title: Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [shRNAscreen]

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institut of Molecular Tumor Biology

institute: University Hospital Münster

summary: Transcription factors (TFs) orchestrating lineage-development also control genes required for cellular survival. One such TF is PU.1, which is essential for myeloid development. Mice with downregulated PU.1 levels develop fatal acute myeloid leukemia (AML). However, because PU.1 is required for expression of growth factor receptors and signaling molecules, it has been unclear how PU.1-downregulated progenitors survive long enough to acquire additional alterations promoting leukemic transformation. Combining a multi-omics approach with a functional genetic screen, we reveal herein that growth of PU.1-downregulated progenitors is secured by shifting survival control from cytokine-dependency towards overactivation of an autophagy-predominated stem cell program. This shift (for which we also find evidence in human AML) is linked to redirected binding of the PU.1 partner TF RUNX1 to chromatin sites previously not co-bound by PU.1. Hence, partner TF reallocation at chromatin can induce autophagy as a cell-autonomous failsafe mechanism to rescue cells from survival deficits caused by TF loss. Such growth-compensatory effects should be taken into account when considering TF as targets in cancer therapy.

overall_design: Focused shRNA screen targeting a specific gene signature (see our manuscript for details) of about 340 genes plus killing (Psma1, Polr2b, Rpl30) and non-targeting (luciferase) controls in three cell lines: HoxWT, HoxURE (both immortalized hematopoietic progenitors from wildtype or UREd/d knockout mice) or B22 (in the manuscript called URE-AML, established from AML blasts of a UREd/d mouse with severe AML). shRNA library was transfected by lentivirus into the cell lines in three independent biological replicates, and either harvested 24h after transfection (input control) or once 10 cell divisions had happened ("final" library). Final vs input counts were used in MAGeCK to define "essential" genes that promote survival and proliferation.

first: Alexander

last: Bender


title: Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [ChIP-seq]

status: Public on Nov 15 2024

country: Germany

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq towards RUNX1 or IgG control in THP-1 cell line. THP-1 either with inducible PU.1 shRNA-mediated knockdown or scramble control.

first: Fuesun

last: Boydere


title: Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [RNAseq_Mice]

type: Expression profiling by high throughput sequencing

overall_design: FACS-sorted LSK and GMP from bone marrow of wildtype and UREd/d knockout mice were subjected to low-input RNA-seq.


title: Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [scRNAseq]

overall_design:
FACS-sorted Lin-negative cKit-positive bone marrow cells (hematopoietic progenitors) were subjected to 10x Chromium v3 scRNA-seq. One 10x reaction was used per sample, in total we assayed 4 samples (2 from WT mice, 2 from UREd/d mice) so 2 vs 2 in terms of biological replicates, total about 20,000 cells. Cells from each replicate are from one mouse, no pooling was performed.

Supplementary files contain both the raw- and normalized counts with column and row annotations for both the "unfiltered" data that went into downstream analysis in R as well as for the "filtered" one which is the data after all processing and filtering in the downstream analysis was applied.


title: Exploring the mechanism of Streptococcus agalactiae infecting tilapia intestinal tissue based on transcriptomics

city: Qinzhou City

first: Xin

last: Lu

address: 12 Binhai Avenue, Qinnan District, Qinzhou City, Guangxi, China

country: China

institute: Beibu Gulf University

summary: The aim of this study is to investigate the mechanism of Streptococcus agalactis invading the intestine of tilapia

overall_design: Comparative gene expression profiling analysis of RNA-seq data for challenge experimental group and control group

first: Xiaohui

last: Cai

first: Yinhui

last: Peng

first: Xiin

first: Xu


title: Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [ATAC-seq]

overall_design: FACS-sorted LSK and GMP from bone marrow of wildtype and UREd/d knockout mice were subjected to ATAC-seq following the OmniATAC protocol.


title: Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [RNAseq_Cell lines]

overall_design: RNA-seq from three cell lines, being two immortalized hematopoietic progenitor lines established from wildtype and UREd/d knockout mice (HoxWT, HoxURE), and an AML blast cell line (B22, in the paper called URE-AML), established from AML blasts of a HoxURE mouse that developed leukemia.


title: Sequential transcriptomic alterations in the cerebral cortex of mice after cerebral venous sinus thrombosis

city: Wuhan

first: Ding

last: rui

address: 99 Zhang Zhidong Street

institute: Renmin Hospital of Wuhan University

summary: To investigate the expression alterations of specific genes that occur after venous stroke

overall_design: We identified differentially expressed genes (DEGs) between sham and damaged cortical tissues at 2 and 7 days after induction of cerebral venous sinus thrombosis (CVST) model via RNA-sequencing (RNA-seq) analysis

first: Rui

last: Ding

first: Jing

last: Chen

first: Huihui

last: Chai

first: Zhibiao


title: Single-cell analysis reveals transcriptomic difference between human hypertrophic scar and keloid

city: Shanghai

first: Jia

last: Zhou

state: --- Select One ---

address: 639 Zhizaoju Road, Shanghai

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

summary:
Background Hypertrophic scars and keloids are both pathological scars with similar appearance and pathological features. Currently, the differential diagnosis of the two mainly depends on the subjective judgment of physicians, and there is a lack of objective diagnostic indicators and treatment methods.
Objectives To provide single-cell level evidence and new approaches for the differential diagnosis and clinical treatment of hypertrophic scars and keloids.
Methods Single-cell RNA sequencing (scRNA-seq) was performed on a hypertrophic scar and a keloid tissue from the same patient to compare the differences in the cellular and tissue microenvironments of the two conditions.
Results ScRNA-seq results depicted the distribution of cell subpopulations and different microenvironments between hypertrophic scars and keloids.
Conclusions The results of the analysis showed significant differences in cell subcluster distribution and cell communication between hypertrophic scars and keloids. This study demonstrated the potential of scRNA-seq to differentiate the two conditions and provide a new approach to refine differential diagnosis and a possible target for therapeutic research.

overall_design: The keloid tissue and the hypertrophic scar tissue from a 34-year-old female patient. The keloid tissue was surgically excised from the anterior chest area and hypertrophic scar tissue from the lower abdomen. Both pathological scar tissues were digested separately into single-cell suspensions and analyzed using droplet-based scRNA-seq.

first: Xinwei

last: Cheng

first: Shengzhou

last: Shan

first: Zhen

last: Gao


title: Transcriptomics of mouse bone marrow erythropoiesis

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

summary: Metabolic requirements vary during tissue development, but little is known whether and how metabolic rewiring orchestrates lineage differentiation and maturation. We discovered an essential metabolic switch from glutamine catabolism to glutamine synthesis during erythropoiesis. Glutamine synthetase (GS), one of the oldest functioning genes, is induced during terminal maturation to promote detoxification of ammonia generated during heme biosynthesis, which is massively upregulated to support hemoglobin production. Loss of GS in mouse erythroid precursors causes ammonia accumulation, oxidative stress, leading to maturation arrest and apoptosis. In β-thalassemia, GS activity is impaired by protein oxidation, causing glutamate and ammonia accumulation, whereas enforced GS expression alleviates the metabolic and pathologic defects. These results identify an evolutionarily conserved metabolic adaptation that may be leveraged to treat common red cell disorders.

overall_design: RNA-seq was performed to determine the transcriptomic changes in flow cytometry-enriched bone marrow (BM) erythroid cells.

first: Yuannyu

last: Zhang


title: SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain

city: Stuttgart

first: Thyagarajan

last: Thiruvanmiyur Chandrasekaran

address: Allmandring 31

department: Biochemistry

institute: University of Stuttgart

summary: SETDB1 is a major H3K9 methyltransferase. It contains a unique Triple Tudor Domain (3TD) which specifically bind the dual modification of H3K14ac in the presence of H3K9me1/2/3. In this study, we explored the role of the 3TD H3K14ac interaction in the H3K9 methylation activity by SETDB1. We generated the 3TD binding reduced F332A mutant and demonstrate in biochemical methylation assays on recombinant nucleosomes containing H3K14ac analogs, that H3K14 acetylation is crucial for the 3TD mediated recruitment of SETDB1. We also see this effect in the cells where SETDB1 binding and activity was globally correlated with H3K14ac, and knock-out (KO) of the H3K14 acetyltransferase HBO1 caused a drastic reduction in the H3K9me3 levels at SETDB1 dependent sites. Further analyses revealed that 3TD was not required for SETDB1 recruitment for regions targeted by KAP1, but at specific target regions, SETDB1 KO could not be efficiently reconstituted by a 3TD mutant of SETDB1 as shown by the finding that H3K9 methylation of L1M repeat elements is highly dependent on an intact 3TD. In summary, our data demonstrate an important role of the 3TD interaction with H3 tails containing K14ac and K9 methylation in the recruitment of SETDB1 to chromatin which is particularly relevant at L1M repeats.

overall_design: Native Chromatin immunoprecipitation-sequencing (ChIP-Seq) of histone modification H3K9me3 and H3K14ac from HCT116 cells

middle: T

last: Chandrasekaran

first: Pavel

last: Bashtrykov

first: Albert

last: Jeltsch


title: Effects of lipid loading on splenic cDC2s

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: To investigate the effect of lipid loading on DCs, cDC2 are isolated from the spleen from mice that are fed a Western-type diet and RNAseq was utilized to analyze the gene expression

overall_design: Gene expression profiling using RNAseq

first: Emiel

last: van der Vorst

first: Erik

last: Biessen

first: Aaron

last: Isaacs


title: Spinal cord bulk RNA sequencing of an EAE mouse model of multiple sclerosis

status: Public on Nov 14 2024

city: Cambridge

first: Timothy

middle: R

last: Hammond

state: MA

address: 350 Water Street

institute: Sanofi

summary: We used the MOG35-55 peptide induction experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis to determine whether Bruton's tyrosine kinase (BTK) inhibition could attenuate disease-relevant changes to central nervous system gene expression.

overall_design: Spinal cord was collected from a C57BL/6 experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis. Bulk RNA sequencing was then performed. A subset of mice had been treated with an inhibitor of Bruton’s tyrosine kinase (BTK) after disease induction.


