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

first: Li

last: Gan

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

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

first: Chloe

last: Lopez-Lee

first: Lay

last: Kodama

last: Fan

first: Daphne

last: Zhu

first: Jingjie

first: Man Ying

last: Wong

first: Pearly

last: Ye

first: Kendra

last: Norman

first: Nessa

last: Foxe

first: Laraib

last: Ijaz

first: Fangmin

last: Yu

first: Hao

first: Gillian

last: Carling

first: Eileen

last: Torres

first: Rachel

last: Kim

first: Dena

middle: B

last: Dubal

first: Shane

last: Liddlelow

first: Subhash

last: Sinja

last: Sinha

first: Wenjie

last: Luo


title: The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming [RNA-seq]

status: Public on Nov 29 2024

city: Shanghai

first: Liping

last: Wang

address: 1239 Siping Road

country: China

institute: Tongji University

type: Expression profiling by high throughput sequencing

summary: Induced pluripotent stem cells (iPSCs) technology offers great promise for scientific research and clinical applications. iPSCs can be generated from various cell types through different strategies. Two different pluripotent states, naive and primed, can be captured in vitro, corresponding to the pre- and post-implantation stages of in vivo development, respectively, with naive pluripotency being considered to possess better developmental potential. We can obtain naïve iPSCs and primed iPSCs through somatic cell reprogramming. Despite well-characterized transcriptional and epigenetic changes, the dynamic of the chromatin landscape during naïve and primed iPSC reprogramming is poorly understood, especially in humans. In this study, we applied ATAC-seq and RNA-seq to delineate the chromatin landscape in the human secondary reprogramming system towards naive and primed pluripotency. We identified several transcription factors and epigenetic factors which were crucial to reprogramming chromatin remodeling. We found that two isoforms of the same gene PRDM1, PRDM1alpha and PRDM1beta, targeted different genomic loci to function in divergent roles during naive reprogramming. We proposed a cross-regulation model of PRDM1alpha and PRDM1beta function. Together, this research highlights the diversity of the transcription factors in determining the chromatin landscape dynamics and regulating pluripotent cell fates.

overall_design: We constructed knockdown and overexpression of PRDM1 in naïve hES cell lines for RNA-seq.

first: Jianfeng

last: Zhou

first: Mingyue

last: Guo


title: LRRK2 G2019S mutation incites increased cell-intrinsic neutrophil effector functions and intestinal inflammation in a model of infectious colitis.

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: Parkinson’s Disease (PD) is a progressive, neurodegenerative disorder characterised by motor and non-motor symptoms. People with PD often present with gastrointestinal dysfunction, such as constipation, and studies have indicated that PD is more common in people with inflammatory bowel disease (IBD). Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) are responsible for approximately 1% of all PD cases and increased risk for inflammatory bowel disease (IBD). Among them, the LRRK2 Gly2019Ser is the most common PD-associated mutation. It is unknown how LRRK2 mutation affects intestinal inflammation susceptibility or pathogenesis of PD. Here we demonstrate that LRRK2 G2019S mutation promotes increased neutrophils migration and differential gene regulation and cell function in these cells in Citrobacter rodentium-infected mice. We found a cell-intrinsic function for LRRK2 G2019S in vivo, in increasing neutrophil chemotaxis, degranulation and NETosis, and an upregulation of Th17 immune responses, which may together contribute to the observed increased colon pathology. Transcriptionally, these neutrophils have a greater pro-inflammatory type I and II IFN response compared to WT mice. Our results increase our understanding of the role of PD-associated genes in immune cells and their contribution to immune dysregulation, which could contribute to the development of pharmacological targets and biomarkers for an easier detection and intervention in PD.

overall_design: Transcriptomic analysis of colonic lamina propria cells in LRRK2 G2019S mice compared to wild type following intestinal microbial infection

first: Pei

last: Jessica

first: Recinto

last: Sheirlyn

first: Gruenheid

last: Samantha

first: Stratton

last: Jo Anne


title: The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming [CUT&Tag]

overall_design: We examined the genomic binding sites of PRDM1alpha and PRDM1beta proteins on day 10 of reprogramming using CUT&Tag technology.


title: MiRNA expression profiling in pancreatic cancer cells compared to normal epihelial cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Expression profiling of 2555 miRNAs was performed using microarray.

overall_design: In the study presented here, we used PDAC cells, Panc-1 and miRNAs expression was analyzed by comparing in HPNE cells

first: Kenji

last: Takahashi

first: Kazuya

last: Koyama


title: The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming [ATAC-seq]

summary: Induced pluripotent stem cells (iPSCs) technology offers great promise for scientific research and clinical applications. iPSCs can be generated from various cell types through different strategies. Two different pluripotent states, naive and primed, can be captured in vitro, corresponding to the pre- and post-implantation stages of in vivo development, respectively, with naive pluripotency being considered to possess better developmental potential. We can obtain naïve iPSCs and primed iPSCs through somatic cell reprogramming. Despite well-characterized transcriptional and epigenetic changes, the dynamic of the chromatin landscape during naïve and primed iPSC reprogramming is poorly understood, especially in humans. In this study, we applied ATAC-seq and RNA-seq to delineate the chromatin landscape in the human secondary reprogramming system towards naive and primed pluripotency. We identified several transcription factors and epigenetic factors which were crucial to reprogramming chromatin remodeling. We found that two isoforms of the same gene PRDM1, PRDM1α and PRDM1β, targeted different genomic loci to function in divergent roles during naive reprogramming. We proposed a cross-regulation model of PRDM1α and PRDM1β function. Together, this research highlights the diversity of the transcription factors in determining the chromatin landscape dynamics and regulating pluripotent cell fates.

overall_design: We collected reprogramming intermediates for RNA-seq and ATAC-seq.


title: Sequencing data of a novel piperine derivative HJ-4 against colorectal cancer

status: Public on Nov 28 2024

city: lianyungang

first: Luyao

last: Zhang

address: tongguan

institute: Jiangsu Ocean University

summary: In order to explore the mechanism of HJ-4, we used RNA-seq technology to extract and analyze the total RNA of cells treated with DMSO and HJ-4, and analyzed the RNA data.

overall_design: After reaching 80% density, HCT116 cells were divided into two groups, with no less than 5×10^6 cells in each group. One group was treated with 32µM HJ-4 drug, and the other group was treated with DMSO as a control. Both groups of cells were incubated at 37°C. One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer. Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

first: Bin

last: Liu


title: RNA sequencing of LT-HSCs from the bone marrow of unirradiated mice after treated with saline or carnosine

city: Chongqing

first: Mengjia

last: Hu

address: Gaotanyan Street 30

institute: Third Military Medical University

summary: Analysis of differentially expressed genes in LT-HSCs from unirradiated mice with or without carnosine treatment.

overall_design: Normal wild type mice without irradiation were treated with saline or carnosine. Then, long-term hematopoietic stem cells (LT-HSCs, Lineage-, Sca-1+, c-Kit+, Flk2-, CD34-) from the bone marrow of these mice were isolated, followed by RNA sequencing analysis.

first: Hao

last: Zeng

first: Naicheng

last: Chen


title: ALKBH1-mediated DNA N6-methyladenine Modification Regulates H3K9me3-dependent Heterochromatin in Neural Tube Development [Cut & Tag]

city: beijing

first: Xuejia

last: He

address: 2 yabao road

institute: Capital Institute of Pediatrics

summary: Neural Tube Defects (NTDs) are a class of severe congenital developmental defects caused by abnormal closure of the neural tube during early embryonic development, including conditions such as anencephaly, spina bifida, and encephalocele. Currently, NTDs are considered to result from the combined effects of genetic and environmental factors, particularly maternal folate intake during pregnancy, leading to widespread epigenetic dysregulation. However, the role of N6-methyladenine (N6-mA) in embryonic neural development remains largely unknown. Here, we found significant upregulation of Alkbh1 and concomitant significant downregulation of overall 6mA in brain tissue of a mouse model of NTDs. Further investigation through MeDIP, CUT&TAG, and single-cell sequencing revealed crosstalk between N6-mA and H3K9me3-marked heterochromatin, primarily impacting the involvement of embryonic glial cells in the formation of the hindbrain during embryonic neural tube development. These findings collectively suggest a potential epigenetic role of N6-mA in mammalian brain development, potentially exhibiting cell type specificity.

