle: P

last: Hammond


title: The SIRT3-DsbA-L-TFAM Axis Suppresses Liver cGAS Signaling and MASH Progression in Male Mice

city: Changsha

first: Jie

last: Wen

address: 87 Xiangya Road, Changsha 410008, Hunan, China

institute: Xiangya Hospital of Central South University

summary: While mitochondrial dysfunction is implicated in metabolic dysfunction associated steatohepatitis (MASH), the precise underlying mechanisms remain obscure. Here, we identify the SIRT3-DsbA-L-TFAM axis as a crucial suppressor for mitochondrial stress-induced cGAS activation in the hepatocytes, thereby alleviating MASH in mice. SIRT3 facilitates the deacetylation of Disulfide-bond-A oxidoreductase-like protein (DsbA-L) at lysine residues (Lys165, Lys167, and Lys177), which promotes the interaction between DsbA-L and mitochondrial transcription factor A (TFAM), essential for the preservation of mitochondrial integrity and function. Hepatocyte-specific knockout of SIRT3 or DsbA-L in male mice promoted mitochondrial DNA release into the cytosol, resulting in activation of the cGAS-STING pathway and exacerbation of MASH characteristics. Conversely, hepatocyte-specific knockout of cGAS or overexpression of DsbA-L mitigated diet- and SIRT3 deficiency-induced MASH progression. Our study underscores the clinical significance of targeting SIRT3 and cGAS as pivotal therapeutic avenues to inhibit the progression of MASH.

overall_design: To investigate whether hepatic STING palys a role in MASH, primary hepatocytes purified from LOXP and liver STING-specific knockout (STINGLKO) mice, and treated with palmitic acid (PA, 0.1 mM) for 24 hours. The hepatocytes were then harvested and subjected to commercial RNA-Seq.

first: Li

last: Hu

first: Juli

last: Bai

first: Feng


title: Characterization of BCR::ABL1-negative NK cells exposed to leukemic microenvironment in a mouse model of Chronic Myeloid Leukemia (https://doi.org/10.1182/bloodadvances.2024014592)

city: Birmingham

first: Valeriya

last: Kuznetsova

state: Al

department: Medicine

institute: The University of Alabama at Birmingham

summary: Natural killer (NK) cells play an integral role in immunosurveillance against myeloid malignancies, with their mature phenotype and abundance linked to prolonged treatment-free remission in chronic myeloid leukemia (CML). However, NK cell function is suppressed during the disease, and the orchestrators of this impairment are not fully understood. Using a chimeric BCR::ABL1+ CML mouse model, we characterized the impact of the leukemic microenvironment on NK cell function and gene transcription. To address the latter, we profiled NK cells from spleen and bone marrow of CML and healthy mice by single-cell RNA sequencing. We revealed an inflammatory cytokine response in CML-exposed NK cells, highlighted by the tumor necrosis factor-a (TNFa)-induced gene signature, upregulation of TNFa receptor TNFR2, and enrichment of SOCS family genes such as Cish, the critical NK cell checkpoint. Ex vivo exposure of healthy NK cells to leukemic soluble factors compromised target-specific NK cell degranulation, which was partially rescued by inhibiting Cish or TNFa - candidate targets reveiled by scRNA-seq. In alignment with these findings, NK cells from healthy donors displayed suppressed cytotoxicity when exposed to plasma from untreated CML patients, with a partial restoration upon Cish or TNFa inhibition. Furthermore, NK cells from newly diagnosed CML patients pre-destined for blast crisis showed an enrichment of the TNFa-induced pro-inflammatory gene signature identified in CML mice. These results suggest that targeting inflammatory signaling could enhance NK cell-based immunotherapies for CML.

overall_design: Sub-lethally irradiated CD45.1+ B6.SJL-Ptprca Pepcb/BoyJ (host) mice were transplanted with CD45.2+ SCL-tTa/BCR-ABL (CML) cells or control CD45.2+ cells lacking the oncogene. Single-cell RNA-sequencing was performed 8-10 weeks after, when CML animals developed leukemia with pronounced myeloid expansion, splenomegaly, and anemia. Bone marrow and splenic NK cells from (2) control and (3) CML mice were isolated by fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq using 10x genomics platform.

first: Robert

middle: S

last: Welner


title: Heat stress-related Exon skip governs Serine/Arginine-rich Splicing Factor SR45a variants underlying plant heat tolerance in Arabidopsis

city: Taian

first: Kang

last: Yan

address: Daizong street 61

institute: Shandong Agricultural University

summary: Heat stress seriously affects the plant development and growth. Increasing evidence points to RNA splicing as co-transcriptional regulations linking heat stresses in plants. However, the mechanism of how heat stress trigger and affect alternative splicing (AS) events through crucial splicing factors is still not clear. Here, we discovered a heat stress-enhancing AS suppression involved in splicing factor SR45a function, whereby SR45a modulates automatic self regulation by strengthen the full length mRNA processing together with CBP20. A SR45a intron splicing–dependent luciferase transgenic line was generated to monitor the intron 4 splicing events. We determined that luciferase activity increases upon heat treatment due to the intron remove, which inhibits the production of SR45a splicing variants. Loss functions of SR45a rendered plants more sensitive to heat stress, whereas overexpresion full length SR45a expression enhanced their tolerance. Full length SR45a is Essential for heat-responsive gene expression and splicing. Interestingly, SR45a modulate self-splicing regulation through branch point recognition together with CBP20. Genetic and molecular experiments identified the CBP20 is a positive regulator under heat stress. In addition, we demonstrate that HSFA2 affects the transcriptional levels of SR45a to act upsteam of SR45a by directly binding SR45a promoter. Our research highlights the heat-responsive self-splicing regulation of SR45a as a novel feedback to enhance plant stress tolerance.

overall_design: Wild-type, SR45a-1a overexpression lines and sr45a plants were grown on ½MS medium under LD conditions.. Two-week-old seedlings were treated with 45℃ for 3 h. Total RNA was isolated with Trizol reagen


title: Single-cell RNA-seq of Bronchoalveolar Lavage Fluid Immune Cells from Padi2/Padi4 Double Knock-out Mice in Pseudomonas aeruginosa Pneumonia-induced Sepsis

city: Ann Arbor

first: Xin

state: Michigan

address: 2800 Plymouth Road.