title: Sec15 Controls STAT3 Traffic Direction to Modulate Hematopoietic Stem Cell Fate

first: Mingdian

last: Tan

state: Shanghai

address: No. 320, Yueyang Rd, Xuhui District

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: To advance the development of our gene expression approach in uncovering regulatory pathways, we utilized whole-genome microarray expression profiling as a discovery platform to identify genes that could illuminate the role of the Sec15 gene. Liver tissues from Sec15 knockout and control mice were collected at six weeks of age to perform comparative analyses. This approach aimed to identify key gene expression changes linked to Sec15 deficiency

overall_design: Sec15 knockout and control mice did not receive any treatment

first: Y

middle: E

last: Chin


title: Single-cell transcriptome unravels spermatogonial stem cells and dynamic heterogeneity of spermatogenesis in seasonal breeding teleost

city: Zhoushan

first: Yang

last: Yang

state: China

address: No. 10,  Tiyu Road

institute: Zhejiang province marine fisheries research institute

summary: We characterized spermatogenesis in the large yellow croaker (Larimichthys crocea), a marine fish of significant commercial value, based on a high-resolution single-cell RNA-seq atlas of testicular cells from three distinct developmental stages- juvenile, adult differentiating and regressed testes. We detailed continuous developmental trajectory of spermatogenic cells, from spermatogonia to spermatids, elucidating the molecular events involved in spermatogenesis. We uncovered dynamic heterogeneity in cellular compositions throughout the annual reproductive cycle, accompanied by strong molecular signatures within specific testicular cells. Notably, we identified a distinct population of SSCs and observed a critical metabolic transition from glycolysis to oxidative phosphorylation, enhancing our understanding of the biochemical and molecular characteristics of SSCs. Additionally, we elucidated the interactions between somatic cells and spermatogonia, illuminating the mechanisms that regulate SSCs development. Overall, this work enhances our understanding of spermatogenesis in seasonal breeding teleost and provides essential insights for the further conservation and culture of SSCs.

overall_design: three samples from fish testicular tissues

first: Yinan

last: Zhou

first: Dongdong


title: A testis-specific long non-coding RNA, 1700052I22Rik, regulates spermatid chromatin condensation in mice

city: Beijing

first: Mengzhen

last: Li

address: 5 DONG DAN SAN TIAO

institute: Peking Union Medical College

summary: Long non-coding RNA (lncRNA), as diverse functional regulators, are abundantly expressed in the testis. However, lncRNAs preferentially or exclusively expressed in the testis remain largely unknown. Here, we report a testis-specific lncRNA, 1700052I22Rik, which exhibits a dynamic expression pattern during spermatogenesis. Our findings demonstrate that knockout of 1700052I22Rik in mice leads to reduced sperm counts and subfertility in males, as well as defective spermatid chromatin condensation. We further elucidate the underlying mechanism by which 1700052I22Rik modulates the translation of protamine 1 (PRM1) through interaction with Y-box binding protein 2 (YBX2). Collectively, our results uncover a crucial role for the testis-specific lncRNA 1700052I22Rik in regulating spermatid chromatin condensation in mice, providing novel insights into the functions of lncRNAs in spermatogenesis and potential targets for the diagnosis and treatment of male infertility.

overall_design: To investigate 1700052I22Rik function in the regulation of spermatogenesis, we conducted RNA sequencing (RNA-seq) analysis of the WT and 1700052I22Rik-KO testes.


title: Leveraging large-scale datasets and single cell omics data to develop a polygenic score for cisplatin-induced ototoxicity

city: Winnipeg

first: Britt

last: Drögemöller

state: Manitoba

address: 309C-745 Bannatyne Avenue

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

summary:
Background
Cisplatin-induced ototoxicity (CIO), characterized by irreversible and progressive bilateral hearing loss, is a prevalent adverse effect of cisplatin chemotherapy. Alongside clinical risk factors, genetic variants contribute to CIO and genome-wide association studies (GWAS) have highlighted the polygenicity of this adverse drug reaction. Polygenic scores (PGS), which integrate information from multiple genetic variants across the genome, offer a promising tool for the identification of individuals who are at higher risk for CIO. Integrating large-scale hearing loss GWAS data with single cell omics data holds potential to overcome limitations related to small sample sizes associated with CIO studies, enabling the creation of PGSs to predict CIO risk.
Results
We utilized a large-scale hearing loss GWAS and murine inner ear single nuclei RNA-sequencing (snRNA-seq) data to develop two polygenic scores: a hearing loss PGS (PGSHL) and a biologically informed PGS for CIO (PGSCIO). The PGSCIO included only variants which mapped to genes that were differentially expressed within cochlear cells that showed differential abundance in the murine snRNA-seq data post-cisplatin treatment. Evaluation of the association of these PGSs with CIO in our target CIO cohort revealed that PGSCIO demonstrated superior performance (P = 5.54 × 10− 5) relative to PGSHL (P = 2.93 × 10− 3). PGSCIO was also associated with CIO in our test cohort (P = 0.04), while the PGSHL did not show a significant association with CIO (P = 0.52).
Conclusion
This study developed the first PGS for CIO using a large-scale hearing loss dataset and a biologically informed filter generated from cisplatin-treated murine inner ear snRNA-seq data. This innovative approach offers new avenues for developing PGSs for pharmacogenomic traits, which could contribute to the implementation of tailored therapeutic interventions. Further, our approach facilitated the identification of specific cochlear cells that may play critical roles in CIO. These novel insights will guide future research aimed at developing targeted therapeutic strategies to prevent CIO.

overall_design: 6-day old CBA/CaJ mice (treatment: n=6, control: n=6; with equal males and females) received intraperitoneal injections of 3mg/kg cisplatin or saline. Mice were euthanized 4-hours post-cisplatin administration, and whole cochlear ducts were dissected from their inner ears.

first: Deanne Nixie

last: Miao

first: Mackenzie

last: Wilke

first: John

last: Pham

first: Feryal

last: Ladha

first: Mansumeet

last: Singh

first: Janilyn

last: Arsenio

first: Emilia

last: Luca

first: Alain

last: Dabdoub

last: Wejian

first: Jun

middle: J

middle: I


title: LeuO fine-tunes the virulence attributable to Salmonella pathogenicity island-2 via repressing ssrA transcription in Salmonella Typhimurium

city: Suwon

first: Eunsuk

last: Kim

address: 206 World cup-ro, Yeongtong-gu

country: South Korea

institute: Ajou University

summary: LeuO, initially identified as a leucine regulator in Escherichia coli, has since been identified as a global regulator required for bacterial pathogenicity in a broad range of bacteria, including gram-negative pathogens, such as Salmonella, Shigella, and Vibrio; and gram-positive bacteria, such as Streptococcus pneumoniae. However, the regulatory roles and targets of LeuO vary among species. In the Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), LeuO represses the transcription of Salmonella pathogenicity island (SPI)-1, thus diminishing the ability of the bacteria to invade host cells. However, its regulatory effect on SPI-2, essential for survival within macrophages, remains poorly understood. This study aimed to determine the regulatory role of LeuO in the intracellular persistence of S. Typhimurium. Overexpression of LeuO repressed the transcription of SPI-2 genes and accordingly decreased its protein levels. Chromatin immunoprecipitation sequencing revealed the genome-wide binding sites of LeuO in S. Typhimurium 14028 and identified a distinctive 23-nucleotide motif with high similarity to that previously discovered in E. coli. Notably, multiple LeuO-binding sites were predicted within SPI-2, primarily adjacent to the ssrA and ssrB loci. In vitro binding assays verified the high binding affinity between LeuO and three specific motifs located at positions -35 to -12 (ssrA1),+231 to +254 (ssrA2) near ssrA, and at positions -622 to -599 (ssrB3) near ssrB, relative to their transcription start sites. Furthermore, LeuO overexpression abolished the transcription of lacZ fused to the ssrA promoter containing ssrA1 and ssrA2, suggesting the direct repression of ssrA via LeuO-binding. The absence of LeuO increased the intracellular survival of S. Typhimurium within macrophages, whereas its overexpression attenuated bacterial persistence, which was presumably associated with the downregulation of SPI-2 by LeuO. This study reveals the versatile regulatory mechanisms of LeuO and underscores its pivotal role in modulating SPI-2 expression, thereby providing key insights into the fine tuning of virulence by Salmonella during systemic infection.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Chromatin immuniprecipitation DNA-sequencing (ChIP-seq) of LeuO in Salmonella Typhimurium 14028

first: Eumnsuk

first: Hyunjin

last: Yoon


title: Effects of LIFR inhibition using EC359 on TNBC cells in obesity conditions

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: In a study using syngeneic BALB/c mice, the impact of a high-fat diet (HFD) on triple-negative breast cancer (TNBC) progression was investigated using 4T1 cells. Mice were fed either a low-fat diet (LFD) or HFD for six weeks before receiving orthotopic injections of 4T1 cells. Post-tumor formation, mice were randomized into three groups: LFD, HFD, and HFD with EC359 treatment. Results indicated that HFD significantly enhanced tumor growth, while EC359 treatment notably reduced HFD-induced TNBC progression. To explore underlying mechanisms, global RNA sequencing was performed on tumor tissues, revealing that HFD altered the expression of 578 genes compared to LFD, with 325 genes differentially expressed between the HFD and HFD + EC359 groups. Gene set enrichment analysis showed that HFD-related genes were linked to cytokine signaling, inflammation, stem cell pathways, TGFβ, metastasis, and epithelial–mesenchymal transition, all of which were downregulated with EC359 treatment.

overall_design: Nine tumors derived from mouse 4T1 syngeneic xenograft models were processed, 3 each for LFD, HFD and HFD+EC359 treatments were processed for transcriptomic profiling and comparisons between different conditions.

first: Suryavathi

last: Viswanadhapalli

first: Panneerdoss

last: Subbarayalu

first: Lai

last: Zhao


title: Farnesyl diphosphate synthase inhibition remodels the tumor immune microenvironment by activating endogenous retroviruses

first: yanyan

last: zhu

state: Beijing

address: 10 Xitoutiao, Youanmen Wai, Fengtai District

institute: Chinese Institutes for Medical Research, Beijing

summary: Farnesyl diphosphate synthase (FDPS) is a crucial enzyme in isoprenoid and cholesterol biosynthesis and the target for nitrogen-containing bisphosphonate (N-BP) drugs widely used for osteoporosis treatment. Here we show that FDPS inhibition overcomes tumor resistance to immune checkpoint blockade (ICB) therapy by activating endogenous retroviruses (ERVs) and promoting a potent type I interferon response. FDPS inhibition, either by genetic knockout or alendronate, enhances the efficacy of ICB therapy substantially in multiple murine tumors by remodeling the immune microenvironment and enhancing lymphocyte infiltration, which is caused by increased type I interferon upregulation. Mechanistically, FDPS inhibition attenuates mitochondrial membrane potential (MtMP), enabling endonuclease G (EndoG) migration from the mitochondria into the nucleus, increasing DNA double-strand breaks and degradation of the heterochromatin maintenance protein TRIM28(KAP1), promoting enhanced ERV transcription and activation of the MDA5/MAVS pathway. The ensuing type I interferon upregulation is responsible for enhanced antigen presentation and sensitization to ICB therapy.