overall_design: 1.Establishment of NTD Mouse Model: MTX is a folate antagonist. Under conditions of low folate diet in pregnant mice, we intraperitoneally injected MTX (1.5 mg/kg) at gestational day 7.5. We began observing the closure status of the neural tube in fetal mice during the neural tube closure window at E9.5-10.5. Normal mice appeared plump and round, with fully closed neural tubes, and were categorized into the normal group. Embryos from mice on low folate diet and injected with MTX exhibited varying degrees of developmental delay, smaller embryos, and primarily showed phenotypes of hindbrain malformations and spina bifida, and were categorized into the NTD group. CUT&Tag was performed on normal and NTD fetal brains to investigate the genomic localization of H3K9me3 and identify genomic regions enriched with H3K9me3. 2.Constructing a low-folate cell line：After resuscitating normal mESCs, Sv129 cells were randomly split into FA4 and FA0. The FA0 group uses folate-free mESCs culture medium.Folate (Sigma) was added to the medium of FA0 as medium of the FA4 group(final concentration: 4 mg/L).  Next, two groups were added correspond medium and were cultured at 37°C with 5% CO2 in a humidified incubator and passaged every 2–3 days. The culture medium was changed daily. CUT&Tag was performed on FA4 and FA0 groups to investigate the genomic localization of H3K9me3 and identify genomic regions enriched with H3K9me3.

first: Jinying

last: Shen

first: Shan


title: Mechanosensing regulates plasmacytoid DCs activation in the skin through NRF2 activation

city: New York

first: Bikash

last: Mishra

state: NY

address: 515 E 71st ST

country: USA

institute: Hospital for Special Surgery

summary: Plasmacytoid dendritic cells (pDCs) infiltrate the skin, chronically produce type I interferon (IFN-I) and promote skin lesions and fibrosis in autoimmune patients. However, what controls their activation in the skin is unknown. Here, we report that increased stiffness, characteristic of the skin microenvironment, inhibits the production of IFN-I by TLR-activated pDCs. Mechanistically, mechanosensing activates stress pathways including the transcription factor NRF2, which, by triggering the pentose phosphate pathway, rewires glycolysis and reduces pyruvate levels, a product necessary for pDC responses. Modulating NRF2 expression in skin-infiltrating pDCs controlled the IFN-I response, leading to either resolution or the sustained activation of pathologic IFN-I pathway in the skin. Moreover, we observed that CXCL4, a pro-fibrotic chemokine that is elevated in fibrotic skin, was able to overcome stiffness-mediated IFN-I inhibition, allowing chronic IFN-I responses by pDCs in the skin. Furthermore, in the skin of patients with systemic sclerosis (SSc), although NRF2 was induced in skin-infiltrating pDCs as compared to blood pDCs, the IFN-response was maintained. Hence, these data identify a novel regulatory mechanism exerted by the skin microenvironment and identify points of dysregulation of this mechanism in patients with skin inflammation and fibrosis.

overall_design: We purified pDC from human buffy coats. pDCs were cultured overnight at 37°C, 5% CO2 in RPMI-1640 medium supplemented with 10% heat-inactivated defined FBS, penicillin-streptomycin, L-glutamine and treated with indicated stimulation.

first: Vidyanath

last: Chaudhary


title: Expression data of miRNAs and lncRNAs from the lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 19

city: Shenyang

first: Zhonghua

last: Yang

address: No.36 street, Heping district

institute: Shengjing hospital of China medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: many dysregulated miRNAs and lncRNAs as the primary factor could be play an important role in the development of lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 17.High-throughput sequencing was utilized to reveal the expression of non-coding RNAs underlying the development of anorectal malformations.

overall_design: The fetal rats with anorectal malformations were successfully established, the  lumbosacral spinal cord  was collected for RNA extraction. This represents the microRNA and lncRNAs component only.

first: Weilin

last: Wang


title: Impact of Vitamin-D3 on the gene expression profile of mouse colon

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary:
Vitamin-D3 (VitD3) exhibits pleiotropic effects in host’s physiology by acting on several organs. To mechanistically understand how VitD3 influences the colon physiology we interrogated the gene expression profile of mouse colon in response to high or low VitD3 bioavailability. VitD3 tissue bioavailability was modulated in mice with the use of diets supplemented with different concentrations of VitD3 (0, 2 or 10 IU/g) and the use of Gc knockout mouse strain in where VitD3 bioavailability is enhanced.
Vitamin-D3 (VitD3) exhibits pleiotropic effects in host’s physiology by acting on several organs. To mechanistically understand how VitD3 influences the colon physiology we interrogated the gene expression profile of mouse colon in response to high or low VitD3 bioavailability. VitD3 tissue bioavailability was modulated in mice with the use of diets supplemented with different concentrations of VitD3 (0, 2 or 10 IU/g) and the use of Gc knockout mouse strain in where VitD3 bioavailability is enhanced.

overall_design: RNA will be extracted from 5 biological replicates (5 individual mice) per condition (20 samples in total). Male mice (8 ½ weeks old) were fed with the following diets 3 ½ weeks :1)C57BL/6J/WT mice that were fed with standard VitD3 diet (2 IU/g) for 3 ½ weeks (n=5), 2) C57BL/6J/WT mice that were fed with high VitD3 diet (10 IU/g) for 3 ½ weeks (n=5), 3) Gc KO mice that were fed with standard VitD3 diet (2 IU/g) for 3 ½ weeks (n=5), 4) Gc KO mice that were fed with VitD3 deficient diet (10 IU/g) for 3 ½ weeks (n=5)

first: Evangelos

last: Giampazolias

first: Caetano

last: Reis e Sousa


title: Expression data of miRNAs and lncRNAs from the lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 17

summary: Many dysregulated miRNAs and lncRNAs as the primary factor could be play an important role in the development of lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 17. High-throughput sequencing was utilized to reveal the expression of non-coding RNAs underlying the development of anorectal malformations.

overall_design: Fetal rats with anorectal malformations were successfully established; the  lumbosacral spinal cord  was collected for RNA extraction. This represents the microRNA and lncRNAs component only.


title: Paired CRISPR screens to map gene regulation in cis and trans (HiChIP)

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center/New York University

summary: In this study, we develop a scalable approach that pairs discovery of cis- and trans-acting elements to systematically decipher the gene regulatory network. We explore the regulation of the immune checkpoint PD-L1 under both basal and IFNγ-stimulated contexts. PD-L1 expression on tumor cells serves as a clinically-actionable diagnostic for immune checkpoint blockade therapy across multiple cancer types.