institute: University of Michigan

summary: Sepsis-induced acute lung injury (ALI) is prevalent in septic patients and has a high mortality rate. Considering ALI’s close link to sepsis, we used a Pseudomonas aeruginosa (PA) pneumonia-induced sepsis mouse model to investigate alveolar microenvironment alterations and lung injury post-sepsis. Peptidyl arginine deiminase (PADI) 2 and PADI4 are highly expressed in immune cells, and play substantial roles in the immune response to sepsis, but their specific functions remain unclear.We employed single-cell RNA sequencing (scRNA-seq) technology to map immune cell populations in bronchoalveolar lavage fluid (BALF) cells from Wild type (WT) and Padi2 and Padi4 double knock-out (DKO)mice in PA pneumonia-induced sepsis and sham conditions.

overall_design: Single cell sequencing of the BALF cells was performed  from WT and Padi2 and Padi4 double knock-out (DKO)mice from PA pneumonia-induced sepsis and sham conditions. For each group a pooled sample of single BALF cell suspension harvested from 3 mice was prepared.

first: Tao

last: Dong

first: Yujing

last: Song

first: Wenlu

last: Ouyang

first: Liujiazi

last: Shao

first: Chao

last: Quan

first: Yongqing

last: Li


title: Molecular remodelling of gene expression profile during differentiation of equine bone marrow-derived MSCs towards adipocytes and chondrocytes

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: Background - The mesenchymal stem cells (MSCs) have a unique self-renewal and developmental potential resulting from their multipotency – the ability to differentiate into particular cell types. It has been confirmed that MSCs have a huge potential and outstanding therapeutic effects in variety of clinical treatments due to the their abilities to differentiate towards ectodermal, endodermal, and mesodermal cell lines.  Objectives - the project aims to identify changes in MSCs transcriptome profile during the process of losing multipotency and acquiring the ability to differentiate cells into adipocytes (ADM) and chondrocytes (CDM) equine cell lines.  Methods - Bone marrow-derived MSCs were differentiated towards adipocytes and chondrocytes using different procedures. The specificity of obtained cell lines was checked using qPCR,  cytometry, and staining approaches. The transcriptome analysis was performed using NGS transcript sequencing on the Illumina HiSeq 3000 platform.  Results - The differential expression analysis allowed us to identify the 2325 DEGs between MSC and ADM groups, while 803 DEGs were detected between MCS and CDM cell lines. According to the comparison of both DEG sets the expression of 320 genes was significantly modified despite the direction of differentiation. The direct related to the transformation of MSCs into adipocytes seems to be fat cell differentiation represented by 47 DEGs and included additional GOs as regulation of fat cell differentiation, regulation of cell differentiation, brown fat cell differentiation, and adipocyte fat development. The results indicated the top DEGs involved in differentiation into adipocytes and previously established as related to adipogenesis: down-regulated - MEOX1, CYYR1, and up-regulated – CYP24A1; LEP; TBX5; FABP4 and GPER1. The obtained data indicated molecular mechanism altered during equine cell remodelling towards chondrocyte differentiation. One of identified GOs was ossification process represented by 35 DEGs with the highest up regulation of two genes was observed - IHH (6.46) and PHOSPHO1 (5.46) involved in chondrocyte proliferation and matrix mineralisation; respectively. The highest down regulation was detected for BMPR1B gene, critical for bone and cartilage formation (-5.98) and together with BMP2 and BMP4 (2.26 and 2.48; respectively) triggered BMP signaling.     Conclusions - The obtained picture of transcriptome differences between primary donor cells and reprogrammed cell lines revealed a range of transcripts important for molecular alterations resulting from substantial phenotypic change of reprogramed cells under special ex-vivo procedures. The study showed the effects of the radical change of cell fate decisions on the molecular level and reinforced further work on efficient procedures to produce MSC-derived reprogrammed cells that have the potential for regenerative medicine of hard connective tissue in horses.

overall_design: Bone marrow-derived MSCs were differentiated towards adipocytes and chondrocytes using different procedures. The specificity of obtained cell lines was checked using qPCR,  cytometry, and staining approaches. RNA was isolated from differentiated lines (n=3 per each line ADM and CDM) and control MSCs line (n=3) the using PureLink™ RNA Mini Kit (Ambion) with DNAse digestion between washing. Its quality and quantity were measured on a NanoDrop2000 and a TapeStation 2200 system (RNA tapes, Agilent). Acceptable samples had an RIN over 9.5. According to the manufacturer's protocol, cDNA libraries cells were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina from 300 ng aliquots of purified RNA samples. The final cDNA library concentration was 10 nM. The quality and quantity of cDNA libraries was assessment using D1000 tapes on TapeStation2200 and on Quibit. The cDNA were sequenced over 150PE cycles on a HiSeq 3000 System (Illumina, San Diego, CA, USA) in outdoor facilities (Admera Health Biopharma Services). The qPCR method and Pearson correlation were applied to validate the RNA-seq results.

first: Katarzyna

last: Ropka-Molik

first: Jolanta

last: Opiela

last: Piórkowska

last: Ząbek

first: Joanna

last: Jurkiewicz

first: Lechosław

last: Gajda

first: Ewelina

last: Semik-Gurgul


title: The effect of cell elongation and alignment via topographical micropatterning on the endothelial transcriptome

city: Portland

first: Meghan

last: Fallon

state: Oregon

address: 3303 S Bond Ave

department: Biomedical Engineering

institute: Oregon Health & Science University

summary: The aim of this study was to investigate the effect of endothelial cell (EC) elongation and alignment, independent of fluid shear stress (FSS), on the endothelial transcriptome. Endothelial cells are continuously exposed to a variety of biomechanical stimuli and must adapt their structure, gene expression, and phenotype to maintain vascular homeostasis. FSS-induced changes in EC morphology are highly associated with functional phenotype. However, to fully investigate EC mechanotransduction pathways, it is essential to decouple cell morphology from FSS. We, therefore, investigated the effects of elongated and aligned endothelial monolayers on the endothelial transcriptome. Baboon carotid artery endothelial cells (ECs) were seeded on either fully non-patterned, planar polyurethane culture substrates or micropatterned (3 µm wide anisotropic ridges and grooves, 1 µm depth) polyurethane culture substrates. We found EC elongation and alignment within static culture induced a highly differential gene transcriptome with a multitude of pro-inflammatory genes downregulated by ECs on micropatterned versus planar substrates. Collectively, our data support that endothelial morphology independently holds a critical role in the genetic transcriptome and may contribute to cardiovascular diseases and inflammation.