overall_design: Because of the synergy observed between FDPS deficiency and ICB treatment, we next sought to characterize the tumor immune microenvironment (TIME) in FDPS-deficient tumors. For this purpose, we sorted CD45+ live immune cells from subcutaneously engrafted control and FDPSKO B16F10 tumors and conducted single-cell RNA sequencing (scRNA-seq).


city: Changchun

first: Xiaorui

last: Yang

address: Xincheng Street

institute: Jilin Agricultural University

summary: Exploring the effect of m6A methylation modification on the progression of bovine ovary tissue before and after the onset of puberty

first: Ziming

last: Wang

first: Wenfa

last: Lu


title: Transcriptomics of SGLT2-positive early proximal tubule segments in mice: response to type 1 diabetes, SGLT1/2 inhibition or GLP1 receptor agonism

city: San Diego

first: Young Chul

address: 3350 La Jolla Village Dr

institute: University of California-San Diego

summary: SGLT2 inhibitors (SGLT2i) and GLP1 receptor (GLP1R) agonists have kidney protective effects. To better understand their molecular effects, RNA sequencing was performed in SGLT2-positive proximal tubule segments isolated by immunostaining-guided laser capture microdissection. Male adult DBA wildtype (WT) and littermate diabetic Akita mice ± Sglt1 knockout (Sglt1-KO) were given vehicle or SGLT2i dapagliflozin (dapa; 10mg/kg diet) for 2 weeks, and other Akita mice received GLP1R agonist semaglutide (sema; 3nmol/[kg body weight*day], s.c.). Dapa (254±11mg/dL) and Sglt1-KO (367±11mg/dL) but not sema (407±44mg/dL) significantly reduced hyperglycemia in Akita mice (480±33mg/dL). The 20,748 detected annotated protein-coding genes included robust enrichment of S1-segment marker genes. Akita showed 198 (~1%) differentially expressed genes vs. WT (DEGs; adjusted p<0.1) including downregulation of anionic transport, unsaturated fatty acid and carboxylic acid metabolism. Dapa changed only 2 genes in WT but restored 43% of DEGs in Akita, including upregulation of lipid metabolic pathway, carboxylic acid metabolism and organic anion transport. In Akita, sema restored ~10% of DEGs, and Sglt1-KO and dapa were synergistic (restored ~61%) possibly involving additive blood glucose effects (193±15mg/dl). Targeted analysis of transporters and channels (t-test p<0.05) revealed that ~10% of 526 detectable transporters and channels were downregulated by Akita, with ~60% restored by dapa. Dapa, dapa+Sglt1-KO and sema also altered Akita-insensitive genes. Among DEGs in Akita, ~30% were unresponsive to any treatment, indicating potential new targets. In conclusion, SGLT2i restored transcription for multiple metabolic pathways and transporters in SGLT2-positive proximal tubule segments in diabetic mice, with a smaller effect also observed for GLP1R agonism.

overall_design: Fourteen week old non-diabetic DBA male mice (Ins2+/+) with Sgl1+/+ or Sglt1-/- were treated with vehicle or dapagliflozin (10mg/kg diet) for 2 weeks, and littermate diabetic DBA male mice (Ins2 Akita/+) with Sglt1+/+ or Sglt1-/- were treated with vehicle, dapagliflozin (10mg/kg idet) or semaglutide (3nmol/kg body weight per day), subcutaneous injection) for 2 weeks. SGLT2-positive early proximal tubules were isolated by laser capture microdissection for RNA sequencing.

first: Vivek

last: Das

first: Sadhana

last: Kanoo

first: Huazhen

last: Yao

first: Stephanie

middle: M

last: Stanford

first: Nunzio

last: Bottini

first: Anil

last: Karihaloo

first: Volker

last: Vallon


title: StitchR: Ribozyme-activated mRNA Trans-ligation and Translation

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

summary: We report that ribozyme cleavage of two separate mRNAs activated their scarless trans-ligation and translation into full-length protein in eukaryotic cells, a process that we named StitchR (for stitch RNA).

overall_design: StitchR 3.0 Nt-GFP and Ct-GFP AAV1-serotyped virus particles were generated and used to co-transduce HEK293T cells. Cells were harvested 48 hours post-transduction.


title: A single-cell atlas of the mouse Multiple Myeloma immune microenvironment during tumor progression

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Here, we mapped the immune compartment in the bone marrow and spleen of the immunocompetent 5T33MM Multiple Myeloma mouse model, using scRNA-seq analysis. This revealed distinct cell types as well as their dynamics in both naive mice and at various disease stages of MM, illustrating the evolving immune landscape during MM progression.

overall_design: scRNA-seq on the 7-AAD- CD45+ 3H2-/CS1- immune cells from bone marrow and spleen of naive and 5T33MM mice.

first: Emma

last: Verheye


title: Effects of AEBP1 knockdown on gene expression profiles in human skeletal muscle myoblasts

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

summary: We recently identified adipocyte enhancer binding protein 1 (AEBP1) as a novel cancer stroma-associated gene and reported that AEBP1 activates cancer-associated fibroblasts in oral cancer. In this study, we show that AEBP1 is negatively associated with skeletal muscle cell differentiation. We found that AEBP1 is downregulated during the diffraction of human skeletal muscle myoblasts (HSMMs). Microarray analysis revealed that knockdown of AEBP1 significantly upregulated a number of genes associated with myogenesis in HSMMs. Notably, co-culture of HSMMs with oral squamous cell carcinoma cells resulted in downregulation of muscle-related genes and upregulation of AEBP1 in HSMMs.

overall_design: For knockdown of AEBP1, 5^10E4 cells were transfected with Silencer Select Pre-designed siRNA (100 pmol each; AEBP1 siRNA1, s1145; AEBP1 siRNA2, s1146; Thermo Fisher Scientific) or Silencer Select Negative Control No. 1 siRNA (Thermo Fisher Scientific) using TransIT-X2 Dynamic Delivery System (Mirus Bio, Madison, WI, USA). Cells were harvested 72 h after transfection. For co-culture experiments, HSMMs (5^10E4 cells/well in 6-well plates) were indirectly co-cultured with OSCC cells (1^10E5 cells in culture inserts) for 72 h.

first: Akira

last: Yorozu


title: Involvement of Wnt/β-catenin Signaling Pathway in Curdione-Induced Reproductive Toxicity Revealed by Multiomics Profiling in HTR-8/SVneo Cells

city: Fuzhou

first: Jiaxin

last: Wen

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

summary: This study aims to explore the mechanism of curdione-induced toxicity damage in HTR-8/SVneo cells through the epigenetics, proteomics, and metabolomics, and experimental verification.

overall_design: Curdione exposure induces ROS accumulation, mitochondrial dysfunction, DNA damage and disruption of tight junctions in HTR-8/SVneo cells.

first: Qibin

last: Wu

first: Mengting

last: Chen

first: Yifan

last: Lin

first: Jian

last: Zhang


title: Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [Hi-C]

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

summary: Medulloblastoma is the most common malignant brain tumor of childhood. The highest-risk tumors are driven by recurrent Myc amplifications (Myc-MB) and experience poorer outcomes despite intensive multimodal therapy. The Myc transcription factor defines core regulatory circuitry for these tumors and acts to broadly amplify downstream pro-survival transcriptional programs. Therapeutic targeting of Myc directly has proven elusive, but inhibiting transcriptional cofactors may present an indirect means of drugging the oncogenic transcriptional circuitry sustaining Myc-MB. Independent CRISPR-Cas9 screens were pooled to identify conserved dependencies in Myc-MB. We performed chromatin conformation capture (Hi-C) from primary patient Myc-MB samples to map enhancer-promoter interactions. We then treated in vitro and xenograft models with the dual CDK9/7 inhibitor zotiraciclib to evaluate effect on Myc-driven programs and tumor growth. Eight CRISPR-Cas9 screens performed across three independent labs identify CDK9 as a conserved dependency in Myc-MB. Myc-MB cells are susceptible to CDK9 inhibition, which is synergistic with concurrent inhibition of CDK7. The dual CDK9/7 inhibitor zotiraciclib disrupts enhancer-promoter activity in Myc-MB and downregulates Myc-driven transcriptional programs, exerting potent anti-tumor effect.

overall_design: Formalin fixed, paraffin embedded primary patient tumor samples were subjected to DNA extraction for chromatin conformation sequencing (Hi-C).

first: Nathan

last: Dahl

first: Rajeev

last: Vibhakar

first: Lays

last: Martin Sobral


title: SeedMatExplorer: The transcriptome atlas of Arabidopsis seed maturation

city: Wageningen

first: Mariana

middle: Aline

last: Silva Artur

address: Droevendaalsesteeg 1

department: Plant Sciences

institute: Wageningen University & Research

summary: During their maturation, seeds acquire traits that are crucial for their survival and that are of extreme importance for seed quality. In this study, we investigate the acquisition of multiple seed quality traits, especially desiccation tolerance and longevity, by analyzing longitudinal RNA-seq data collected for various stages of seed maturation. The data was acquired for several mutants, predominantly affected in abscisic acid biosynthesis and signalling, which vary in their ability to acquire seed quality traits.

overall_design: Seeds were harvested during their maturation stage, from 12 DAP to 26 DAP, in 2 days intervals. This was done for several abscisic acid biosynthesis and signalling related mutants, that show reduced acquisiton of seed quality traits.

middle: A

first: Robert

last: Koetsier

first: Leo

middle: W

last: Willems

first: Lars

last: Bakermans

first: Annabel

last: van Driel

first: Joram

last: Dongus

first: Bas

last: Dekkers

first: Alexandre

middle: C

last: Silva de Santana Marques

first: Harm

last: Nijveen

first: Leónie

last: Bentsink

first: Henk

last: Hilhorst

first: Renake

last: Nogueira Teixeira


title: High-throughput sequencing for lacrimal sacs from chronic dacryocystitis patients and normal controls

city: Shanghai

first: yue

last: li

state: None Selected

address: No.639 Zhi Zao Ju Road, 200011, Shanghai, P.R. China

institute: Shanghai Jiaotong University

summary: We report the application of whole transcriptome sequencing technology for high-throughput profiling of lacrimal sacs from chronic dacryocystitis patients and normal controls.  Differently expressed mRNAs and circRNAs were used for co-expression analysis.   The expression levels of mRNAs and circRNAs in control and chronic dacryocystitis samples were validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Among all the 3909 circRNAs predicted from RNA sequencing data, 25 circRNAs (20 up regulated and 5 down-regulated) were differentially expressed in chronic dacryocystitis samples. Besides, 1486 differentially expressed mRNAs were identified.  This study identified statistically significant differences between circRNAs and mRNAs of lacrimal sac samples of chronic dacryocystitis patients and control individuals. Of these differently expressed circRNAs and mRNAs, eight were validated by qRT-PCR, including MYH2, DSP, CD27, CCL5, FN1, has_circ_0004792, has_circ_0001062 and has_circ_0115476. This study suggested the differentially expressed circRNAs might participate in pathogenesis of chronic dacryocystitis, and it is therefore reasonable to consider circRNAs as potential therapeutic targets in treating chronic dacryocystitis patients.