overall_design: H3K27ac HiChIP for untreated and IFNγ-treated BxPC-3 human pancreatic adenocarcinoma cells

first: Zoran

last: Gajic

first: Christina

last: Caragine

first: Mateusz

last: Legut

first: Conor

last: Walker

first: James

last: Kim

first: Xiao

first: Rachel

middle: E

last: Yan

first: Hans-Hermann

last: Wessels

first: Congyi

last: Lu

first: Neil

last: Bapodra

first: Gamze

last: Gursoy

first: Neville

last: Sanjana


title: Paired CRISPR screens to map gene regulation in cis and trans


title: Paired CRISPR screens to map gene regulation in cis and trans (CUT&RUN)

overall_design: Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for SRF, BPTF, and H3K4me3 in BxPC3 human pancreatic adenocarcinoma cells


title: Transcriptomic analysis of early-stage basal cell carcinomas in murine skin following ablative fractional laser and vismodegib treatment

city: Copenhagen

first: Kristian

middle: Kåber

last: Pedersen

address: Bispebjerg Bakke 23

department: Department of Dermatology

country: Denmark

institute: Copenhagen University Hospital – Bispebjerg

summary: Recent studies have demonstrated that ablative fractional laser (AFL) can inhibit the hedgehog pathway, enhance immune infiltration, and clear basal cell carcinomas (BCCs) in murine models. In this study, we applied RNA sequencing to further characterize the impact of AFL on the transcriptome of murine skin containing early-stage microscopic BCCs, contrasting it with the effects of the FDA approved hedgehog inhibitor vismodegib. Our results showed that BCC induction in murine skin was primarily linked to gene upregulation. Both AFL and vismodegib treatments were able to reverse this upregulation with vismodegib demonstrating superior performance by reversing the most genes (AFL: 59/277; vismodegib 180/277). Surprisingly, Ingenuity Pathway Analysis revealed that both treatments also caused considerable immune cell infiltration. Based on gene set enrichment analysis and cell type deconvolution, AFL treatment resulted in the largest immune cell recruitment, which for both treatments primarily consisted of infiltrating neutrophils, macrophages, and monocytes. In conclusion, the distinct effects observed in BCC skin following AFL and vismodegib treatment highlight key differences between the two interventions. Future applications of AFL or vismodegib treatments could leverage their individual effects, for example by combining AFL’s effects on the immune system with other topical treatments.

overall_design:
Our goal was to investigate the effects of ablative fractional laser and topical vismodegib treatment on a mouse that develops basal cell carcinomas following induction with tamoxifen and x-ray treatment (Ptch1+/- K14-CreER2 p53fl/fl).
We treated 1cm2 skin pieces containing early-stage BCCs with AFL and vismodegib. As controls, we included healthy skin (non-induced) and BCC skin (induced skin).

middle: K

first: Merete

last: Hædersdal

first: Uffe

middle: H

last: Olesen

first: Thomas

last: Litman


title: RNA sequencing of LT-HSCs from the bone marrow of irradiated mice after treated with saline or carnosine

first: Mengjia

last: Hu

summary: Analysis of differentially expressed genes in LT-HSCs from irradiated mice with or without carnosine treatment.

overall_design: Normal wild type mice were subjected to 5.0 Gy total body irradiation and then treated with saline or carnosine. Subsequently, long-term hematopoietic stem cells (LT-HSCs, Lineage-, Sca-1+, c-Kit+, Flk2-, CD34-) from the bone marrow of these mice were isolated, followed by RNA sequencing analysis.

first: Naicheng

last: Chen


title: Paired CRISPR screens to map gene regulation in cis and trans (ATAC-seq)

first: Xinhe

last: Xue

overall_design: Assay for transposase-accessible chromatin with sequencing  (ATAC-seq) for untreated and IFNγ-treated BxPC-3 human pancreatic adenocarcinoma cells

first: Zoran

last: Gajic

first: Christina

last: Wang


title: Expression data of miRNAs and lncRNAs from the lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic days 17 and 19

first: Zhonghua

last: Yang


title: cDNA sequencing of rRNA from mouse tissues and human matched normal-tumor samples.

city: Barcelona

first: Ivan

last: Milenkovic

state: Catalonia

address: Dr. Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

summary: Mammalian ribosomal RNA (rRNA) molecules are highly abundant RNAs, decorated with over 220 different rRNA modifications, changing their chemical and biological properties. Previous works have shown that some types of rRNA modifications can be dynamically regulated; however, a comprehensive analysis of how the mammalian rRNA modification landscape is remodeled across time, cell types and upon disease conditions, remains largely unexplored. Here, we employ direct RNA nanopore sequencing to generate maps of human and mouse rRNA modifications across tissues, developmental stages, cell types and disease conditions. Our analyses reveal multiple rRNA sites that are differentially modified in a tissue- and/or developmental stage-specific manner. Notably, the adult brain exhibits the most distinct rRNA modification patterns, including previously unannotated rRNA modified sites. We then demonstrate that dynamic rRNA modification patterns can be used for tissue and cell type identification, which we hereby term ‘epitranscriptomic fingerprinting’. We then explored rRNA modification patterns in normal-tumor matched samples from lung cancer patients, finding that rRNA epitranscriptomic fingerprinting accurately classified clinical samples into normal and tumor groups from only 250 reads per sample, demonstrating the potential of rRNA modifications as diagnostic biomarkers, and revealing rRNA modifications as a rich source of information for tissue, cell type and disease identification.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Novoa, Eva Maria

first: Milenkovic

last: Ivan

first: Cruciani

last: Sonia

first: Llovera

last: Laia

first: Medina

last: Rebeca


title: Correlation between JA and jasmonic acid receptor COI1 in tobacco

city: Qingdao

first: Fuzhu

last: Ju

address: Laoshan District No.11 Forth Longitudinal Keyuan Rd.

institute: Chinese Academy of Agricultural Sciences Institute of Tobacco research

summary: JA-signaling in plants is manipulated by COI1 that recruits the protein complex perceiving JA signal . To determine JA correlated with the function of tobacco COI1, NtCOI1-silenced and control before and after MeJA treatment were analyzed using microarray chip.

overall_design: Two-condition experiment, Ctrl vs. NtCOI1-RI, Ctrl-JA vs. Ctrl,  NtCOI1-RI-JA vs. NtCOI1-RI, NtCOI1-RI-JA vs. Ctrl-JA, Biological replicates: 3control replicates, 3 transgenesis replicates.

first: Hongbo

last: Zhang


title: Gene expression profile at single cell level of  terminal ileum tissues from healthy humans and  atopic dermatitis

city: guangzhou

first: yalan

last: wu

address: guangzhou

institute: guang zhou university of China medicine

summary: Atopic dermatitis is one of the most common inflammatory disorders characterized by intense itch and widespread inflammatory eczematous lesion, while the exact mechanism underlying the pathogenesis of AD, remains not completely clear. Moreover, whether there is a certain degree of intestinal changes in patients with AD also remains to be further studied. scRNA-seq enables specific profiling of cell populations at single-cell resolution. Here, we analyzed cells from AD and matched healthy adult terminal ileums at single-cell resolution

overall_design: Single-cell mRNA profiles of p terminal ileum tissues from healthy humans and  atopic dermatitis were generated by Single-cell RNA sequencing, using BD Rhapsody system.

first: L

last: Wu

first: Y

last: Liu


title: Alpha-ketoglutarate dehydrogenase is a therapeutic vulnerability in acute myeloid leukemia [KL974_shOGDH]

status: Public on Nov 27 2024

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Perturbations in intermediary metabolism contribute to the pathogenesis of acute myeloid leukemia (AML) and can produce therapeutically actionable dependencies. Here, we probed whether alpha-ketoglutarate (aKG) metabolism represents a specific vulnerability in AML. Using functional genomics, metabolomics, and mouse models, we identified the aKG dehydrogenase complex, which catalyzes the conversion of aKG to succinyl CoA, as a molecular dependency across multiple models of adverse-risk AML. Inhibition of 2-oxoglutarate dehydrogenase (OGDH), the E1 subunit of the aKG dehydrogenase complex, impaired AML progression and drove differentiation. Mechanistically, hindrance of aKG flux through the tricarboxylic acid (TCA) cycle resulted in rapid exhaustion of aspartate pools and blockade of de novo nucleotide biosynthesis, while cellular bioenergetics was largely preserved. Additionally, increased aKG levels following OGDH inhibition impacted the biosynthesis of other critical amino acids. Thus, this work has identified a previously undescribed, functional link between certain TCA cycle components and nucleotide biosynthesis enzymes across AML. This metabolic node may serve as a cancer-specific vulnerability amenable to therapeutic targeting in AML and perhaps in other cancers with similar metabolic wiring.