overall_design: To investigate cell elongation and alignment on the endothelial transcriptome, primary carotid artery endothelial cells isolated from a single male, juvenile baboon (Papio anubis) were cultured on either fully non-patterned or topographically micropatterned (3 µm wide ridges and grooves, 1 µm depth) polyurethane substrates. After 24 hours in static culture, endothelial cells were lysed

first: Anthony

last: Barnes

first: Monica

middle: T

last: Hinds


title: COMMD10-deficiency in adipose tissue macrophages attenuates obesity and insulin resistance by boosting mitochondrial and antioxidant functions

city: Rehovot

first: Paula

last: Abou Karam

address: Herzl St 234

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann institute of Science

summary: During obesity, adipose tissue macrophages (ATM) colonize the white adipose tissue (WAT), where they adapt inflammatory and metabolically activated phenotypes. Here, we demonstrate that COMMD10 is a key regulator of macrophage oxidative capacity in response to chronic caloric excess. Mice with COMMD10-deficiency targeted to macrophages were fed with high-fat-diet (HFD) for 12 weeks. They gained less weight despite similar food intake, and showed improved systemic metabolic indices, sustained adipose tissue insulin sensitivity, increased lipolysis and reduced adipocyte hypertrophy and liver steatosis. COMMD10-deficient ATM directly improved insulin sensitivity and increase lipolysis in co-cultured adipocytes. COMMD10-deficient ATM exhibited increased oxidative respiration and mitochondrial membrane potential after short term (five weeks) and chronic (12 weeks) HFD. Their oxidative respiration was fueled by both glucose and lipids. They better adapted to mitochondrial activation by upregulating NRF2-dependent antioxidant transcriptional module. their increase in mitochondrial activity was furthered supported by COMMD10 modulation of cellular copper-iron balance and interaction with various oxidative phosphorylation related proteins. Our study illuminates COMMD10 as a pivotal regulator of mitochondrial energy production in ATM during constant energy surplus.

overall_design: To investigate the regulatory role of COMMD10 in metabolically activated macrophage, we established a mouse model with COMMD10 depletion in macrophage by crossing conditional Commd10fl/fl  mice with Cx3cr1cre/+ mice (Cx3cr1∆Commd10). Cx3cr1∆Commd10 mice and their littermate control Commd10fl/fll mice were placed on HFD for 12 weeks. Subsequently, metabolically activated ATM (CD9+) were sorted from epiWAT. Comparative gene expression profiling analysis was performed by  RNA-seq of  5 control samples and 3 COMMD10 depleted ATM samples

first: Chen

last: Varol

first: Nathan

last: Gluck

first: Shani

last: Ben-Shlomo


title: Next generation sequencing analyses shed light on the cold adaptation mechanisms of Saposhnikovia divaricata (Turcz.) Schischk

city: Qiqihar

first: Ming

last: Jiang

address: No.333, Bukui Street, Jianhua Distric

institute: Qiqihar Medical University

summary: Purpose:Next generation sequencing has been done to compare differrent transcriptome profiling between control groups and cold treated groups of Saposhnikovia divaricate (Turcz.) Schischk. Methods:Retinal mRNA profiles of 48d-old control samples (CK)and 6h/48h cold treated under 4°C were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000 Platform.                       Results: Using an optimized data analysis workflow, we obtained 6.1 GB of clean reads with an impressive Q30 percentage > 91.58%. We mapped about 20 million sequence reads per sample.                     Conclusions: Our study represents the first detailed analysis of Saposhnikovia divaricate (Turcz.) Schischk trascriptomes, with biologic replicates.

first: Hui

first: Kanchao

last: Yu

first: Yanshi

last: Ma


title: Subcommissural organ (SCO) contributes to brain development via SCO-secreted peptides.

city: beijin

first: Tingting

last: Zhang

address: Beijin

institute: CIBR

summary: To explore the mechanism of SCO-derived peptides, we performed RNAseq in cultured neurons added with SCO peptide and control neurons which added with DPBS to identify the expression of some  unique genes and possible pathway related to the function of SCO derived peptides. We cofirmed  the role of SCO derived peptide which contribute in neuronal development,especially projection developent and cell survival. development and neuronal survival .

overall_design: Differential expression analysis and Gene Set Enrichment Analysis of RNA seq data. We performed differential expression analysis and Gene Set Enrichment Analysis of RNA seq data obtained from cultured neurons added with SCO-derived peptides and  cultured neurons added with DPBS

first: Daosheng

last: Ai

first: Pingli

last: Wei

first: Woo-ping

last: Ge


title: Effect of ablation of trophoblast-derived signals on gene expression in the decidua of early pregnancy

city: Xiamen

first: Yang

last: Sun

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

summary: Maternal-embryonic interactions play a critical role in successful pregnancy, with particular emphasis on the decidual-trophoblast interaction, which have been long recognized to exert a paracrine influence through the trophoblast cells on the progression of decidualization and the function of decidual cells. Despite this knowledge, the full extent of the embryo's impact on the decidua remains largely unexplored. To investigate the influence of embryonic signals on the maternal decidua, we utilized Prl3d1Cre/Cre mice mated with R26DTA/DTA mice, resulting in the generation of Prl3d1Cre/+, R26DTA/+ conceptus. In these conceptuses, the primary trophoblast giant cells (pTGCs) were selectively ablated by diphtheria toxin A (DTA). The pTGCs are the key embryonic cells that directly interact with the maternal decidua. Following the ablation of pTGCs, we observed impaired decidualization, as indicated by altered expression of genes related to decidualization or decidual function, such as Prl8a2, Wnt4, Bmp2, Alpl, and Hsd11b2, as well as a reduction in the interferon response in the decidua on day 6.5 of early pregnancy. Additionally, we found significant downregulation of numerous lipid-related biological effects in both deciduae on day 6.5 and day 8 of early pregnancy. These findings shed light on the complex interactions between the maternal and embryonic components during early pregnancy and underscore the importance of embryonic-derived influences on decidual lipid metabolism.

overall_design: we employed a mouse model with selective ablation of pTGCs using the pTGC-specific Prl3d1-Cre driven Rosa26-DTA expression system. RNA sequencing was performed on two biological replicates of WT and DTA deciduae, after removing myometrium and embryo tissues from the whole uteri

first: Ningjie

last: Yang


title: Epithelial barrier function and its underlying mechanical regulation affects the biology of Macro-Metastasis Parenchyma Interface (MMPI).