overall_design: High-throughput sequencing of lacrimal sacs from 3 chronic dacryocystitis patients and 3 normal controls

first: Yue

last: Li

first: Xueru

last: Liu

first: Leilei

last: Zhang

first: Caiwen

last: Xiao


title: Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [CUT&RUN]

first: Pluto

last: Bio

overall_design: Myc-amplified D458 cell line was established in culture and then treated with either  TG02 or equivalent DMSO control.  We then performed CUT&RUN analysis for chromatin profiling.

first: Nathan

last: Dahl

first: Rajeev

last: Vibhakar

first: Lays

last: Martin Sobral


title: Patch-Seq of seven 5-HT neuronal subpopulations in zebrafish whole brain

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

summary: The goals of this study is to compare transcriptome profiles (RNA-seq) of seven 5-HT neuronal subpopulations in zebrafish whole brain. Tg(tph2:GFP) fish at 7 dpf were fixed in a recording chamber containing extracellular solution. The somata of 5-HT neurons from seven subpopulations (PT, SR-R, SR-M, SR-C, IR-R, IR-C, MO) were visualized under a fluorescence microscopy, then targeted and collected separately using glass electrode. For each sample, 10-12 neurons were collected and transferred to lysis buffer solution. Total RNA was extracted for construction of cDNA libraries, involving fragmentation, PCR enrichment, N7 index linking, and purification. A total of 71 QuantSeq libraries (N=9-12 samples for each subpopulation) were prepared using the Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina according to the manufacturer’s instructions. Sequencing was carried out using Illumina NovaSeq 6000 with 150 bp paired-end reads. Gene expression level analysis was performed using R (Version 4.3.1) package Seurat (Version 5.0.2), and the mean gene expression matrix of all samples was obtained after processing by NormalizeData function. For marker gene analysis of each subpopulation, FindAllMarkers function in Seurat was used, with parameters set as min.pct=0.1 and logfc.threshold=0.25. Differential expression analysis revealed that each subpopulation expressed a set of featured genes, including specific markers for neurotransmitters, axon projection, neuron development, synapse, and ion channels, suggesting that seven 5-HT neuronal subpopulations display distinct genetic profiles.  We demonstrated that seven 5-HT neuronal subpopulations are molecularly discriminative by expressing distinct molecular markers.

overall_design: To compare transcriptome profiles (RNA-seq) of seven 5-HT neuronal subpopulations in zebrafish whole brain, Tg(tph2:GFP) fish at 7 dpf were fixed in a recording chamber containing extracellular solution, and neurons were collected separately with glass pipette. A total of 71 QuantSeq libraries (N=9-12 samples for each subpopulation) were prepared using the Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina according to the manufacturer’s instructions.

first: Jianren

last: Song

last: Guan

first: Ziqi

first: Chunxiao


title: ATP Citrate Lyase Drives Vascular Remodeling Diseases Development Through Metabolic-Epigenetic Reprograming.

city: Quebec city

first: Francois

last: Potus

address: 2725 Ch Ste-Foy

institute: IUCPQ-Laval university

summary: Our study explores the previously uncharted role of ATP-citrate lyase (ACLY) in vascular remodeling within the pulmonary and coronary circulations, providing novel insights into the pathogenesis of pulmonary hypertension and coronary artery diseases. ACLY, known for its involvement in de novo lipid synthesis and histone acetylation, emerges as a key regulator in sustaining vascular smooth muscle cell proliferation and survival. Utilizing rare human coronary and pulmonary artery tissues, our findings reveal an upregulation of ACLY expression during vascular remodeling processes. Inhibition of ACLY, achieved through pharmacological and molecular interventions in humans primary cultured vascular smooth muscle cells, leads to decreased proliferation, migration, and resistance to apoptosis. Mechanistically, these effects are associated with diminished glycolysis, lipid synthesis, GCN5-dependent histone acetylation, and FOXM1 activation. In vivo experiments, combining pharmacological and VSMC-specific ACLY knockout mice, ACLY inhibition demonstrate its efficacy in mitigating systemic vascular remodeling and reducing pulmonary hypertension. Notably, initiating ACLY inhibition post-disease onset reverses pathological conditions, positioning ACLY as a promising therapeutic target. Human ex-vivo tissue culture further supports our findings, showcasing reduced vascular remodeling in cultured human coronary artery rings and a reversal of pulmonary artery remodeling in precision-cut lung slices upon ACLY inhibition. This study introduces a groundbreaking concept, linking disparate abnormalities in vascular diseases to a common pathogenetic denominator, ACLY. The identified "multiple-hit" therapeutic approach presents potential targets for addressing complex vascular diseases, offering avenues for future clinical interventions.

overall_design: Our study delineates the pivotal role of ATP-citrate lyase in pulmonary hypertension and coronary artery diseases.

first: Boucherat

last: Olivier

first: Bonnet

last: Sebastien


title: The epitranscriptional factor PCIF1 orchestrates CD8+ T cell ferroptosis and activation to govern anti-tumor immunity

city: ,Wuhan

first: Bolin

last: Xiang

address: Donghu Road, No. 115, Wuchang District

institute: Medical Research Institute and Frontier Science Center for lmmunology and Metabolism of Wuhan University

summary: Pcif1 KO mice can significantly inhibit tumor growth. We attempted to explore the changes in tumor immune microenvironment of tumor-bearing mice after Pcif1 KO by single-cell sequencing.

overall_design: The tumors of the LLC subcutaneous tumor model of Pcif1 KO and WT mice were ground into single-cell suspension, and single-cell sequencing was performed


title: Spatial transcriptomics reveals molecular cues underlying the site specificity of the adult mouse oral mucosa and its stem cell niches

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

summary: The oral cavity is a multifunctional organ composed of structurally heterogeneous mucosal tissues that remain poorly characterised. Oral mucosal tissues are highly stratified and segmented along an epithelial–lamina propria axis. Here, we performed spatial transcriptomics (tomo-seq) on the tongue, cheeks, and palate of the adult mouse to understand the cues that maintain the oral mucosal sites. We define unique and shared molecular markers of cellular niches and differentiation programmes across oral sites. Using a comparative approach, we identify fibroblast growth factor (FGF) pathway components as potential niche factors for oral epithelial stem cells. Using organoid technology, we validated three FGF ligands (FGF1, FGF7, FGF10) as regulators of site-specific stemness in the dorsal and ventral tongue epithelium. Our dataset of the spatially resolved genes across major oral sites represents a comprehensive resource for unravelling the molecular mechanisms underlying the adult homeostasis of the oral mucosa and its stem cell niches.

overall_design: RNA sequencing data generated using RNA extracted from tissue sections of mouse oral mucosal tissues (tomo-seq)

first: Anna

last: Seubert

first: Marion

last: Krafft

first: Sarah

last: Bopp

first: Moutaz

last: Helal

first: Pranjali

last: Bhandare

first: Elmar

last: Wolf

last: Alemany

first: Angela

last: Riedel


title: Effect of IL-33 in bone marrow derived eosinophils

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

institute: Chiba University

summary: This study aimed to investigate the effect of IL-33 in eosinophil in the context of arthritis. To address this, bone marrow derived eosinophils were generated and treated with or without IL-33 for 3 hours. Then total RNAs were subjected to the study.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBS treated (N = 3) and IL-33 (2.5ng/mL, N = 3).

first: Koto

last: Hattori

first: Hiroshi

last: Nakajima


title: Cellular responses in the airway ciliary microenvironment from mouse models of primary ciliary dyskinesia with central pair apparatus defects

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

summary: Dysfunction of motile cilia can impair mucociliary clearance in the airway and result in primary ciliary dyskinesia (PCD), a pediatric syndrome characterized by chronic respiratory infection and bronchiectasis, as well as infertility, laterality defects, and occasionally hydrocephalus due to defects in cilia in other organ systems.  We have previously shown that mutations in genes encoding components of the ciliary central pair apparatus (CPA) perturb ciliary motility and result in PCD in mouse models.  However, little is known about how epithelial cell types in the ciliary microenvironment of the upper airway respond to defects in ciliary motility and mucociliary clearance.  In this study, we have used a single-cell RNA sequencing (scRNA-seq) approach to investigate the effects of ciliary dysfunction on the tracheal epithelial cells from mouse models with mutations in CPA genes Cfap221 (also known as Pcdp1), Cfap54, and Spef2.  Expected cell types were identified in the tracheal epithelial samples, including basal cells, suprabasal cells, secretory cells, deuterosomal cells, ciliated cells, tuft cells, ionocytes, and neuroendocrine cells, as well as an unidentified cell type that does not express markers of typical airway cells.  The deuterosomal cells were found to exist in two states that differ largely in expression of genes involved in differentiation into the ciliated cell type.  Differentially expressed genes (DEGs) were identified for each cell type, and functional enrichment analysis revealed a variety of important cellular functions altered in mutant cells.  Overlapping DEGs shed light on general cellular responses to cilia dysfunction, while unique DEGs indicate that some responses may be specific to the individual mutation and ciliary defect.  These analyses uncover new information about cellular responses to mucociliary clearance defects in the airway and pathogenesis of PCD.

overall_design: Single-cell RNAseq libraries were prepared from isolated trachea from mice with the following mutations: nm1054 line lacking Cfap221, bgh line with a mutation in Spef2, and the Cfap54gt/gt line with a gene-trapped allele of Cfap54. All were maintained on the 129S6/SvEvTac (129) background.

first: Casey

last: McKenzie

first: Reesa

last: Wilcox

first: Oduduabasi

last: Isaiah

middle: S

first: Lance

last: Lee


title: High resolution analysis of heterogeneous alveolar type II cells in emphysema and health reveals an airway origin of impaired alveolar regeneration

status: Public on Nov 19 2024

city: Columbus

first: Yan

last: Hu

state: OH

address: 575 Children’s Crossroad, RB3 6th Floor WB6271

department: Pediatrics

institute: Nationwide Children's Hospital

summary: Emphysema is a major pathological phenotype of chronic obstructive pulmonary disease (COPD) that is characterized by progressive and irreversible alveolar tissue destruction caused by several stressors, such as tobacco smoke and air pollution. It remains incurable in part due to an incomplete understanding of cellular and molecular mechanisms underlying the failure of tissue repair. Here, we have generated a single cell RNA sequencing dataset of enriched epithelial cells from emphysematous parenchymal lung tissue of COPD patients and from healthy controls.  Using this dataset, we performed high resolution analysis of 78,699 ATII cells and reveal novel ATII cell subsets in severe emphysema and health. These include two ATII sub-clusters expressing various secretoglobin mRNAs (SCGBpos) in COPD that present distinct transcriptomic profiles compared to healthy sub-clusters. These ATII sub-clusters that are present in human COPD are also found in a mouse emphysema model.  Importantly, the COPD specific ATII cells from both species demonstrate airway origins and fail to undergo alveolar differentiation in organoid cultures, thereby suggesting that a common mechanism in emphysema pathogenesis.