overall_design: RNA sequencing of murine p53-mutant AML cell lines was perfored at days 0, 2, and/or 4 after induction of the indicated BFP-linked shRNAs with doxycycline. Two independent shRNAs targeting Ogdh (shOgdh346 and shOgdh2081) and a control shRNA (shRen713) were used. Sorted, induced (BFPplus) cells are included for all shRNAs. Undinduced (BFPmin) cells at each timepoint are included for control samples.

first: Scott

last: Millman

first: Almudena

last: Chaves-Perez

first: Sudha

last: Janaki-Raman

first: John

middle: P

last: Morris IV

first: Varun

last: Narendra

first: Chi-Chao

first: Benjamin

middle: T

last: Jackson

first: Jossie

middle: J

last: Yashinskie

first: Riccardo

last: Mezzadra

first: Tessa

middle: I

last: Devine

first: Valentin J

middle: A

last: Barthet

first: Michelle

last: Saoi

first: Timour

last: Baslan

first: Sha

last: Tian

first: Zohar

last: Sachs

first: Lydia W

middle: S

last: Finley

first: Justin

middle: R

last: Cross

middle: W

last: Lowe


title: Alpha-ketoglutarate dehydrogenase is a therapeutic vulnerability in acute myeloid leukemia [RN2_shOGDH]

first: Yu-Jui

last: Ho

overall_design: RNA sequencing of murine MLL-fusion AML cell lines was perfored at days 0 and 4 after induction of the indicated shRNAs with doxycycline. Two clonal isolates of two independent shRNAs targeting Ogdh (shOgdh346 and shOgdh2081) and a control shRNA (shRen713) were used.

first: Scott

last: Millman

last: Chen


title: Global gene expression changes in Sendai virus-derived feline induced pluripotent stem cells (iPSCs) during differentiation into mesenchymal stromal cells

city: Ithaca

first: Muhandiram

middle: Prasanna

last: Weeratunga

address: 121 Pleasant Grove Rd, 911 Hasbrouck Apartments

department: Baker Institute for Animal Health

institute: Cornell University

summary: Induced pluripotent stem cells (iPSCs) are a valuable resource in veterinary regenerative medicine and cellular therapy, particularly for advancing species-specific applications such as feline medicine. This study employs RNA sequencing (RNA-seq) to investigate the transcriptomic profiles of feline iPSCs generated using the Sendai virus method and mesenchymal stem cells (MSCs) derived from these iPSCs. The comparative analysis reveals unique expression patterns linked to the Sendai virus reprogramming approach, identifying key regulatory pathways and gene networks characteristic of Sendai virus-derived iPSCs. Furthermore, the distinct transcriptome of iPSC-derived MSCs showcases markers associated with mesenchymal lineage commitment and MSC functionality. These findings provide valuable insights into the impact of Sendai virus reprogramming on feline iPSC properties and contribute to advancing stem cell-based therapies tailored to feline-specific needs.

overall_design: To compare the gene expression profiles of Sendai virus-derived feline iPSCs and their corresponding iPSC-derived MSCs, RNA sequencing was performed for each of the following cell lines: SV-IPSCs (including SV-IPSCs-1 and SV-IPSCs-2) and IPSC-MSCs (including IPSC-MSCs-1 and IPSC-MSCs-2). To assess transcriptional differences across cell types, comparisons focused on SV-IPSCs vs IPSC-MSCs, highlighting gene expression changes during the differentiation process from SV-derived IPSCs to MSCs. Differential expression analysis was performed using the DESeq2 package in R. This experimental design facilitates the identification of distinct gene expression patterns, key regulatory pathways, and markers associated with differentiation.

first: Prasanna

first: Rebecca

middle: M

last: Harman

first: Gerlinde

last: Van de Walle


title: Gene expression profiling (total RNA-Seq) of HCV susceptibility Cells, Huh7.5 cell lines and primary human hepatocyte cells

city: Iksan-Si  Jeonbuk

first: Hee-Jeong

last: Han

country: South Korea

institute: Korea Zoonosis Research Institute  Jeonbuk National University

summary: To elucidate the underlying causes associated with HCV infection and proliferation, total RNA sequencing was conducted to compare transcriptome levels in primary human hepatocytes (PHH) and Huh7.5 cells, which differ in HCV susceptibility.

overall_design: Corning® Gentest™ Plateable Human CryoHepatocytes (Cat. no 454541, Lot no 393B) were utilized for primary human hepatocytes (PHH), and the Huh7.5 cell line was used for the human hepatoma cells. Total RNA was isolated from both cell types using Trizol reagent (Invitrogen), followed by total RNA sequencing.


title: Molecularly defined and functionally distinct subcircuits of the medial mammillary nucleus

city: Wuhan

first: Youming

last: Lu

state: Hu Bei

address: No. 13, Hangkong Road, Qiaokou District

department: School of Basic Medicine and Tongji Medical College

institute: Huazhong University of Science and Technology

summary:
we dissectede the PV positive neurons and Drd2 positive neurons from transgene mouse brains for single-cell RNA sequencing (RNA-seq)
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 biological replicates of PV-positive and Drd2-positive neurons .

first: Lanfang

last: Li

first: Yiqing

last: Guo


title: Gene expression proﬁling of MDA-MB-231 cells treated Compound 28, a CDK9 degrader

city: Shanghai

first: Jingya

last: Sun

state: Shanghai

address: No.501 Haike Road

institute: Shanghai Institute of Materia Medica CAS: Shanghai Institute of Materia Medica Chinese Academy of Sciences

summary: Triple-negative breast cancer (TNBC) is highlyaggressive with very limited treatment options due to the lack of eﬃcient targeted therapies and thus still remains clinically challenging. Targeting CDK9 to remodel transcriptional regulation shows great promisein cancer therapy. We synthesized new series of heterobifunctional molecules ashighly selective and eﬃcacious CDK9 degraders, enabling potentinhibition of TNBC cell growth and rapidly targeted degradationof CDK9. Moreover, the CDK9 degrader (compound 28) was used to treat on TNBC cell lines and the gene expression profile was performed by RNA-seq.

overall_design: MDA-MB-231 cell line were seed into 6 well plate at densities of 5×105 cells/well, the culture medium was replaced 24 h later, and MDA MB 231 cell line were incubated with 500 nM of 28 for 4 h, then the RNA of the cell line is extracted for RNA-seq.

first: Dan

last: Wei

first: Hanlin

last: Wang

first: Qinghe

last: Zeng

first: Ruimin

last: Huang

first: Jia

first: Xiao-Hua


title: Thyroid hormone-responsive genes in primary cultures of rat hepatic cells

city: Hiroshima

first: Nariaki

last: FUJIMOTO

state: Hiroshima

address: 1-2-3 Kasumi

department: RIRBM

institute: Hiroshima University

summary: cDNA microarray analysis was applied to primary cultures of rat hepatic cells treated with triiodothyronine (T3) at 10-9 M for 24 hrs to identify the differentially expressed genes. A limited number of genes were listed, and only 3 of them, pyridoxal kinase (Pdxk), phosphoe-nolpyruvate carboxykinase 1 (Pck1), and solute carrier family 17 member 2 (Slc17a2), were con-firmed to be up-regulated by quantitative RT-PCR.

overall_design: Primary cultured rat hepatocytes were treated with or without T3 at 10-9 M for 24 h. Total RNA was extracted with NucleoSpin RNA II. Total RNA from control and T3-treated cells was subjected to cDNA microarray analysis using a GeneChip Array (Rat Genome 230 2.0).