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

summary: Already years ago, the histopathological growth pattern (HGP) of liver metastases at the macro-metastases parenchyma interface (MMPIliver) was included in pathological guidelines. Brain metastases also differ in their HGPs at the MMPIbrain. However, there is no existing biological concept for these differences. Pathophysiological, the MMPI is an interface between an emerging metastatic tissue and the host organ, which both protect themselves from each other. Thus, it would be not surprising that carcinomas reactivate their original function, the epithelial barrier at this interface. However, differences in epithelial barrier were never been taking into account for different HGPs at the MMPI. Here, we systematically compared models with epithelial infiltration (Epi-models) with diffuse infiltrating models (Diff-models) at the MMPIbrain. Using this stratification, we revealed fundamental differences in mechano-transduction via YAP, Ca2+ distribution and the epithelial barrier function. Moreover, these features have effects on immune cell infiltration and druggable immune checkpoints. Finally, we clustered human brain and liver metastases by using an Epi- and a Diff-gene signature into four clusters: the Epi-, Diff-, Mixed- and Unclassified-cluster. These also revealed enormous differences in pathways, responsible for epithelial barrier formation, extracellular matrix and immune response. Moreover, it also revealed YAP as an important transcriptional co-activator in this context. Taken together, we report about fundamental differences in barrier function and mechano-regulation at the MMPI, which could have implications for therapy decisions of metastasized patients in future.

overall_design: We collected 28 brain metastatic samples from patients (one sample per patient) previously diagnosed with colon cancer (n=16) and rectal cancer (n=12), and characterized them by RNA-Seq.

first: Tobias

last: Pukrop

first: Daniela

last: Sparrer

first: Raquel

last: Blazquez

first: Tim

last: Beißbarth

first: Annalen

last: Bleckmann


title: Spermidine promotes meiotic maturation of porcine oocytes

city: Nan Jing

first: Qian

last: Gao

address: No 1, Weigang

institute: Nanjing Agricultural University

summary: Spermidine is involved in a variety of biological processes, including DNA metabolism, autophagy and aging. Previous studies have shown that spermidine can increase the percentage of mouse oocytes developing into blastocysts after in vitro fertilization. However, none of the past studies elucidated the effects of spermidine supplementation on porcine oocyte maturation. Here, we choose appropriate dose of spermidine to be added to the maturation medium during in vitro maturation (IVM) to verify whether spermidine can actively promote the maturation of porcine oocytes. Our study provided substantial evidence that spermidine exposure promoted the porcine oocyte meiotic maturation. In addition, single-cell transcriptome analysis identified the target effectors of spermidine actions in porcine oocytes, further demonstrating that spermidine exposure enhanced mitochondrial distribution and function, leading to a reduced excessive oxidative stress-induced DNA damage and early apoptosis of porcine oocytes. These findings demonstrate that spermidine not only delays ageing and cancer treatment, but also improves the quality of germ cells, which may be less likely to suffer from sterility or infertility in humans and animals.

overall_design: Transcriptomic analysis of matured oocytes was carried out using a protocol for RNA-Seq. The constructed library was sequenced with Illumina platform.

first: Xiaotong

last: Zhu

first: Yilong

last: Miao


title: Subcommissural organ (SCO) contributes to brain development via SCO-secreted peptides

summary: To explore the role of SCO and its functional mechanism, we performed RNAseq between SCO and hippocampus at  different stage to identify the expression of some  unique genes and possible pathway related to the function of SCO. We cofirmed  the role of SCO in neuronal development and identified  three SCO-derived peptides which can contributed to neurite development and neuronal survival .

overall_design: Differential expression analysis and Gene Set Enrichment Analysis of RNA seq data. We performed differential expression analysis of RNA seq data obtained from SCO and hippocampus of adult mice and Gene Set Enrichment Analysis obtained from SCO and hippocampus of P0 mice.


title: Transcriptional profiling of chickpea genes differentially expressed in response to drought stress using high density oligonucleotide microarray

city: Nanjing

first: xian-sheng

last: wang

address: Weigang No.1

institute: NJAU

summary: Chickpea (Cicer arietinum L.) is an important pulse crop grown mainly in the arid and semi-arid regions. Due to its taxonomic proximity with the model legume Medicago truncatula and its ability to grow in arid soil, chickpea has its unique advantage to understand how plant responds to drought stress.  This microarray was used for analyze the transcriptomic profiles of unigenes in leaf and root of chickpea seedling under drought stress, respectively.   Microarray data showed that 4805 differentially expressed unigenes were either greater than 2 fold up- or less than 0.5 fold down-regulated in at least one of the 5 time points during drought stress. 2003 and 3488 unigenes were time-dependent differentially expressed in root and leaf, respectively. 110 pathways in two tissues were found to respond to drought stress. Compared to control, 88 and 52 unigenes were expressed only in drought-stressed root and leaf, respectively, while nine genes were expressed in both tissues. 2484 function-unknown unigenes were found to be remarkably regulated by drought stress.  The expression profiles of these time-dependent differentially expressed unigenes were useful in furthering our knowledge of the drought tolerance mechanism of plant.

overall_design: Total RNA from the control root and leaf and drought-stressed root and leaf of chickpea were used to generate target cDNA, and then hybridized to Agilent Chickpea Gene Expression Microarray representing about 6000 unigenes.

first: Xiansheng

last: Wang

first: Shubing

last: Shi

first: Hao


title: Dynamics of de novo heterochromatin assembly and disassembly at replication forks ensures fork stability

city: Rotterdam

first: Calvin

last: Lo

address: Doctor Molewaterplein 40

department: Molecular Genetics

country: Netherlands

institute: Erasmus MC

summary: Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here, we discover a checkpoint regulated cascade of chromatin signaling that activates the histone methyltransferase EHMT2/G9a to catalyze heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fiber approaches, we show that G9a together with SUV39h1 induces chromatin condensation by accumulating the silent mark, H3K9me1/2/3, in the vicinity of stressed replication forks. This closed conformation is also favored by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering ssDNA gaps formation and sensitizing cells towards chemotherapeutic drugs. These findings may help explaining chemotherapy resistance and poor prognosis observed in cancer patients displaying elevated level of G9a/H3K9me3.modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (sixfold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (for example, a >15-fold enrichment of dimethylated H3K79me2). Nuc-MS is highly concordant with chromatin immunoprecipitation-sequencing (ChIP-seq) and offers a new readout of nucleosome-level biology.