overall_design: Single cell RNA-seq profiling of murine COPD model

first: Kent

last: Riemondy

first: Melanie

last: Koenigshoff


title: Lipid-restricted culture media reveals unexpected cancer cell sensitivities

city: Adelbert Rd

first: Matthew

last: Atala Pleshinger

state: Ohio

institute: Case Western Reserve University

summary: Cancer cell culture models frequently rely on fetal bovine serum as a source of protein and lipid factors that support cell survival and proliferation; however, serum-containing media imperfectly mimics the in vivo cancer environment.  Recent studies suggest that typical serum-containing cell culture conditions can mask cancer dependencies, for example on cholesterol biosynthesis enzymes, that exist in vivo and emerge when cells are cultured in media that provides more realistic levels of lipids.  Here we describe a high-throughput screen that identified fenretinide and ivermectin as small molecules whose cytotoxicity is greatly enhanced in lipid-restricted media formulations.  Mechanism of action studies indicate that the ivermectin-induced cell death involves oxidative stress, while fenretinide likely targets DEGS1, a lipid desaturase necessary for ceramide synthesis, to induce cell death.  Notably, both fenretinide and ivermectin have previously demonstrated in vivo anticancer efficacy despite their low cytotoxicity under typical cell culture conditions.  These studies reveal ceramide synthesis as a targetable vulnerability of cancer cells cultured under lipid-restricted conditions and suggest a general screening strategy for identifying additional cancer dependencies masked by culture conditions unrepresentative of the in vivo environment.

overall_design: DLD1 cells were cultured in 10% FBS or lipoprotein deficient serum and treated with Fenretinide or Ivermectin


title: The epitranscriptional factor PCIF1 orchestrates CD8+ T cell ferroptosis and  activation to govern anti-tumor immunity

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

summary: T cell-based cancer immunotherapies have revolutionized cancer treatment, yet durable responses remain elusive. Here, we report that PCIF1, an RNA N6, 2’-O-dimethyladenosine (m6Am) methyltransferase, negatively regulates CD8+ T cell anti-tumor responses. Whole-body or T cell-specific Pcif1 knockout (KO) significantly reduces tumor growth in mice. Single-cell RNA sequencing reveals heightened tumor-infiltrating cytotoxic CD8+ T cells in Pcif1-deficient mice. Mechanistically, proteomic and m6Am-sequencing analyses pinpoint that Pcif1 KO elevates crucial m6Am-modified targets, specifically ferroptosis suppressor genes (Fth1, Slc3a2), and T cell activation gene Cd69, imparting resistance to ferroptosis and enhancing CD8+ T cell activation. Of note, Pcif1-deficient mice with tumors exhibit enhanced responses to anti-PD-1 immunotherapy, and Pcif1 KO CAR T cells demonstrate improved tumor control. Clinically, cancer patients with low PCIF1 expression in T cells exhibit enhanced responses to immunotherapies. These findings suggest that PCIF1 suppresses CD8+ T cell activation and targeting PCIF1 as a promising strategy to boost anti-tumor immunity.

overall_design: In order to investigate the regulatory role of epitranscriptional factor PCIF1 in controlling anti-tumor immunity, we studied downstream regulated genes of m6Am through m6Am-seq and RNA-seq.

first: Meiling

last: Zhang

first: Bolin

last: Xiang


title: HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

summary: Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through cophase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF-HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.

overall_design: Refer to individual Series

first: Guoqiang

first: Yaqi

last: Miao

first: Yuan

last: Song

first: Yawei

first: Yuanxiang

last: Zhu

first: Wenxin

first: Qinmiao

last: Sun

first: Dahua

last: Chen


title: IKKα signaling in the nucleus or cytoplasm of keratinocytes leads to opposite skin phenotypes.

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: The skin exerts essential roles for the organism survival, such as environmental barrier and immune functions. IKKα is known as an essential protein for skin homeostasis. However, the functions performed by IKKα in the skin and the mechanisms it employs are largely unknown, leading to contradictory interpretations and results regarding the consequences of its deregulation in pathologies such as non-melanoma skin cancer (NMSC). Here, using our previously generated transgenic mouse models which express IKKα in the cytoplasm (C-IKKα mice) or in the nucleus (N-IKKα mice) of basal keratinocytes, we demonstrate that at each subcellular localization, IKKα distinctly regulates signaling pathways important for maintaining the balance between keratinocyte proliferation and differentiation, as well as the inflammatory response of the skin. As a result, N-IKKα mice show an atrophic epidermis with exacerbated terminal differentiation, reminiscent of alterations observed in patients with ichthyosis. Conversely, C-IKKα mice display a hyperplastic epidermis with impaired epidermal differentiation and pustular inflammation, resembling patients with pustular psoriasis. Interestingly, C-IKKα keratinocytes are almost devoid of nuclear IKKα due to endogenous IKKα downregulation. However, these changes in the skin of C-IKKα mice do not lead to the development of squamous cell carcinomas (SCCs), unlike N-IKKα mice, which develop spontaneous SCCs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for skin from wild type or transgenic mice expressing exogenoues IKKalpha  in the nucleus (N-IKKα mice) and in the cytoplasm (C-IKKα mice) of keratinocytes.

first: Manuel

last: Navarro

first: M

middle: L

last: Casanova

first: Josefa

middle: P

last: Alameda

first: Verónica

last: García-García


title: The characterization of circulating extracellular vesicles and small non-coding RNAs cargo in idiopathic inflammatory myopathies reveals differences across clinically diagnosed myositis subsets

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

summary: Objective. To investigate the epigenetic footprint of idiopathic inflammatory myopathies (IIM) through characterization of circulating extracellular vesicles (EVs) and the expression of EV-derived small non-coding RNAs (sncRNAs).

overall_design: In this cross-sectional study, EVs were isolated by size-exclusion chromatography from plasma of patients with IIM and matched healthy donors (HD). EV-derived sncRNAs were sequenced and quantified using Next-Generation Sequencing (NGS). Following quality control and normalization, filtered count reads were used for differential microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs) expression analyses. Putative gene targets enriched for pathways implicated in IIM were analyzed. Patients’ clinical and laboratory characteristics at the time of sampling were recorded.

first: Alessandra

last: Giannella


title: Transcriptional profiling of CD4+ T cells with high, intermediate and low PD-1 and ICOS co-expression from HCV infected chimpanzees

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: A sustained CD4+ T cell response is required for resolution of acute HCV infection but remains poorly characterized.  Here, CD4+ T cells with high PD-1 and ICOS co-expression expanded in the blood of chimpanzees during acute HCV infection.  The peak response was comprised primarily of HCV-specific populations and temporally associated with acute hepatitis, seroconversion, and initial control of HCV replication. Circulating PD-1hiICOShi CD4+ T cells differentially expressed genes associated with Tfh, Th1, and cytotoxic signatures.  Co-production of Tfh (CXCL13, IL-21) and Th1 (IFN-) effector molecules was observed after HCV antigen stimulation. HCV-specific Tfh1 CD4+ T cells infiltrated liver, consistent with expression of chemokine receptors that mediate homing to inflamed tissues. Most were CXCR5-negative and therefore resembled Tph/Tfhx13 CD4+ T cells recently described in cancer and autoimmune conditions. Detailed transcriptional, phenotypic, and functional analysis of the protective CD4+ T cell response presented here is expected to aid HCV vaccine development.

overall_design: CD4+ T cells from HCV infected chimpanzees were sorted into 3 sub-populations PD-1/ICOS low (n=4), PD-1/ICOS intermediate (n=4) and PD-1/ICOS high (n=5) and transcriptional profililng was performed

first: Heather

last: Blasczyk

first: Bill

last: Bremer

first: Yan

last: Zhou

first: David

last: Bowen

first: Zhaohui

last: Xu

first: Robert

last: Lanford

first: Naglaa

last: Shoukry

first: Arash

last: Grakoui

first: Nicole

last: Skinner

first: Chris

last: Walker


title: Single-cell sequencing reveals cellular heterogeneity of nucleus pulposus in intervertebral disc degeneration

city: Jining

first: Shu

last: Jia

state: Shandong

address: No. 133, Hehua Road, Taibai Lake New District, Jining City

department: Clinical Research Team for Spinal Cord Disorders

institute: Affiliated Hospital of Jining Medical University

summary: Nucleus pulposus (NP) plays a vital role in intervertebral disc degeneration (IVDD). Previous studies have revealed cellular heterogeneity in the NP tissue during IVDD progression. Here, we used single cell RNA sequencing (scRNA-seq) to analyze the cellular and molecular alterations of diverse cell clusters during IVDD.

overall_design: NP tissues were obtained from patients diagnosed with lumbar disc herniation at L4/L5 or L5/S1 levels, who were undergoing endoscopic lumbar discectomy. The removed NP tissues were digested into single cell suspension and analyzed using scRNA-seq.

first: Tao

last: Yang

first: Chunyang

last: Meng


title: Adipose tissue retains an epigenetic memory of obesity after weight loss [snRNAseq]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Reducing body weight to improve metabolic health and related comorbidities is a primary goal in treating obesity. However, maintaining weight loss is a considerable challenge, especially as the body appears to retain an obesogenic memory that defends against body weight changes. Overcoming this barrier for long-term treatment success is difficult because the molecular mechanisms underpinning this phenomenon remain largely unknown. Here, by using single-nuclei RNA-sequencing, we show that both human and mouse adipose tissue retain cellular transcriptional changes after appreciable weight loss. Furthermore, we find persistent obesity-induced alterations in the mouse adipocyte epigenome, negatively affecting their function and response to metabolic stimuli. Mice carrying this obesogenic memory show accelerated rebound weight gain, and the epigenetic memory can explain future transcriptional deregulation in adipocytes in response to further high-fat diet feeding. In summary, our findings indicate the existence of an obesogenic memory, largely based on stable epigenetic changes, in mouse adipocytes, and likely other cell types. These changes appear to prime cells for pathological responses in an obesogenic environment, contributing to the problematic "yo-yo" effect often seen with dieting. Targeting these changes in the future could improve long-term weight management and health outcomes.