first: N

last: Fujimoto

first: S

last: Kitamura


title: NOTCH3 Promotes Malignant Progression of Bladder Cancer by Directly Regulating SPP1 and Activating PI3K/AKT Pathway

first: Changxue

last: Liu

state: Shandong

address: Qingdao, Shandong, China

institute: The Affiliated Hospital of Qingdao University

summary: The biological role and precise molecular mechanisms of Notch receptor 3 (NOTCH3) in the malignant progression of bladder cancer (BLCA) remain unclear. In this study, we found that NOTCH3 was significantly upregulated and associated with poor prognosis in BLCA patients. Functional experiments demonstrated that NOTCH3 knockdown inhibited BLCA cell proliferation, migration, invasion and significantly suppressed tumor growth and metastasis in vivo as well. Mechanically, chromatin immunoprecipitation and dual-luciferase reporter assays confirmed that NOTCH3 could promote the transcription of secreted phosphoprotein 1(SPP1), a potential downstream target gene of NOTCH3，by binding to the CSL elements in the SPP1 promoter. Moreover, we also found that targeting NOTCH3 inhibited BLCA growth and metastasis by suppressing the SPP1-PI3K/AKT axis. Our study highlights the critical role of NOTCH3-SPP1-PI3K/AKT axis in the malignant progression of BLCA, suggesting that NOTCH3 may be a potential therapeutic target for BLCA.

overall_design: T24 cells with validated stable knockdown of NOTCH3 and their control group were cultured in 6-well plates for 24 hours, and 5×106 T24 cells were collected (n=3 per group). Cells were then lysed using TRIzol reagent (Invitrogen, USA) for RNA sequencing.

first: Huaixi

last: Ge

first: Chengquan

last: Shen

first: Ding

last: Hu

first: Xinzhao

last: Zhao

first: Ruize

last: Qin

first: Yonghua


title: CHI-KAT8i5 suppresses ESCC tumor growth through inhibiting KAT8 mediate c-Myc stability

city: Zhengzhou

first: Dandan

last: Zhang

address: Dongming road

institute: China-US (Henan) hormel cancer insititute

summary: The integrated analysis of histone modifier enzymes in solid tumor, especially in esophageal squamous cell carcinoma (ESCC) is still inadequate. Here, we investigate the expression levels of histone modifier enzymes in ESCC tissues. Notably, KAT8 is identified as a prognostic and therapeutic biomarker in ESCC. Esophageal tissue-specific deletion of KAT8 mice exhibite less tumor burden after induction of tumorigenesis via 4NQO treatment compared with wild-type mice. Meanwhile, silencing KAT8 significantly suppresses tumor growth in CDX and PDX model. Mechanically, we confirm that KAT8 regulates c-Myc protein stability by directly binding it. Furthermore, we design and screen a specific KAT8 inhibitor (CHI-KAT8i5) that significantly attenuate tumor growth in vitro and in vivo, providing promising potential for clinical application. Thus, our work identify KAT8 could serve as a potential clinically relevant biomarker and therapeutic target in patients with ESCC disease and optimize KAT8 inhibitor is a promising lead candidate for ESCC therapy.

overall_design: To investigate the potential mechanism of KAT8.The scramble and shKAT8  cell line were used for transcriptome sequencing.

first: Zigang

last: Dong

first: Ming

last: Jiang


title: Nonylphenol and Cetyl Alcohol Polyethoxylates Disrupt Thyroid Hormone Receptor Signaling to Promote Metabolism Disrupting Effects

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

summary: Surfactants are molecules with both hydrophobic and hydrophilic structural groups that adsorb at the air-water or oil-water interface and serve to decrease the surface tension. Surfactants combine to form micelles that surround and break down or remove oils, making them ideal for detergents and cleaners. Two of the most important classes of nonionic surfactants are alkylphenol ethoxylates (APEOs) and alcohol ethoxylates (AEOs). APEOs and AEOs are high production-volume chemicals that are used for many industrial and residential purposes, including laundry detergents, hard-surface cleaners, paints, and pesticide adjuvants. Nonylphenol ethoxylates (NPEOs) comprise ~80% of the total annual production of nonionic surfactants. Commensurate with better appreciation of the toxicity of APEOs and the base alkylphenols, use of AEOs has increased, and both sets of compounds are now ubiquitous environmental contaminants. Using a well-established in vitro model of adipogenesis, we recently demonstrated that diverse APEOs and AEOs induce triglyceride accumulation and/or pre-adipocyte proliferation. Both sets of contaminants have also been demonstrated as obesogenic in a developmental exposure zebrafish model, promoting increased body weights, increased adiposity (preferentially in visceral depots), and/or disrupting energy expenditure or behavioral responses. While these metabolic health effects are consistent across models and species, the mechanisms underlying these effects are less clear. This study sought to evaluate causal mechanisms through reporter gene assay assessments, relative binding affinity assays, co-exposure experiments, and use of both human cell and zebrafish models. We report that antagonism of thyroid hormone receptor signaling appears to mediate at least a portion of the polyethoxylate-induced metabolic health effects. These results suggest further evaluation is needed, given the ubiquitous environmental presence of these thyroid hormone system disrupting contaminants and reproducible effects in human cell models and vertebrate animals.

overall_design: A transcriptome was determined from Zenbio-sourced human bone marrow derived mesenchymal stem cells to assess whether thyroid hormone receptors and associated machinery was expressed in these cells. A sample of pre-differentiated hMSCs was submitted for transcriptome assessment.

first: Christopher

last: Kassotis

first: Roxanne

last: Berube

first: Brooklynn

last: Murray

first: Thomas

last: Kocarek


title: The ion channel mechanisms of the subthreshold inward depolarizing currents in the VTA dopaminergic neurons and their roles in the depression-like behavior

city: Shijiazhuang

first: Jing

last: Wang

address: No.466 ZhongshanRoad

institute: Hebei Medical University

summary: The dopaminergic (DA) neurons in the ventral tegmental area (VTA) of middle brain play important role in emotion related behaviour, and the alteration of excitability of VTA DA neurons are believed to be the key determinants in behaviours of depression and drug addictions. The excitability of VTA DA neurons controls the release of DA in the projection fiber terminals thus controls the function of VTA DA neurons. After many years hard work, we begin to understand how the excitability of VTA DA neurons are regulated, but these achievements are far from satisfactory. Furthermore, with recent progress and realization that property of VTA DA neurons, against the classical view that VTA DA neurons are homogeneous population, are distinctly different, thus the accumulated limited knowledge on the mechanism of excitability modulation of VTA DA neurons is especially short of expectation. The most outstanding indications of the heterogeneity of VTA DA neurons are represented by the distinctly different electrophysiological properties among VTA DA neurons projecting to different brain regions. However the underlying mechanism is not clear. In this application we plan to investigate the underlying mechanism determining the distinct excitability of VTA DA neurons projecting to the cortical and the limbic regions of the brain by single cell RNA sequencing (scRNA-seq). The main focus of the study will be on the intrinsic ion channels and the related modulation mechanism of VTA DA neuron excitability. On the basis of this we will further study the mechanism which underlie alteration of excitability of VTA DA neurons in condition of depression state, and still further the related depression behaviour.

overall_design: After retrobeads injection, following brain slice preparation and recording, the recorded and retrobeads-labelled VTA neurons were aspirated into the patch pipette and then sequenced using Illumina HiseqXten.