overall_design: TIG3 cells for the indicated conditions were cross-linked for 10 min in 1% formaldehyde and chromatin was fragmented by sonication using Bioruptor Sonicator (Diagenode). Chromatin immunoprecipitation was performed as previously described (Jakobsen et al. 2013) with antibodies against H3K9me3 (Abcam, ab8898) and H3 (Abcam, ab10799). Replicates of 2 have included.  Raw reads were aligned to the human genome (hg19 assembly excluding non-canonical chromomes i.e. random, unknown and haplotype variant chromosomes)

first: Nazaret

last: Reverón-Gómez

first: Zuzana

last: Jasencakova

first: Vincent

last: Gaggioli


title: M6A Demethylase FTO-mediated downregulation of DACT1 mRNA stability promotes Wnt signaling to facilitate osteosarcoma progression

city: guangzhou

first: DONGMING

last: LV

address: guangzhou,china

institute: the first affiliated hospital of sysu,guangzhou,china

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

overall_design: Refer to individual Series


title: Tlr7 Drives Sex Differences in Age- and AD-related Demyelination [spatial transcriptomics]

status: Public on Nov 29 2024

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Alzheimer’s disease (AD) and other age-related disorders associated with demyelination exhibit sex differences. Here, we used single-nuclei transcriptomics to dissect the contributions of sex chromosomes and gonads in demyelination and AD. In a mouse model of demyelination, we identified the role of sex chromosomes and gonads in modifying microglia and oligodendrocyte responses before and after myelin loss. In an AD-related mouse model expressing APOE4, XY sex chromosomes heightened interferon response and tau-induced demyelination. The X-linked gene Toll-like receptor 7 (Tlr7) regulated sex-specific interferon response to myelin. Deletion of Tlr7 dampened sex differences while protecting against demyelination. Administering TLR7 inhibitor mitigated tau-induced motor impairment and demyelination in male mice, indicating that Tlr7 plays a role in the male-biased IFN-I response in aging- and AD-related demyelination.

overall_design: Spatial transcriptomic sequencing of mouse hemi brains  investigating the effects of biological sex, sex hormones, and sex chromosomes on either cuprizone-induced demyelination or tau pathology

first: Chloe

last: Lopez-Lee

first: Lay

last: Kodama

last: Fan

first: Daphne

first: Jingjie

first: Man Ying

last: Wong

first: Pearly

last: Ye

first: Kendra

last: Norman

first: Nessa

last: Foxe

first: Laraib

last: Ijaz

first: Fangmin

last: Yu

last: Chen

first: Gillian

last: Carling

first: Eileen

last: Torres

first: Rachel

last: Kim

first: Dena

last: Dubal

first: Shane

middle: A

last: Liddlelow

first: Subhash

last: Sinja

middle: C

last: Sinha

first: Wenjie

last: Luo


title: mRNA profiles of DNT cells in primary biliary cholangitis patients

city: Beijing

first: Tingting

last: Lv

address: No. 95 Yong-An Road

institute: Beijing Friendship Hospital

summary:
Primary biliary cholangitis (PBC) is an autoimmune liver disease of unknown pathogenesis. We find a decreased number and immunosupressive function of double nagative T (DNT) cells in PBC patients. To further unveil the mechanism by which suppressive function and quantity of DNT cells in PBC patients was impaired, we performed a whole-transcriptome analysis on DNT cells isolated from 13 PBC patients and 6 HCs. Total RNA of DNT cells from HCs and PBC patients were isolated and assessed. Transcriptome sequencing libraries were then generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Differentially expressed genes with a fold change of >=2.0 and p < 0.05 between HC and PBC patients were submitted to GO and KEGG enrichment analysis.
Thie biologic processes of GO enrichment analysis showed that cell co-stimulations, cell migration, apoptotic process, cell activation and cell cytotoxicity were enriched, which helped to explain the alterations in number and suppressive function of DNT cells between HCs and patients from a mRNA level. Meanwhile, we observed that T cell receptor signaling pathway was enriched in DEGS and  all identified genes with GSEA. Additionally the leading-edge genes of this pathway exhibited downregulation in PBC patients, subsequently supported by real-time PCR. PIK3R1 and MAP3K8 exhibited more significant reduction in DNT cells from PBC patients.

overall_design: mRNA profiles of DNT cells from 6 healthy controls and 13 PBC patients were generated by deep sequencing with Illumina Hiseq platform.

first: Dong

last: Zhang

first: Jidong

last: Jia


title: B cells enhanced the anti-U251/U373 activity of EphA2-CAR T cells

first: yi

last: hu

address: No.10 Yangfangdian Road

institute: Beijing Shijitan Hospital

summary: Chimeric antigen receptor (CAR) T cell therapy is a powerful adoptive immunotherapy against blood cancers, but the therapeutic effect was not efficient enough on solid tumors. B cells have been reported to play a critical role in regulating memory T differentiation and cytotoxic T development. However, as of yet the influence of such B cells on CAR T cells has not been discussed. In this study, using ephrin type-A receptor 2 (EphA2) specific CAR T cells, we cultured B cells successfully to stimulate T cells in vitro, and investigated the cell differentiation and anti-tumor efficiency. We observed that EphA2-CAR T cells stimulated by B cells performed enhanced anti-tumor ability with more interferon γ (IFN γ) production and higher OX40 expression. The differentiation of CAR T cells was arrested after B cells stimulation for more than 7 days with the percentage of central memory T cells (Tcm) increasing. In addition, next generation sequencing was performed. The top expressed genes clustered in activation, leukocyte migration and chemokine signaling pathway contributed to the anti-glioblastoma (GBM) activity of CAR T cells stimulated by B cell. In conclusion, these results indicated the importance of B cells in retarding CAR T cells differentiation and enhancing anti-tumor activity, which paves the way for the rapid exploitation of EphA2-CAR T cells against GBM in the future.

overall_design: EphA2-CAR T cells stimulated with or without B cells were co-cultured with U251 or U373 (1:1). The suspended cells were collected and washed with PBS for three time.  CD3+ T cells were isolated using Dynabeads™ CD3 (Invitrogen). Total RNA was extracted from cells attached on the beads using TRIzol Reagent (Invitrogen). The culture dish was washed with PBS for three times and RNAs of adherent cells were collected using TRIzol reagents. Samples containing 2 µg total RNA each were used as input material for generating the sequencing libraries by company.

first: Ying

first: Zhijing

last: An

first: Can

first: Yi

last: Hu


title: Tlr7 Drives Sex Differences in Age- and AD-related Demyelination [snRNAseq]

first: Li

last: Gan

overall_design: Droplet-based single nuclear RNA sequencing  of various hippocampal tissues investigating the effects of biological sex, sex hormones, and sex chromosomes on either cuprizone-induced demyelination or tau pathology

first: Chloe

last: Lopez-Lee

first: Lay

last: Kodama

last: Fan

first: Daphne

last: Zhu

first: Jingjie

first: Man Ying

last: Wong

first: Pearly

last: Ye

first: Kendra

last: Norman

first: Nessa

last: Foxe

first: Laraib

last: Ijaz

first: Hao


title: Immunogenic clearance combined with programmed cell death protein-1 blockade elicits antitumor effect by promoting the recruitment and expansion of the effector memory-like CD8+ T cell

city: Seongbuk-gu

first: In-San

last: KIM

address: 5, Hwarang-ro 14-gil

institute: Korea Institute of Science and Technology

summary: Inducing immunogenic clearance enhances the phagocytosis of dying cancer cells and activates antigen-presenting cells, facilitating the immune system against cancer. This approach can potentially generate robust systemic antitumor immune responses and increase tumor responsiveness to anti-programmed cell death protein 1 (αPD-1) therapy. However, the precise mechanisms underlying this antitumor response induced by immunogenic clearance remain unclear. We used single cell RNA sequencing (scRNA-seq) to understand the underlying mechanism of the therapeutic strategy of immunogenic clearance.