overall_design: Male C57BL/6J were subjected to high fat diet (HFD) feeding for 12 or 25 weeks while controls received low fat diet. Thereafter, obese mice were switched to chow diet for 8 weeks. Mice that had been on HFD for 12 weeks and lost weight during 8 weeks and their respective conrols, were subjected to 4 weeks HFD feeding. Epididymal adipose tissue at each time point from treated group and age matched controls was snap frozen and then used for snRNAseq. 5 mice were pooled per sample.

first: Laura

last: Hinte

first: Daniel

last: Castellano-Castillo

first: Ferdinand

last: von Meyenn


title: Adipose tissue retains an epigenetic memory of obesity after weight loss

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


title: IL17A-induced OPN from tumor cells promotes tumor progression by inducing tissue-resident TAM proliferation via LYVE1 [II]

city: Changchun

first: Lei

last: zhao

state: Jilin

address: No. 908 Mingde Street, Changchun City, Jilin Province

department: The First Hospital of Jilin University

institute: Jilin University, Changchun, China

summary: To further understand the downstream mechanism of IL17/IL17R signaling in tumor cells, we performed transcriptome sequencing analysis of 4T1 cells treated with rIL17A

overall_design: KEGG analysis showing the top ten pathways predicted using genes changed significantly in LYVE-1+ TAMs between 4T1WT group and 4T1Opn-KO group. All genes were statistically changed (|log2(FC)|>1.2 & Pvalue <0.05).

last: Zhao

first: Zonghan

last: Wang

first: Yuying

last: Tan

first: Jianan

last: Ma


title: Next Generation Sequencing Quantitative Analysis of exosomes of hepatocellular carcinoma patients and healthy people

city: Guangzhou

first: MinQiang

last: Lu

state: Guangdong

address: No.1, Panfu Road, Yuexiu District

department: HBP II Surgery

institute: Guangzhou First People's Hospital

summary: We report the application of miRNAs analysis in exosomes based on second-generation high-throughput sequencing. Plasma samples from 3 hepatocellular carcinoma patients and 3 healthy controls were collected, and exosomes were isolated by ultra-centrifugation. MiRNAs in exosomes were then extracted and high-throughput sequencing was performed.By comparing the sequencing data, we screened out differentially expressed miRNAs and validated them with qRT-PCR in exosome samples, establishing and verifying the diagnostic panel of hepatocellular carcinoma composed of miR-212-5p, miR-519b-3p, miR-1248 and miR-1250-5p.

overall_design: Plasma exosome miRNAs from 3 hepatocellular carcinoma patients and 3 healthy volunteers

first: XiaoYuan

last: Hu

first: JiYou

last: Yao


title: Adipose tissue retains an epigenetic memory of obesity after weight loss [TRAP]

overall_design: AdipoERCre x NuTRAP mice received two times tamoxifen at age of 4-5 weeks. After a 2 week washout period mice  were subjected to high fat diet feeding for 12 or 25 weeks (controls received control diet). Subsequently, mice were put on control diet for 8 weeks. Epididdymal adipose tissue was snap frozen at each time point. Labelled ribosomes were pulled down with translation RNA and RNA was isolated for RNAseq. Each replicate is an individual biological replicate


title: Adipose tissue retains an epigenetic memory of obesity after weight loss [CUT&TAG]

overall_design: AdipoERCre x NuTRAP mice received two times tamoxifen at age of 4-5 weeks. After a 2 week washout period mice  were subjected to high fat diet feeding for 12 or 25 weeks (controls received control diet). Subsequently, mice were put on control diet for 8 weeks. Epididdymal adipose tissue was snap frozen at each time point. Nuclei of labelled adipoctytes were isolated and used for Cut and Tag of four histone marks.. 3 biologcial replicates per condition.


title: Adipose tissue retains an epigenetic memory of obesity after weight loss [ATAC-seq]

overall_design: AdipoERCre x NuTRAP mice received two times tamoxifen at age of 4-5 weeks. After a 2 week washout period mice  were subjected to high fat diet feeding for 12 or 25 weeks (controls received control diet). Subsequently, mice were put on control diet for 8 weeks. Epididdymal adipose tissue was snap frozen at each time point. Nuclei of labelled adipoctytes were isolated and used for ATACseq. Each replicate is an individual biological replicate


title: Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia [spatial transcriptomics]

status: Public on Nov 18 2024

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

summary: We performed spatial and single-cell transcriptomics on male mouse brains to map out the molecular and cellular processes governing the response to ischemic stroke during the first week after the injury. Focusing on glial cells, we documented their activation, the formation of the glial scar, and significant changes in cell–cell communication patterns. Interestingly, we identified various activated populations of oligodendrocytes that, while similar in their anti-inflammatory properties, differ in their immunogenic and metabolic characteristics. This challenges the long-held belief that oligodendrocytes play a passive role in neuropathologies. Altogether, we present a major contribution to the current understanding of the role of glial cells in stroke pathobiology, comprehensively mapping their acute response and role in the formation of the glial scar.

overall_design: To invesigate ischemic brain injury, mouse model of permanent middle cerebral artery occlusion was used. Screened timepoints include control, day 1, 3, and 7 post the injury. Coronal sections were sampled  from bregma -1.3 mm and processed using the 10X Genomics Visium platform with the 55-um spot resolution.

last: Zucha

first: Pavel

last: Abaffy

first: Denisa

last: Kirdajova

last: Jirak

first: Mikael

last: Kubista

first: Miroslava

last: Anderova


title: Differential expression of genes upon E-cadherin loss of function

city: Paris

first: Rene-Marc

last: Mege

address: 15 Rue Helene Brion

country: France

institute: Institut Jacques Monod

summary: In this work by growing monolayers upto 70-80% confluency we study the differential expression of genes upon E-cadherin loss of function

overall_design: MDCK WT and E-cadherin knock out cells were grown on tissue culture dishes until they reached confluency. Each condition had n=3 samples.

first: Lakshmi

last: Balasubramaniam

first: Benoit

last: Ladoux


title: Arabidopsis acton binding proteins WLIM2A links PAMP-triggered immunity and cytoskeletal organization

city: Thuwal

first: Prabhu

last: Manickam

state: Jeddah

address: 4700 KAUST

department: BESE

country: Saudi Arabia

institute: KAUST

summary: MAPKs are a family of highly conserved serine/threonine protein kinases that link upstream receptors to their downstream targets which can be localized in the cytoplasm or the nucleus. Pathogens produce pathogen-associated molecular patterns (PAMPs) that trigger the activation of MAPK cascades in plants. Phosphoproteomic analysis of PAMP-induced Arabidopsis plants led to the identification of several putative MAPK targets. WLIM2A is a putative phosphorylation target of MAPKs, but so far little is known about the function of WLIM2A in plant immunity. We investigated the role of WLIM2A in immunity via a reverse-genetics approach generating wlim2a knockout lines using CRISPR-Cas9, as well as complementation and phosphosite mutated WLIM2A expression lines in the wlim2a background. The wlim2a lines were compromised in their response to Pst DC3000 but showed enhanced resistance to fungal infection by Botrytis cinereae. Transcriptome analyses revealed that immune hormone signaling and biosynthesis genes of salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) are differentially regulated in the wlim2a knockout lines. Pathogen assays with Pst DC3000 showed altered stomatal phenotypes in wlim2a mutants. Importantly, WLIM2A phosphomutants had opposing stomatal behaviour and resistance phenotypes in response to Pst DC3000 infection. Overall, these data show that WLIM2A is a MAPK target and that phosphorylation of WLIM2A regulates stomatal immunity.

overall_design: To characterize the function of WLIM2A in the regulatuion of gene expression, we acrried out a global transcriptome analysis on the wlim2a-1 mutrants plants in response to flg22 treatment

first: Aala

last: Abdulfaraj

first: Hanna

last: Alhoraibi

first: Alaguraj

last: Veluchamy

first: Naganand

last: Rayapuram

first: Heribert

last: Hirt


title: Mitochondria drive neuronal differentiation by metabolising nuclear-encoded RNA [RNA-seq]

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

country: Australia

institute: University of Sydney

summary: In this study, we show that within minutes of exposure to differentiation cues and activation of the electron transport chain, the mitochondrial outer membrane transiently fuses with the nuclear membrane of neural progenitors, leading to efflux of the nuclear-encoded RNAs (neRNA) into the positively charged mitochondrial intermembrane space. Subsequent degradation of mitochondrial neRNAs by Polynucleotide phosphorylase 1 (Pnpt1) residing in the intermembrane space curbs the transcriptomic memory of progenitor cells. Further, phosphorolysis by Pnpt1 indirectly suppresses ATP production by depriving ATP synthase of inorganic phosphate, resulting in delayed recovery of the attenuated transcriptomic memory. Collectively, these events force the progenitor cells towards a “tipping point” characterised by emergence of a competing neuronal differentiation program.

overall_design: mRNA profiles of isolated mitochondria and nuclei at baseline, 1h post induction of differentiation, and 2h post-induction of differentiation, Biological replicates: 2/group

last: Farahani


title: Mitochondria drive neuronal differentiation by metabolising nuclear-encoded RNA


title: Mitochondria drive neuronal differentiation by metabolising nuclear-encoded RNA [ATAC-seq]

overall_design: ATAC-seq profiles of NPCs at baseline, 1h post induction of differentiation, and 2h post-induction of differentiation, Biological replicates: 1/group


title: Multifaceted roles of RAP80 during the Herpes simplex virus 1 life cycle

status: Public on Nov 13 2024

city: Beijing

first: jie

last: Wang

address: 5 Summer Palace Road, Haidian District, Beijing

institute: school of Life science

summary: Herpes simplex virus 1 (HSV-1) is a widespread human pathogen that establishes lifelong infections, but understanding precise activity at each infection stage remains challenging. HSV-1 utilizes ubiquitination pathways to modulate cellular factors to facilitate its replication cycle, however, elucidating the cascades that follow host protein degradation and the subsequent impact on the host-virus equilibrium continues to be a complex endeavor. Here we reveal the multifaceted role of the DNA damage response protein RAP80 throughout HSV-1’s infection cycle. In early stages, RAP80 inhibits HSV-1 transcription by directly binding to the viral genome, blocking ICP4 (viral protein) binding to transcription factors. This interaction is regulated by phase separation via an intricate interplay between RAP80 and ICP0/ICP4. As infection progresses, the viral E3 ligase ICP0 degrades RAP80, dissolving phase separation, and allowing the formation of a mature viral replication compartment. In late infection stages, RAP80 is deubiquitinated by the viral deubiquitinase UL36USP, which restores cellular homeostasis and promotes HSV-1 survival. This process involves modulating the R-loop-cGAS-apoptosis pathway. These findings underscore the dynamic interplay between viral and host factors and the complex mechanisms used by HSV-1 to subvert host defenses, offering practical implications for the future development of antiviral strategies.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RAP80 in HeLa cells infected by HSV-1 at 3h and 20h post-infection.