first: Hailin


title: CRISPR-SaCas9-KKH targeting of miR-21 through a single adeno-associated virus vector prolongs survival of GB-bearing mice

city: Charlestow

first: Lisa

last: Nieland

state: Massachusetts

address: 149 13th street

department: Neurology

institute: Massachusetts General Hospital

summary: Glioblastoma (GB), the most aggressive tumor of the central nervous system (CNS), has poor patient outcomes with limited effective treatments available. MicroRNA-21 (miR-21) is a known oncogene, abundantly expressed in many cancer types. MiR-21 promotes glioblastoma progression, and lack of miR-21 reduces tumorigenic potential of tumor. Here, we propose a single adeno-associated virus (AAV) vector strategy targeting miR-21 using the Staphylococcus aureus Cas9 ortholog (SaCas9) guided by a single-guide RNA (sgRNA). Our results demonstrate that AAV8 is a well-suited AAV serotype to express SaCas9-KKH/sgRNA at the tumor site in an orthotopic glioblastoma model. The SaCas9-KKH induced a genomic deletion, resulting in lowered miR-21 levels in the brain, leading to reduced tumor growth and improved overall survival. In this study we demonstrated that a single AAV-mediated mir-21 disruption influences glioma development resulting in beneficial anti-tumor outcomes in GB-bearing mice.

overall_design: To investigate the therapeutic effect of targeting microRNA-21 in a glioma context we peformed Next Generation Sequencing analysis to confirm gene-editing of the targeted microRNA-21. A wild-type (WT) non-edited cell line and/or SaCas9 only condition were the controls. 1) Co-transfected in vitro in glioma cell lines (CT2A and GL261) with SaCas9 and sgRNA to knockdown miR-21. 2) Tested a single construct containing both SaCas9 and sgRNA to target miR-21 in vitro cell lines. 3) designed a single AAV vector to CRISPR-edit microRNA-21 in vivo in a glioblastoma mouse model. The AAV was delivered locally by injecting it intratumorally in the mice brain. We then analysed FACS sorted tumor tissue for CRISPR-editing of microRNA-21 by Next Generation Sequencing. 4) We screened 5 potential off-targets in the mouse genome of the specific sgRNA we used in this study by Next Generation Sequencing.

first: Anne

last: B Vrijmoet

first: Isabelle

last: W Jetten

first: David

last: Rufino-Ramos

first: Alexandra

last: J.E.M. de Reus

first: Koen

last: Breyne

first: Benjamin

last: P Kleinstiver

first: Casey

last: A Maguire

first: Marike

last: L.D. Broekman

first: Xandra

last: O Breakefield

first: Erik

last: R Abels


title: Investigate the effect of MSCs treatment on the glomeruli of mice with lupus nephritis by RNA sequencing

city: Nanjing

first: Qixiang

last: Zhang

address: Tongjiaxiang #24, Nanjing, Jiangsu Province, China

institute: China Pharmaceutical University

summary: Human umbilical cord mesenchymal stem cells (hUC-MSCs) have shown potential as a therapeutic option for lupus nephritis (LN), particularly in patients refractory to conventional treatments. Despite extensive translational research on MSCs, the precise mechanisms by which MSCs migrate to the kidney and restore renal function remain incompletely understood. Here, we aim to clarify the spatiotemporal characteristics of hUC-MSC migration into LN kidneys and their interactions with host cells in microenvironment. This study provides valuable insights into the significant involvement of CXCL10-CXCR3 axis in hUC-MSC migration to the LN kidneys and the subsequent remodeling of renal immune microenvironment.

overall_design: We set up a blank control group of mice, a lupus nephritis model group of mice (MRL/lpr mice), and MRL/lpr mice treated with MSCs, and then isolated the mice's glomeruli and performed single-cell sequencing.

first: Fang

last: Zhou


title: Tracking changes in functionality and morphology of repopulated microglia in young and old mice [RNA-Seq]

city: Warsaw

first: Patrycja

last: Rosa

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

summary: Microglia (MG) are resident myeloid cells in the central nervous system (CNS) that perform homeostatic or pathological functions. Microglia self-renewal is controlled by the macrophage colony-stimulating factor-1 (CSF-1). Inhibitors of CSF-1 receptor (i.a. BLZ-945) by blocking the CSF1R signaling deplete 99% of microglia in 21 days and after cessation of treatment microglia rapidly repopulate and restore normal density within 1 week in adult mice. The functions of these repopulated microglia are poorly known and they can vary according to age. To investigate the microglia repopulation process, we compared samples of repopulated microglia from old (18-22 months) mice against undepleted controls using RNA sequencing (RNA-seq).

overall_design: We compared BLZ-945 depleted microglia from old (18-22 months) GFP-M::Cx3cr1-CreERT2fl/fl::Rosa26-tdTomatotg/tg mice against undepleted controls. For both conditions, separate RNA-seq libraries from three animals were constructed.

first: Zuzanna

last: Luczak-Sobotkowska

first: Maria

last: Banqueri Lopez

first: Aleksander

last: Jankowski

first: Bozena

last: Kaminska


title: PTEN depletion reduces global levels of H3K27me3 to promote epithelial-to-mesenchymal transition in epithelial colorectal cancer cells [ATAC-seq]

city: Bloomington

first: Ahmed

last: Ghobashi

state: IN

institute: Indiana University

summary: Epithelial-to-mesenchymal (EMT) transition is one of the best-known examples of tumor cell plasticity. EMT enhances cancer cell metastasis, which is the main cause of colorectal cancer (CRC)-related mortality. Therefore, understanding underlying molecular mechanisms contributing to the EMT process is crucial to finding druggable targets and more effective therapeutic approaches in CRC. In this study, we demonstrated that activation of AKT induces EMT in epithelial CRC. Activation of AKT through Phosphatase and tensin homolog (PTEN) knockdown (KD) modulated chromatin accessibility and reprogrammed gene transcription to mediate EMT in epithelial CRC cells. Active AKT can phosphorylate EZH2 on serine 21, which switches EZH2 from a transcriptional repressor to an activator. Interestingly, PTEN KD reduced the global level of trimethylation of histone 3 at lysine 27(H3K27me3) in an EZH2-phosphorylation-dependent manner. Additionally, EZH2 phosphorylation at serine 21 reduced the interaction of EZH2 with another polycomb repressive complex 2 (PRC2) component, the Suppressor of Zeste 12 (SUZ12), suggesting that the reduced H3K27me3 levels in PTEN KD cells were due to a disruption of the PRC2 complex. Overall, we demonstrated that PTEN KD modulates changes in gene expression to induce the EMT process in epithelial CRC cells by phosphorylating EZH2 and activating different transcription factors such as activator protein 1 (AP1).

overall_design: Investigating how PTEN  KD altered chromatin accessibility in HT29. ATAC-seq in PTEN KD and EV HT29 with and without EZH2 inhibitor

first: Heather

last: O'Hagan


title: The effect of neutrophil extracellular trap (NETs) on BMDMs

city: Beijing

first: Xuan

last: Zhao

address: 45 Changchun Street, Xicheng District, Beijing

institute: xuanwu hospital capital medical university

summary: To investigate the altered gene expression levels in BMDMs treated with or without NETs. Each group had a biological repeat (n=3). Results provide insight into the effect of NETs on BMDMs.

overall_design: Three groups of BMDMs treated with NETs (NETs-treated group) versus three groups of normal BMDMs (Control group).


title: Tracking changes in functionality and morphology of repopulated microglia in young and old mice

summary: Microglia (MG) are resident myeloid cells in the central nervous system (CNS) that perform homeostatic or pathological functions. Microglia self-renewal is controlled by the macrophage colony-stimulating factor-1 (CSF-1). Inhibitors of CSF-1 receptor (i.a. BLZ-945) by blocking the CSF1R signaling deplete 99% of microglia in 21 days and after cessation of treatment microglia rapidly repopulate and restore normal density within 1 week in adult mice. The functions of these repopulated microglia are poorly known and they can vary according to age. To investigate the microglia repopulation process, we compared samples of repopulated microglia from young (3 months) and old (12 months) mice using single cell RNA sequencing (scRNA-seq).