overall_design: Here, we employed a B16F10 murine melanoma model, which is resistant to immune checkpoint blockade (ICB). We administered doxorubicin (Dox), an anthracycline that induces immunogenic cell death, and fasudil, a ROCK inhibitor that enhances phagocytosis, to induce immunogenic clearance. We determined the effect of a novel triple combination therapy (Dox+fasudil and αPD-1) on the tumor microenvironment (TME) using single-cell transcriptome profiling.


title: Spatial transcriptomics reveals key differences in Alport disease progression and potential targets of hEV treatment in Alport disease

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Alport syndrome is a glomerular disease. To understand the disease progression of alport syndrome and potential therapeutical effects of hEV derived from AFSCs, we performed spatial transcriptomics to profile the  heterogeniety of cell populations in kidneys of mouse of AS through disease progression and hEV treated AS mice as well. Our analysis sheds light on key functional parts of the kidney responsible in disease progression as well as potential targets of hEV therapy.

overall_design: WT, Early and late stage alport syndrome mouse models were used to profile the spatial transcriptomics of the disease progression. Early treated 5m AS and Late treated 5m AS were used to profile the spatial trascriptomics of the hEV treated AS


title: Mutant FUS induces chromatin reorganization in the hippocampus and alters memory processes

city: Strasbourg

first: Anne-Laurence

last: Boutillier

address: 12 rue Goethe

department: LNCA

country: France

summary: This project aims to assess the transcriptomic signature of FUS∆NLS/+ (FUS) vs FUS+/+ (WT) mice, by identifying differentially expressed genes in basal conditions and also during learning. Cytoplasmic mislocalization of the nuclear Fused in Sarcoma (FUS) protein is associated to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS accumulation is recapitulated in the frontal cortex and spinal cord of heterozygous Fus∆NLS/+ mice. We show that in these mice, the hippocampus, a critical structure involved in learning and memory, paradoxically displays nuclear FUS accumulation. FUS binds to a set of genes characterized by the presence of an ETS/ELK-binding motifs, and involved in RNA metabolism, transcription, ribosome/mitochondria and chromatin organization. Importantly, hippocampal nuclei showed a decompaction of the neuronal chromatin at highly expressed genes and an inappropriate transcriptomic response was observed after spatial training of Fus∆NLS/+ mice. Furthermore, these mice lacked precision in hippocampal-dependent spatial memory task. These studies shows that mutated FUS affects epigenetic regulation of the chromatin landscape in hippocampal neurons, which could participate in FTD/ALS pathogenic events.

overall_design: Total RNAs were extracted from the dorsal hippocampus (HD) of 4-5 month-old FUS+/+ (WT) and FUS∆NLS/+ (FUS) mice at basal state (Home Cage, HC) and after 3 days of training in the Morris Water Maze (MWM). In total, we have 4 groups : WT and FUS mice Home Cage, and WT and FUS mice after learning. Each group includes 3 samples for sequencing with a total of 12 samples for dorsal hippocampus. Data were generated by deep sequencing using Illumina Hiseq 4000.

first: Luc

last: Dupuis


title: Palmitoyltransferase ZDHHC21 regulates oxidative phosphorylation to induce AML differentiation block and chemoresistance

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

summary: Acute myeloid leukemia (AML) is an aggressive hematological malignancy. Nearly 50% of the patients who receive the most intensive treatment develop leukemia relapse. AML cells are highly dependent on mitochondrial oxidative phosphorylation (OXPHOS) for survival, especially refractory leukemia, but how OXPHOS contributes to the leukemia progression is unclear and noncytotoxic strategy to inhibit OXPHOS is lacking. Here, we demonstrate for the first time that ZDHHC21 palmitoyltransferase serves as a key regulator to regulate the OXPHOS hyperactivity in AML cells. The depletion of ZDHHC21 effectively inhibited OXPHOS activity and induced the myeloid differentiation of AML cell lines and patient-derived AML specimens. Mechanistically, ZDHHC21 specifically catalyzes the palmitoylation of mitochondrial kinase AK2 and further activates OXPHOS to arrest myeloid differentiation. Moreover, inhibition of ZDHHC21 eradicated the AML blasts and prolonged the survival of NOD/SCID mice inoculated with AML cell lines and PDX-AML cells. Besides, targeting ZDHHC21 to suppress OXPHOS markedly enhances the chemotherapy efficacy in refractory leukemia. Together, these findings not only uncover the new biological function of palmitoyltransferase ZDHHC21 in regulating AML oxidative phosphorylation, but also indicate ZDHHC21 inhibition as a potential therapy for patients with AML especially refractory leukemia.

overall_design: HL60 cells infected with lentivirus-shZDHHC21 (#1 and #2) or shAK2 (#1 and #2) for 4 and 7 days

first: Meidan

last: Ying

first: Aixiao

last: Xu


title: Loss of RPA1 impairs peripheral T cell homeostasis and exacerbates inflammatory damage through triggering T cell necroptosis

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: The peripheral T cell pool is maintained at dynamic homeostasis throughout life. This is achieved through fine-tuning of thymic output and self-renewal of naïve T cells. Dysregulation of T cell homeostasis has been implicated in autoimmune diseases, yet little is known about the homeostatic mechanisms. Here, we report that the replication protein A1 (RPA1) is upregulated during T cell activation. Utilizing T cell-specific Rpa1-deficient (Rpa1fl/fl Cd4-cre) mice, we find that loss of Rpa1 restrains peripheral CD8+ T cell population and limits TCR repertoire diversity. Clinical analysis reveals that the mRNA level of RPA1 is reduced in patients with ulcerative colitis. Accordingly, Rpa1fl/fl Cd4-cre mice exhibit increased susceptibility to inflammatory diseases, including colitis and hepatitis. Mechanistically, RPA1 deficiency triggers necroptotic T cell death following TCR engagement, which in turn results in damage-associated molecular patterns (DAMPs) leakage and leukocyte recruitment, consequently exacerbating inflammatory damage. These studies thus uncover that RPA1 acts as a guardian of T cell clonal expansion that is essential for T cell homeostasis.