first: Jie

first: TingTing

last: Li

first: Yi

last: Chi

first: Yujing

last: Deng

first: Xiaofeng

last: Zheng

first: Dong

last: Xing


title: Transcriptome-Wide Analysis of the 5' Cap Status of RNA Using 5' Monophosphate-Dependent Exonuclease Digestion and RNA Sequencing

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: Eukaryotic mRNAs carry an N7-methylguanosine (m7G) cap structure at their 5' extremity, which protects them from the degradation by 5'-3' exoribonucleases and plays a pivotal role in mRNA metabolism, promoting splicing, nuclear export, and translation. Decapping, the enzymatic process that removes this structure, is a key event during cytoplasmic mRNA 5'-3' decay, leading to the degradation of the transcript body by Xrn1. In this chapter, we describe a procedure to assess the cap status of RNA at the transcriptome level. It is based on a treatment of total RNA extracts with a 5' monophosphate-dependent exonuclease, which like Xrn1 specifically degrades decapped RNAs harboring 5' monophosphate extremities, but not RNAs with intact m7G cap. The digested RNAs are then analyzed by RNA sequencing.

overall_design: To determine the capping status of the RNAs that accumulate upon CHX treatment and/or NMD inactivation, we performed strand-specific total RNA-seq in control (DMSO) and CHX-treated WT and upf1 mutant cells, including a treatment of the RNA extracts with the Terminator 5´-Phosphate-Dependent Exonuclease, which degrades RNAs with 5’-monophosphate ends but not those with an intact m7G cap (2 biological replicates per condition).

last: WERY

first: Ugo

last: SZACHNOWSKI

first: Sara

last: ANDJUS

first: Antonin

last: MORILLON


title: The transcriptome analysis of synovium-infiltrating regulatory T cells in collagen-induced arthritis model

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

institute: Chiba University

summary: This study aimed to understand the characteristics of synovium-infiltrating regulatory T cells (Treg) during arthritis. Treg cells were  collected from the synovium and draining lymph nodes of arthritic mice. Treg cells of control draining lymph nodes were also subjected to the study.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 1) synovial Tregs of arthritic mice (N = 3), 2) draining lymph node Tregs of arthritic mice (N = 3), 3) draining lymph node Tregs of control mice (N = 3).

first: Koto

last: Hattori

first: Hiroshi

last: Nakajima


title: IL17A-induced OPN from tumor cells promotes tumor progression by inducing tissue-resident TAM proliferation via LYVE1 [I]

first: Lei

last: zhao

overall_design: 4T1 tumor cells treated with or without recombinant IL-17A cytokines.

last: Zhao

first: Zonghan

first: Yuying

last: Tan

first: Jianan

last: Ma


title: Combined inhibition of histone methyltransferases EZH2 and DOT1L is an effective therapy for neuroblastoma

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: The child cancer, neuroblastoma (NB), is characterised by a low incidence of mutations and strong oncogenic embryonal driver signals. Many new targeted epigenetic modifier drugs have failed in human trials as monotherapy. We performed a high‐throughput, combination chromatin‐modifier drug screen against NB cells. We screened 13 drug candidates in 78 unique combinations. We found that the combination of two histone methyltransferase (HMT) inhibitors: GSK343, targeting EZH2, and SGC0946, targeting DOT1L, demonstrated the strongest synergy across 8 NB cell lines, with low normal fibroblast toxicity. High mRNA expression of both EZH2 and DOT1L in NB tumour samples correlated with the poorest patient survival. Combination HMT inhibitor treatment caused activation of ATF4‐mediated endoplasmic reticulum (ER) stress responses. In addition, glutathione and several amino acids were depleted by HMT inhibitor combination on mass spectrometry analysis. The combination of SGC0946 and GSK343 reduced tumour growth in comparison to single agents. Our results support further investigation of HMT inhibitor combinations as a therapeutic approach in NB.

overall_design: SK‐N‐BE(2)‐C and KELLY neuroblastoma cell lines were seeded in T25 flasks. Following 24 h of incubation cell culture medium was replaced with medium containing either DMSO, 12.8 μM SGC0946, 12.8 μM GSK343 or a combination of both drugs. Treated cells were incubated for 6 h, followed by total RNA extraction and quantitation. RNA from treated samples were then subject to microarray profiling via the PrimeView Human Genome U219 Array (#901605 Applied Biosystems) according to manufacturer instructions, by the Ramaciotti Centre for Genomics (UNSW, Australia).


title: Non-canonical Hedgehog signaling via GLI2 promotes pancreatic stellate cell activation and fibrosis in chronic pancreatitis

city: Chengdu

first: Linrui

last: Peng

state: Sichuan

address: No37 Guoxue Alley Wuhou District

institute: West China Hospital

summary: Excessive Hedgehog (Hh) signaling activity contributes to fibrosis in multiple organs, however, its role in pancreatic stellate cell (PSC) activation and fibrosis development during chronic pancreatitis (CP) remains unclear. We demonstrate that GLI2 is upregulated in activated PSCs from CP patients and animal models. Specific deletion of Gli2, but not Smo, significantly alleviated fibrosis in CP models, indicating that CP is driven by non-canonical Hh signaling. Experiments on culture-activated primary PSCs reveal early nuclear translocation and increased GLI2 expression promptly after in vitro culture, with GLI2 being essential for PSC activation. SMO inhibition only reduces GLI2 activation in the short term, while activation of GLI2 by TGF-β/SMAD3 signaling explains the SMO-independent mechanisms leading to Hh activation in PSCs. Altogether, our data demonstrate the activation of the non-canonical Hh pathway in PSCs and indicate that GLI2 represents a promising therapeutic target for CP.

overall_design: To elucidate the molecular mechanisms underlying the antifibrotic effects of GLI2, we performed bulk RNA sequencing (RNA-seq) of primary PSCs isolated from Gli2fl/fl:Pdgfrb-CreERT2 (Gli2△PSC) mice and Gli2fl/fl mice. The genetically modified mice were intraperitoneally injected with tamoxifen at a dose of 100 mg/kg body weight for 5 consecutive days. After a 1-week interval, PSCs were isolated and then cultured in vitro for 4 days, as GLI2 reached its peak abundance by day 4 of culture.  We then performed gene expression profiling analysis from data obtained from RNA-seq of D4 PSCs isolated from Gli2△PSC and Gli2fl/fl mice.

first: Yuchen

last: Hu

first: Yuwei

last: Zhang


title: Brain-targeting liposome-based APOE2 gene delivery exacerbates soluble amyloid-β accumulation in AppNL-G-F mice

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Alzheimer’s disease (AD) is the most common cause of late-life dementia characterized by progressive neurodegeneration and brain deposition of amyloid-β (Aβ) and phosphorylated tau. The APOE ε2 encoding apolipoprotein E (APOE2) is a protective allele against AD among the three genotypes (APOE ε2, ε3, ε4), while APOE4 is the strongest genetic factor substantially increasing AD risk. APOE regulates brain lipid homeostasis and maintaining synaptic plasticity and neuronal function, where APOE2 has a superior function compared to APOE3 and APOE4. Gene therapy that increases APOE2 levels in the brain is, therefore, a promising therapeutic strategy for AD treatment. We previously reported that PEGylated liposomes conjugated with transferrin and a cell-penetrating peptide Penetratin sufficiently deliver chitosan-APOE2 cDNA plasmid complex into the brain of wild-type mice. Here, we investigated how brain-targeting liposome-based APOE2 gene delivery influences Aβ)-related pathologies in amyloid model AppNL-G-F knockin mice at 12-month-old. We found a trend of reductions of insoluble Aβ levels in the mouse cortices 1 month after APOE2 gene therapy. Furthermore, in the AppNL-G-F knockin mice that received the APOE2 gene therapy, brain transcriptome analysis through RNA-sequencing identified the upregulation of genes/pathways related to neuronal development. This was supported by increases of Dlg4 and Syp mRNAs coding synaptic proteins in the experimental group. On the other hand, we found that APOE2 gene delivery increased soluble Aβ levels, including oligomers, as well as exacerbated neurite dystrophy and decreased synaptophysin. Together, our results suggest that brain-targeting liposome-based APOE2 gene therapy is potentially beneficial for synaptic formation at the transcriptional level. Forced APOE2 expressions, however, may exacerbate Aβ toxicity by increasing the dissociation of Aβ oligomers from aggregates in the presence of considerable amyloid burden.

overall_design: We performed bulk RNA sequencing of amyloid model AppNL-G-F knockin mice and investigated changes in gene expression and pathway alternations.

first: Ni

last: Wang

first: Takahisa

last: Kanekiyo


title: Differentially Expressed Genes in C-33A and CaSki Cells Overexpressing miR-124-3p, miR-23b-3p, or miR-218-5p Modulate Processes and Pathways Involved in Cervical Cancer Progression

city: Chilpancingo

first: Gloria

last: Fernández Tilapa

state: Guerrero

address: Ciudad Universitaria Sur, Av. Lázaro Cárdenas S/N

country: Mexico

institute: Autonomous University of Guerrero

summary: Aberrant expression of oncomicroRNAs and tumor suppressor miRNAs (tsmiRs) contributes to the carcinogenesis and progression of cervical cancer (CC). miR-124-3p, miR-23b-3p, and miR-218-5p are tsmiRs that modulate oncogenes regulating cellular processes implicated in CC progression. This research aimed to explore transcriptomic changes in C-33A and CaSki cells following the overexpression of miR-124-3p, miR-23b-3p, and miR-218-5p, and to identify the biological processes (BPs) and pathways modulated by differentially expressed genes (DEGs). A total of 100 nM of miR-124-3p, miR-23b-3p, and miR-218-5p mimetics were transfected into C-33A and CaSki cells, and transcriptome changes were analyzed using RNA-seq. The Galaxy and R-Studio platforms were employed to identify DEGs, while BPs and pathways regulated by DEGs were identified through the DAVID platform. Transcriptional changes revealed both differences and similarities between cell lines and miRNAs. In C-33A cells, miR-124-3p and miR-218 regulated direct and indirect targets involved in the cell cycle and apoptosis. In CaSki cells, apoptosis and viral carcinogenesis were regulated by genes modulated directly or indirectly by miR-124-3p and miR-23b-3p. These tsmiRs demonstrated synergistic activity, regulating multiple transcripts that modulate processes and pathways involved in CC progression, with or without HPV. These findings suggest that miR-124-3p, miR-23b-3p, and miR-218-5p may represent promising therapeutic alternatives for CC treatment.

overall_design: To analyze the effect of miR-124-3p, miR-23b-3p or miR-218-5p in gene expression of C-33A and CaSki cells, and to identify the biological processes (BPs) and pathways modulated by differentially expressed genes (DEGs).