overall_design: We compared BLZ-945 depleted microglia from young (3 months) and old (12 months) GFP-M::Cx3cr1-CreERT2fl/fl::Rosa26-tdTomatotg/tg mice against undepleted controls. Four scRNA-seq libraries (Rep1 to Rep4) were constructed, each combining four animals representing all experimental conditions (control young, control old, repopulated young, repopulated old).

first: Natalia

last: Ochocka


title: PTEN depletion reduces global levels of H3K27me3 to promote epithelial-to-mesenchymal transition in epithelial colorectal cancer cells [RNA-seq]

overall_design: Investigating how PTEN  KD altered gene transcription in HT29. RNA-seq in PTEN KD and EV HT29 with and without EZH2 inhibitor


title: Targeting Pyk2 inhibition enhances bone restoration

city: Sapporo

first: Ji-Won

last: Lee

state: Does Not Apply

address: N13W7, Kita-Ku

department: Graduate school of Dental Medicine

institute: Hokkaido University

summary: Understanding the intricate cellular interactions involved in bone restoration is crucial for developing effective strategies to promote bone healing and mitigate conditions such as osteoporosis and fractures. Here, we provide compelling evidence supporting the anabolic effects of a pharmacological Pyk2 inhibitor (Pyk2-Inh) in promoting bone restoration. Using an ovariectomized mouse model, we administered Pyk2-Inh orally, resulting in increased bone mass characterized by reduced bone resorption, increased bone formation and decreased bone marrow fat. In vitro, Pyk2 inhibition significantly impedes osteoclast differentiation and bone resorption. In a co-culture system comprising osteoblasts and osteoclasts, Pyk2-Inh effectively suppressed osteoclast differentiation, accompanied by a substantial increase in the transcriptional expression of Tnfrsf11b and Csf1 in osteoblasts. Additionally, Pyk2 signaling inhibition markedly enhances alkaline phosphatase (ALP) activity, a hallmark of osteoblast differentiation, through an increase in canonical Wnt/β-catenin signaling. Notably, analysis of human mesenchymal stem cells through RNA-seq revealed a novel candidate, SCARA5, identified through Pyk2-Inh treatment. We demonstrate that Scara5 plays a crucial role in suppressing the differentiation from stromal cell into adipocytes, and accelerates lineage commitment to osteoblasts, establishing Scara5 as a negative regulator of bone formation. These results suggest Pyk2 as a potential therapeutic target for both adipogenesis and osteogenesis in bone marrow. Our findings underscore the importance of Pyk2 signaling inhibition as a key regulator of bone remodeling, offering promising prospects for the development of novel osteoporosis therapies.

overall_design: To assess the impact of Pyk2 signaling on the transcriptomic profile, primary human mesenchymal cells (hMSCs) were cultured in 24-well plates with or without Pyk2 inhibitor. Cells were divided into two groups as control and Pyk2 inhibitor treatment (concentration: 50 nM).


title: Effect of treatment with IFN-β on miRNA expression in extracellular vesicles secreted by mesenchymal stem cells

first: Meng

last: Yuan

state: Jiangsu

address: 22 Hankou Road, Nanjing, Jiangsu 210093

institute: Nanjing University

summary: MSC-EVs have emerged as a promising cell-free therapeutic tool with tremendous potential for treating a variety of diseases. Studies have demonstrated that MSCs exhibit enhanced immune regulatory abilities when stimulated by inflammatory factors. Notably, the presence of IFN-β in MSC culture has been shown to impact the expression of chemokines and their receptors in human MSCs, leading to a significant increase in the secretion of immunomodulatory molecules and their immune modulatory effects. We found that the enhanced immune function of MSCs induced by IFN-β can be presented by their secreted EVs in line with the evidence that the contents of extracellular vesicles were reflective of the physiological or pathological states of the cells from which they derived. These nanoscale vesicles, composed of natural phospholipid bilayer membranes, can encapsulate various biologically active substances, including nucleic acids (RNA, DNA, non-coding RNA), proteins, and lipids. Through these cargoes, EVs can regulate the physiological functions of distal recipient cells, facilitating the exchange of information between cells and tissues.

overall_design: To investigate the effect of IFN-β treatment on miRNA expression in extracellular vesicles secreted by mesenchymal stem cells, EVs were purified by multiple ultracentrifugation steps from the conditioned media obtained from MSCs cultured with or without IFN-β stimulation for a duration of 2 days. We performed gene expression profiling using data obtained from miRNA-seq in two groups of extracellular vesicles.


title: Deficiency of lysophosphatidic acid receptor 3 decreases the erythropoietin production in hypoxic mouse kidney

last: Yin

address: 19 Xinjiekouwaida Street

department: College of Life Science

institute: Beijing Normal University

summary: As a simple lipid mediator, Lysophosphatidic acid (LPA) exerts its function by binding to 6 GPCRs (LPAR1-6) on the cell membrane. Among the 6 LPA receptors, LPAR3 is highly expressed in mouse kidney, where it has only been found to play a harmful role in kidney ischemia-reperfusion injury and diabetic nephropathy. Our previous research and other researchers found the correlation between the ATX-LPA-LPAR axis and hypoxia-related biological processes. The kidney is one of the most susceptible organs to hypoxia. It is therefore interesting to identify the function of LPAR3 in hypoxic mice kidneys. In this study, the wild-type (WT) and Lpar3-/- mice were put into a normobaric hypoxic installation and RNA sequencing analysis showed that Lpar3-/- mice showed a significant decrease in hypoxia-induced EPO expression in the kidney compared with WT mice. The impaired EPO gene expression resulted in reduced plasma EPO levels and lower hematocrit and hemoglobin levels. The KEGG enrichment analysis revealed the reduced accumulation of HIF-2α caused by LPAR3 deficiency may be the reason for insufficient hypoxic renal EPO production. In in-vitro hypoxic cell models (Hep3B cells and HK2 cells), targeting LPAR3 can also regulate HIF-2α and EPO expression. KEGG analysis revealed that the PI3K/Akt signaling pathway was involved in the regulation of LPAR3 on HIF-2α-EPO, which was validated at the tissue level and cell level. Taken together, this study demonstrates that the murine renal LPAR3 promotes HIF-2α accumulation to maintain renal EPO production by activating the downstream PI3K/Akt pathway, ensuring the generation of red blood cells in mice and plays an important role in the body's adaptation to hypoxia.

overall_design: To investigate the physiological function of LPAR3 in hypoxic mice kidneys, the wild-type (WT) and Lpar3-/- mice were put into a normobaric hypoxic installation (8% O2) for 12 h and the kidneys were harvested for RNA sequencing.

first: Junjie

last: zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of HCC Cell Line HepG2 Cells with Inhibited P2X7 Receptor Signaling by Antagonist A740003 or A438079

city: Xi'an

first: Xiao

last: Yang

state: Shaanxi

address: 157#, Xiwu Road, Xincheng District

department: The Second Affiliated Hospital

institute: Xi'an Jiaotong University

summary: The goals of this study aim to reveal the role of P2X7 receptor signaling in HCC

overall_design: Compare transcriptomes of HepG2 cells treated with PBS (Control), A740003 (P2X7 specific antagonist) or A438079 (P2X7 specific antagonist)


title: Effect of depletion of NEDD4L on gene expression in EC9706 esophageal squamous cell carcinoma cells

city: Xinxiang

first: zhen

last: chen

state: China

address: Hongqi District

institute: Xinxiang Medical Universty

summary: NEDD4L plays a dual role in cancer. In order to verify its role in esophageal squamous cell carcinoma and the impact of NEDD4L deletion on different signaling pathways and gene expression, we used siRNA to transfect EC9706 cells to explore the role of NEDD4L deletion in esophageal squamous cell carcinoma.

overall_design: To examine the effect of deleting NEDD4L on gene expression in EC9706 esophageal squamous cell carcinoma cells, we transfected three groups of siRNA and sicontrol respectively.