overall_design: Study of colon infiltration immune cells from WT or CKO mice in the context of experimental colitis using 10x scRNA-seq technologies.

first: Xin

last: Zhang

first: Dan

last: Lu


title: The rice anther transcriptomes responded to low temperature [RNA-seq]

city: Sapporo

first: Yuji

last: Kishima

address: Kita-ku Kita 9 Nishi 9 W105

country: Japan

institute: Hokkaido University

summary: The booting stage of rice shows the most sensitivity to cold stress, and low-temperature stress causes irreversible pollen sterility. We performed transcriptome analysis using RNA-seq to investigate the response of rice anthers to low-temperature stress. In this RNA-seq analysis, to validate the results of transcriptome analysis of anthers from 13 rice lines using microarrays, four cultivars were selected for analysis from the 13 tested for microarrays.

overall_design: The four rice lines exposed to the low temperature at 12℃ for four days, were used for the RNA-seq. RNA was extracted from the anthers after the cold-treated and non-treated anthers with two replicates.

first: Y

first: K

last: Yamamori


title: M6A Demethylase FTO-mediated downregulation of DACT1 mRNA stability promotes Wnt signaling to facilitate osteosarcoma progression [MeRIP-seq]

first: DONGMING

last: LV

summary: Despite advances in clinical diagnosis and treatment, the prognosis of patients with osteosarcoma (OS) remains poor, and the treatment efficacy has plateaued. Therefore, it is important to identify new therapeutic targets for OS. N6-methyladenosine (m6A) modification has been reported to participate in tumor malignancy. In this study, functional screening found that the m6A demethylase FTO could be a candidate therapeutic target for OS. Upregulated FTO in OS could predict a poorer prognosis. FTO promoted the growth and metastasis of OS in vitro and in vivo. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed to identify DACT1 as a potential target of FTO. In vitro assays demonstrated that FTO could reduce the mRNA stability of DACT1 via m6A demethylation, which decreased DACT1 expression and further activated the Wnt signaling pathway. The oncogenic effect of FTO on OS was dependent on DACT1. In addition, the m6A reader IGF2BP1 was validated to participate in the regulation of DACT1. Entacapone, a conventional drug for Parkinson's disease, was confirmed to suppress OS via m6A-mediated regulation through the FTO/DACT1 axis. Our findings demonstrate that FTO may be a novel therapeutic target and that entacapone has the preclinical value to be repurposed for OS.

overall_design: MeRIP-seq of FTO knockdown and control 143B cells

first: Dongming

last: Lv

first: Xianbiao

last: Xie


title: NKG2C and NKG2A coexpression defines a highly functional antiviral NK population in spontaneous HIV control

city: Barcelona

first: Maria

middle: José

last: Buzón

state: Barcelona

address: Passeig Vall d'Hebron 119-129

department: Infectious Diseases

institute: Vall d'Hebron Research Institute

summary: Elite controllers (ECs), a unique group of people with HIV (PWH), exhibit remarkable control of viral replication in the absence of antiretroviral therapy. In this study, we comprehensively characterized the NK cell repertoire in ECs after long-term viral control. Phenotypic profiling of NK cells revealed profound differences compared with other PWH, but marked similarities to uninfected individuals, with a distinctive prevalence of NKG2C+CD57+ memory-like NK cells. Functional analyses indicated that ECs had limited production of functional molecules upon NK stimulation and consequently reduced natural cytotoxicity against non-HIV target cells. Importantly, ECs showed an exceptional ability to kill primary HIV-infected cells by the antibody-dependent cell cytotoxicity adaptive mechanism, which was achieved by a specific memory-like NK population expressing CD16, NKG2A, NKG2C, CD57, and CXCR3. In-depth single-cell RNA-seq unveiled a unique transcriptional signature in these NK cells linked to increased cell metabolism, migration, chemotaxis, effector functions, cytokine secretion, and antiviral response. Our findings underscore a pivotal role of NK cells in the immune control of HIV and identify specific NK cells as emerging targets for immunotherapies.

overall_design: Three distinct NK cell populations (NKA, NKB, and NKC) were isolated from PBMCs obtained from an HIV EC individual by Fluorescence-activated cell sorting (FACS) according to the expression of selected receptors: NKA (NKG2A+ NKG2C+ CD57+ CXCR3+), NKB (NKG2A- NKG2C+ CD57+ CXCR3+), and NKC (NKG2A+ NKG2C- CD57+ CXCR3+) and analyzed using scRNAseq.

first: Maria J

first: Nerea

last: Sanchez-Gaona


title: Modular organization of mouse prefrontal  cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIEDER-Seq

city: Wuhan

first: Hu

last: Zheng

state: Hubei

address: shizishan street No.1

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

summary: Deciphering the connectome, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a cost-effective Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate a comprehensive integrated single-cell spatial molecular, cellular and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated projectomic atlas with their distinct spectrum of neurotransmitter/neuropeptide and the receptors-related gene profiles and depicted PFC neural signal transmission network. By which, we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, we predicted neuron projections with high accuracy by combining gene profiles and spatial information via machine learning. This study facilitates our understanding of brain multi-modal network and neural computation.

overall_design: We injected rAAV2-retro viruses with different barcodes into multiple target brain areas of the prefrontal cortex of c57bl/6 mice. One months later, the prefrontal cortex of the mice was dissected and the cells were sorted for BD Rhapsody scRNAseq. A total of 3 mice were included in this study.

first: Leqiang

last: Sun


title: Next Generation Sequencing facilitates to identify the differential expression genes between tumor (T1-8) and non-tumor tissue (NT1-8) from HBV-infected hepatocellular cacinoma (HCC) patients.

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

summary: To find the key gene regulating HBV-infected hepacellular cacinoma genesis and development. We selected tumor (T1-8) and non-tumor tissue (NT1-8) from HBV-infected hepatocellular cacinoma (HCC) patients perform next-generation sequencing (NGS).  Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest  the key gene regulating HBV-infected hepacellular cacinoma genesis and development.

overall_design: We selected 8 non-tumor liver tissue as control and 7 hepatoma tissue from HBV-infected hepatocellular cacinoma (HCC) patients.

first: Xiufang

last: Weng


title: Transcriptional profiles of heterozygous and homozygous Pdp1-p205 larvae

city: Houston

first: Marco

last: Sardiello

state: TX

address: One Baylor Plaza

department: MHG

institute: Baylor College of Medicine

summary: homozygous Pdp1-p205 larvae are severely growth delayed and die before pupation, whereas Pdp1-p205 heterozygous larvae and adults display no apparent phenotype. We compared the transcriptional profiles of heterozygous and homozygous Pdp1-p205.