first: Merlin

last: Cruz de la Rosa

first: Hober

middle: N

last: Núñez Martínez

first: Hilda

last: Jiménez Wences

first: Manuel

last: Romero López

first: Judit

last: Alarcon Millan

first: Oscar

last: Peralta Zaragoza


title: Glycolytic enzyme PKM2 regulates cell senescence but not inflammation in the process of osteoarthritis.

city: Shanghai

first: Liu

last: Bo

address: 180 Fenglin Road

department: 1Department of Orthopedic Surgery

institute: Zhongshan Hospital, Fudan University

summary: Chondrocyte senescence is an important mechanism underlying osteoarthritis in the senile population and is characterized by reduced expressions of the extracellular matrix proteins. The involvement of glycolysis and the tricarboxylic acid cycle in the development of osteoarthritis is inclusive. The present study aims to investigate the role of the glycolytic enzyme M2 isoform of pyruvate kinase (PKM2) in chondrocytes in senescence and inflammation. Primary chondrocytes are isolated from the knee joints of neonatal mice. Small interfering RNAs (siRNAs) against PKM2 are transfected using lipofectamine. RNA sequencing is conducted in primary chondrocytes with the PKM2 gene deleted. Cell apoptosis, autophagy, reactive oxygen species measurement, and senescent conditions are examined. The glycolytic rate in cells is measured by Seahorse examination. Interleukin 1-β (IL-1β) increases the protein expressions of matrix metallopeptidases (MMP)13 and PKM2 and reduces the protein expression of collagen type II (COL2A1) in primary chondrocytes. Silencing of PKM2 alters the protein expressions of MMP13, PKM2, and COL2A1 in the same pattern in quiescent and stimulated chondrocytes. RNA sequencing analysis reveals that PKM2 silencing reduces senescent biomarker p16INK4a expression. Compared with low-passage chondrocytes, high-passage chondrocytes exhibit increased expression of p16INK4a and reduced expression of COL2A1. Silencing of PKM2 reduces SA-β-Gal signals and increases COL2A1 expression in high-passage chondrocytes. Seahorse assay reveals that PKM2 deletion favors the tricarboxylic acid cycle in mitochondria in low- but not in high-passage chondrocytes. In summary, the glycolytic enzyme PMK2 modulates chondrocyte senescence but does not participate in the regulation of inflammation.

overall_design: To understand the role of PKM2 in chondrocytes, RNA sequencing was conducted in primary mouse chondrocytes with siRNA-mediated Pkm2 silencing.

first: Bo

last: Liu

first: Chenzhong

first: Yi

last: Shi

first: Chi


title: A Novel Hidden Protein p-414aa Encoded by circSETD2(14,15) Inhibits Vascular Remodeling

city: haikou

first: shaoguang

last: sun

state: hainan

address: No. 3 Xueyuan Road

institute: hainan medical university

summary: The phenotypic switching of vascular smooth muscle cells (VSMCs) leads to neointimal hyperplasia, which is the underlying cause of vascular remodeling diseases such as atherosclerosis and hypertension. Novel hidden proteins encoded by circular RNAs (circRNAs) play crucial roles in disease progression. Our study identified a new protein derived from a circRNA in VSMCs and demonstrated its potential role in regulating vascular remodeling. We discovered a novel hidden protein, p-414aa, encoded by circSETD2(14,15), which can inhibit vascular remodeling. Both circSETD2(14,15) and p-414aa may serve as potential therapeutic targets for vascular remodeling diseases. In this study, we demonstrated that the new protein p-414aa encoded by circSETD2(14,15) inhibits VSMC proliferation and neointimal hyperplasia through the HuR/C-FOS axis. In summary, our data provide a molecular framework for the phenotypic switching of vascular smooth muscle cells.

overall_design: To identify potential mRNA targets regulated by p-414aa, we performed RNA sequencing (RNA-seq) analysis in human aortic smooth muscle cells (HASMCs) with or without p-414aa overexpression. For overexpression, we used the pcDNA3.1(+) plasmid to overexpress p-414aa in HASMCs, with the pcDNA3.1-EGFP plasmid serving as a control.

first: Shaoguang

last: Sun

first: Jiajie

last: Lin

first: Shuyan

last: Yang

first: Sifan

first: Liyun

first: Anqi

last: Zhao

first: Zhaoyi

first: Sen

first: Miao

last: Gong

first: Mingqi

last: Zheng

first: Gang


title: A Transcriptome Analysis of the Lifecycle of Anthrobots

city: Medford

first: Michael

last: Levin

state: MA

address: 200 Boston Ave

department: Biology

institute: Tufts University

summary: The goal of this study was to quantify transcriptomic differences between sphereoids made from bronchial epithelial cells at different stages of their lifecycle. These differences in their transcriptome were then compared with the transcriptomes of their progenitor cells, normal human bronchial epithelial cells (NHBEs).

overall_design: The samples of this study fall into several major groups. The first are the normal human bronchial epithelial progenitor cells (NHBEs); these are the cells used to make the Anthrobots, airway organoids. There are several passages collected, denoted by "P + No." and these are the times the cells were passaged following thaw from the original frozen stock. The next set collected was the RNA from Anthrobots at various stages of their lifecycle. The RNA of the day 0 bots was collected immediately upon their being dissolved from their Matrigel suspension. The following day 10, day 25 bots were collected 10 and 25 days post-Matrigel respectively. The Bridge Bots were where we dissolved an entire well into a 60mm dish to allow for better aggregation between bots; the bots are capable of aggregating to form larger organoids, and the normal method is to divide the contents of a single well among two 60mm dishes to discourage aggregation

first: Gizem

last: Gumuskaya

first: Nikolai

last: Davey

first: Pan

last: Hui

first: Jonathan

last: Dreyfuss


title: Immune Infiltration Correlates with Transcriptomic Subtypes in Primary ER+ Invasive Lobular Breast Cancer

city: Boston

first: Fangyuan

last: Chen

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Understanding interplay of breast cancer and microenvironment is critical. Here we identified two transcriptomic subtypes and five immune infiltration patterns from RNA-seq and multiplex immunohistochemistry from 21 ER+/HER2- ILCs. We found proliferative subtype associated with increased suppressive immune infiltration, and defined a signature associated with lower proliferative, pro-inflammatory TAM infiltration, and improved survival in ER+ breast cancer. Our work identified genes related to ILC immune microenvironment and prognosis. This GEO submission is related to RNA-seq section of this study.

overall_design: For the 21 cases, formalin-fixed paraffin-embedded (FFPE) blocks of primary ER+/HER2- ILC tumors were acquired from University of Pittsburgh Biospecimen Core, and clinical information was queried from the UPMC Cancer Registry. For each block, three sections (at the top, bottom and middle of the block) were stained with hematoxylin and eosin (H&E) and inspected by pathologist to circle out regions with tumor epithelial cell proportion ≥40%. 5 sections (of 10uM thickness each) were used for RNA extraction and sequencing at these circled regions. Sample RNA was extracted with Qiagen tissue DNA/RNA kit from FFPE sections, assessed with High Sensitivity RNA TapeStation for quality and concentration, and sequenced with Illumina Nextseq 500 75 bp pair-end in 150 cycles at University of Pittsburgh Health Sciences Sequencing Core. For RNA-seq data, we used FastQC for FASTQ data quality control, trimmomatic for adapter trimming, Hisat2 for alignment to human genome 38 (hg38), and HTSeq for quantification, to generate normalized expression in transcripts per million (TPM).

first: Sayali

last: Onkar

first: Peter

last: Lucas

first: Yujia

last: Li

first: Jian

last: Zou


title: Inducible deletion of Ezh2 in CD4+ T cells inhibits kidney T cell infiltration and prevents interstitial nephritis in MRL/lpr lupus-prone mice

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Systemic lupus erythematosus is a remitting relapsing autoimmune disease characterized by autoantibody production and multi-organ involvement. T cell epigenetic dysregulation plays an important role in the pathogenesis of lupus. We have previously demonstrated upregulation of the key epigenetic regulator EZH2 in CD4+ T cells isolated from lupus patients. To further investigate the role of EZH2 in the pathogenesis of lupus, we generated a tamoxifen-inducible CD4+ T cell Ezh2 conditional knockout mouse on the MRL/lpr lupus-prone background. We demonstrate that Ezh2 deletion abrogates lupus-like disease and prevents T cell differentiation. Single-cell analysis suggests impaired T cell function and activation of programed cell death pathways in EZH2-deficient mice. Ezh2 deletion in CD4+ T cells restricts TCR clonal repertoire and prevents kidney-infiltrating effector CD4+ T cell expansion and tubulointerstitial nephritis, which has been linked to end-stage renal disease in patients with lupus nephritis.

overall_design: To investigate the file of EZH2, we generated EZH2 wild type and knockout mice and performed TotalSeq-C profiling of kidney and spleen cells

first: Xiaoqing

middle: G

first: Luis

last: Espinoza

first: Sheldon

last: Bastacky

first: Amr

middle: H

last: Sawalha


title: Host Genetics and Gut Microbiota Influence Lipid Metabolism and Inflammation: Potential implications for ALS Pathophysiology in SOD1 G93A Mice

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary:
Running Head: Genetics, Gut Microbiota, and ALS Progression
We investigate the interplay among genetic background, GM composition, metabolism, and immune response in two distinct ALS mouse models: 129Sv_G93A and C57Ola_G93A, representing rapid and slow disease progression, respectively.

overall_design: Total DNA was extracted from the stool of mice with genotype 129Sv or C57Ola, with or without the mutation G93A, at three consecutive time points (namely PS,OS and SY). The DNA has been amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei

first: Leandro

last: Di Gloria

first: Elena

last: Niccolai


title: The ex vivo productionofmature neutrophils depends on the sourceofCD34+ human hematopoietic progenitors

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

summary: we propose a two-stage procedure for pre-expanding hematopoietic progenitor cells and subsequent ex vivo differentiation for potential granulocyte transfusion. We compared three distinct donor sources, UCB, BM live donor, and BM deceased donor, and tested two expansion different expansion protocols. Donor sources were evaluated based on proliferation during expansion and differentiation phases, neutrophil cell yield, and function. We show that cell for cell, UCB is the most proliferative and give the greatest neutrophil yield. Further, our ex vivo-generated neutrophils of all three donor sources have an enhanced propensity for opsonin-recognizing functions relative to primary neutrophils, which may influence future treatment.

overall_design: Single-cell RNA-seq library preparation and sequencing: Single live cells were counted and processed using Honeycomb Single Cell RNA Sequencing platform HIVE. The samples were prepared for library preparation according to the manufacturer's protocol, and were then sequenced on an Illumina NextSeq500 sequencer.