overall_design: We performed 3 indipendent hybridization comparing the transcriptome of the homozygous Pdp1-p205 (considered as KO) vs heterozygous Pdp1-p205 (considered as WT) larvae.

first: Remo

last: Sanges

first: Guglielmo

last: Roma


title: M6A Demethylase FTO-mediated downregulation of DACT1 mRNA stability promotes Wnt signaling to facilitate osteosarcoma progression [RNA-seq]

overall_design: RNA-seq of FTO knockdown and control 143B cells


title: Induction of MASH in Three-Dimensional Bioprinted Human Liver Tissue

city: La Jolla

first: David

last: Brenner

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys

summary: Non-alcoholic steatohepatitis (NASH) represents a significant and growing public health concern worldwide, characterized by hepatic steatosis, inflammation, and varying degrees of fibrosis. In vitro models of NASH play a crucial role in elucidating the underlying mechanisms of disease pathogenesis, identifying potential therapeutic targets, and evaluating the efficacy of pharmacological interventions. Several preclinical models of MASH have been developed and are being used extensively to study these areas. While standard cell culture models allow for elucidation of certain molecular pathways involved in MASH pathogenesis, they lack three-dimensional architecture and cellular heterogeneity observed in native liver tissue, potentially limiting their physiological relevance and inability to fully capture the multifactorial nature of the disease Precision cut liver slices from MASH livers retain the complex multicellular architecture of the liver including hepatocyte arrangement, sinusoidal structure, and cellular interactions, but the metabolism deteriorates over a short period of time (usually reported as 2 days). Human liver organoids from iPSCs (induced pluripotent stem cells) retain the genetics of the patients but fail to fully differentiate into hepatocytes or have the liver architecture. Human liver spheroids incubated in a MASH cocktail develop several phenotypic characteristics of a MASH liver, but the small spheroid size precludes extensive histological comparisons to MASH livers. Microphysiological systems (MPS) or “liver on a chip” in which 3D cultures are perfused, maintain many of the physiological functions of the liver owing to precise control over microenvironmental parameters, including fluid flow, nutrient gradients, and mechanical cues. However, MPS are difficult to scale up and have not been developed to reproduce a MASH phenotype.  In comparison, bioprinted liver tissues for MASH have many advantages. Organovo’s 3D bioprinted liver tissues are comprised of all major primary liver cells including hepatocytes, endothelial cells, stellates and Kupffer cells, mixed in physiologically relevant ratios. These cells are then bioprinted in precise pre-defined liver specific geometries to recapitulate complexity of the hepatic microenvironment.. This mimicking of tissue architecture enables more accurate representation of cellular interactions, spatial organization, and microenvironmental cues crucial for MASH pathogenesis. The liver tissues developed using this method maintain differentiation and metabolism over several weeks. In this paper, we further demonstrated that upon treatment with a MASH induction cocktail, these liver tissues respond accurately by developing steatosis and fibrosis Tissue response varies depending in response to the complexity of the MASH cocktail.

overall_design: To investigate similarities between MASH human bioprinted tissues and two previous studies of transcriptomic differences between human MASH livers and human healthy livers, MASH tissues were bioprinted using primary liver cells and treated with a MASH induction cocktail. Healthy controls followed the same protocol but were not treated with a MASH induction cocktail.

first: Vaidehi

last: Joshi

first: Alice

last: Chen

first: Keith

last: Murphy

first: Daisy

last: Chilin-Fuentes

first: Sara

last: Rosenthal

first: Kathleen

middle: M

last: Fisch

first: Tatiana

last: Kisseleva


title: The rice anther transcriptomes responded to low temperature

first: Yuji

last: Kishima

summary: Transcriptome analysis using a microarray equipped with probes for genes and repetitive sequences has been performed to examine the expression change in rice anther. We performed transcriptome analysis in 13 rice lines with different cold tolerances at the booting stage because the low temperature at this stage resulted in pollen sterility. From our study, it was found that genome-wide expression is negatively correlated with the degree of cold tolerance.

overall_design: The 13 rice lines exposed to the low temperature at 12℃ for four days, were used for the microarray analyses. RNA was extracted from the anthers after the cold-treated and non-treated anthers with two replicates.

first: Y

first: K

last: Yamamori


title: Exosomes derived from TREM-2 knocked-out macrophages alleviated renal fibrosis via HSPa1b/AKT pathway

city: Whhu

first: Xiao

last: Zihao

state: Anhui

address: 92# West Zhe Shan Road

department: Nephrology

institute: Yi Ji Shan hospital affiliated to Wan Nan Medical college

summary: Macrophages are recognized as the vital players in renal fibrosis, with a high degree of heterogeneity and plasticity, and triggering receptor expressed on myeloid cell-2(TREM-2) was highly expressed on macrophages and participated in the progression of tissue fibrosis. However, the mechanism by which TREM-2 mediate the progress of renal fibrosis is still unclear. Our study have found the exosomes derived from TREM-2 deficient (TREM-2-/-) macrophages could suppress the progression of fibrosis, showing a higher matrix metalloproteinase-9 (MMP-9) / tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) ration at protein level in secreted exosomes than exosomes from WT（wild type）macrophages in the fibrotic microenvironment. Besides, renal tubular epithelial cells (TECs) engulfed theses nanoscale vesicles, the expression of collagen I and α-smooth muscle actin (α-SMA) (fibrosis related marker) was obviously decreased. Through the RNA-seq, we found that TREM-2-/- macrophages upregulate the MMP-9/TIMP-1 ratio in its exosomes via HSPa1b/AKT pathway. Furthermore, it’s noteworthy that the renal fibrosis was effectively alleviated in the obstructed kidney from mice received a renal pelvis injection of adeno associated virus (AAV-shTREM-2) containing the sequence of silencing TREM-2. However, VER-155008 (inhibitor of HSPa1b) and Ly294002 (inhibitor of AKT) reversed this effect. Moreover, polyclonal antibodies against TREM-2 also effectively relieved the UUO-induced renal fibrosis. Above all, we have validated that the knocking down TREM-2 expression can inhibit the progression of renal fibrosis through a macrophage exosome-dependent pathway in vitro and vivo. Hence, our finding suggest TREM-2 is potential therapeutic target for CKD.

overall_design: To investigate the mechanism by which TREM-2 knockout macrophages-derived exosomes could alleviate the renal fibrosis, and to identify the differentially expressed genes between the TREM-2 knockout and WT macrophages.

first: Zihao

last: Xiao

first: Yajie

last: Wang

first: Yuye

first: Ling

last: Jin

first: Cong

last: Fu

first: Yuhan

last: Cao