title: miR-10a-3p as a potential non-invasive biomarker for NSCLC patients’ survival

city: Vilnius

first: Linas

last: Kunigėnas

address: Santariškių str. 1

country: Lithuania

institute: National Cancer Institute

summary: Lung cancer is the most currently diagnosed cancer type among adults and the most common cause of death from cancer worldwide. Poor lung cancer patients’ outcomes and survival rates demand   discovery of new biomarkers for the specific, significant, and non-invasive detection of non-small cell lung cancer (NSCLC) progression. Determination of cell lines' relationship to genomic changes in tumors could be valuable for functional and therapeutic discoveries. Human cell line models with different aggressiveness statuses may play an important role in the investigation of NSCLC. In addition, miRNA expression patterns that are reliable in predicting NSCLC patients’ survival rates are highly promising cancer biomarkers. The aim of the present study was to investigate the potential of miRNA expression as biomarkers in NSCLC.

overall_design: In order to determine miRNA expression pattern related to lung cancer aggressiveness total RNA were extracted from HBEC3, H1299, A549, Calu-1, and H23 cultured as multicellular spheroids for miRNA sequencing.

first: Julija

last: Šimienė

first: Rimvilė

last: Prokarenkaitė

first: Daiva

last: Dabkevičienė

first: Eglė

last: Strainienė

first: Saulius

last: Cicėnas

first: Kęstutis

last: Sužiedėlis


title: LncRNA/mRNA expression profiling for diabetic and reversal rat retina samples

first: Pooja

last: Malaviya

state: Michigan

address: 4717 St Antoine, Kresge eye institute Room#404

institute: Wayne state university

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We employed LncRNA/mRNA expression profiling as a discovery platform identify aberrantly expressed LncRNAs that fail to reverse back after hyperglycemia is terminated. Using rat model of diabetic retinopathy- metabolic memory, LncRNA array was performed in the retina of rats diabetic for eight months, or in poor glycemic control for four months followed by good glycemic control for four additional months. Expression of selected LncRNAs and their associated genes from these profiles were confirmed by quantitative real-time PCR.

overall_design: Differential expression profiling for LncRNA/mRNA was measured for normal, diabetic (8 months) and reversal (diabetic for four months followed by good glycemic controlfor four months) rat retina samples. Each group had 6-7 animals.

first: Renu

last: Kowluru

first: Jay

last: Kumar

first: Ghulam

last: Mohammad


title: IgE plasma cells differentially regulate antibody secretion, ER stress and tissue-specific longevity relative to other isotypes

city: Tarrytown

first: Joseph

middle: Cooper

last: Devlin

address: 777 Old Saw Mill River Rd

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

summary: Understanding the transcriptional signature of IgE producing cells is fundamental to plasma cell biology. IgE PCs from bone marrow (BM) upregulated genes associated with pro-survival, and BM homing, whereas IgE PCs from draining lymph nodes (dLN) expressed genes associated with recent class-switching and differenatiation. Finally, IgE PCs exhibited higher expression of ER stress and protein coding compared to IgG1.

overall_design: The TRAPnSeq protocol was performed on bone marrow and draining lymph nodes of mice exposed to HDM for 15 weeks, and of mice exposed to HDM and treated with anti-IL4Ra. Single cell sequencing was performed on bone marrow of allergic donors.

first: Andrea

last: Vecchione

last: Cooper Devlin

first: Seblewongel

last: Asrat

first: Carley

last: Tasker


title: Transcriptomics of A. mexicanum Regeneration: A Comparative Study Reveals Key Proteins And Pathways for Limb Regeneration.

city: Mexico City

first: Ernesto

last: Soto-Reyes

state: Delegación Cuajimalpa de Morelos

address: Av. Vasco de Quiroga 4871

country: Mexico

institute: Universidad Autónoma Metropolitana

summary: The axolotl is an animal with remarkable regenerative abilities, making it an ideal model for studying potential regenerative therapies in mammals, including humans. However, the molecular mechanisms involved in regeneration remain unclear. We conducted a transcriptomic analysis of juvenile axolotls' limbs and their blastema and compared the results with aged axolotls that failed to regenerate after amputation. We identified a set of genes involved in cell differentiation, transcriptional regulation, cartilage development, bone morphogenesis, and extracellular matrix remodeling. Four highly expressed genes (FSTL1, ADAMTS17, GPX7, and CTHRC1) were identified in regenerating tissue, but underexpressed in aged axolotls. Structural and homology analysis showed that these genes are conserved and have important roles in development, bone morphogenesis, and cartilage formation. Our findings propose a novel set of key axolotl genes involved in tissue regeneration that could be a starting point for further studies in other vertebrates.

overall_design: Total RNA from the inferior limbs of five juvenile axolotls, aged 8 months, as well as from two aged axolotls, aged 8 years. Blastema was collected 10 days post-amputation from juvenile axolotls, whereas aged axolotls did not display any development of blastema tissue.

first: Aylin

last: del Moral-Morales

first: Cynthia

last: Sámano

first: José

last: Ocampo-Cervantes

first: Maya

last: Topf

first: Jan

last: Baumbach

first: Rodrigo

last: González-Barrios


title: 5-methylcytosine modification profiling of messenger RNA in breast cancer brain metastasis

city: Liaocheng

first: Bo

last: Fu

address: 67 Dongchang West Road

institute: Liaocheng People's Hospital

summary: We performed m5C MeRIP-seq to clarify the role of m5C RNA modification in the pathogenesis of BCBM

overall_design: Sample: cell line; Group: breast cancer brain metastasis (BCBM) vs breast cancer (BC),each with 3 replicates; Methods:m5C RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China). Briefly, m5C RNA immunoprecipitation was performed with the GenSeqTM m5C RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m5C IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

first: Peiying

last: Cai

first: Jichao

last: Li

first: Wei

last: Zhang

first: Yan

last: Liu


title: Epigenetic signature of human vitamin D3 and IL-10-conditioned regulatory DCs

city: Pittsburgh

first: Shuchang

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

type: Methylation profiling by high throughput sequencing

summary: To define the epigenetic signature of human DCregs generated in vitamin 14 D3 (vitD3) and IL-10 compared to immune stimulatory DCs (sDCs), we measured levels of DNA methylation by whole genome bisulfite sequencing (WGBS). Distinct DNA methylation patterns were acquired by DCregs compared to sDCs. These patterns were located mainly in transcriptional regulatory regions. Genes associated with these programs were enriched in STAT3-signaling and valine catabolism in DCregs; conversely, pro-inflammatory pathways e.g., pattern recognition receptor signaling, were enriched in sDCs. Further, DCreg differentially-methylated regions (DMRs) were enriched in binding motifs specific to the immunomodulatory transcription factor KLF11, while AP1 (Fos:Jun) transcription factor binding motifs were enriched in sDC DMRs. Using publicly-available data22 sets, we defined a common epigenetic signature shared between DCregs generated in vitD3 and IL-10, dexamethasone or vitD3 alone. These insights may help pave the way for design of epigenetic-based approaches to enhance production of DCregs as effective therapeutic agents.

overall_design: Leukapheresis products were obtained under an IRB-approved protocol (Institute for Transfusion Medicine, Pittsburgh, PA). Monocyte-enriched, elutriated fractions recovered from 6 normal human donor leukapheresis products were used for generation of DCregs and monophosphoryl lipid A (MPLA; TLR4 ligand low toxicity derivative of bacterial lipopolysaccharide (LPS))-matured sDC. In instances where the elutriated monocyte fraction purity was <90%, CD14-specific immunobeads (Miltenyi, San Diego, CA) were used according to the manufacturer’s protocol to increase monocyte purity to >90%. After 7 days culture, monocyte-derived DCreg and sDC were harvested. The viability of DCregs and sDCs, determined by trypan blue staining, was routinely > 95%. A portion of each DC group was snap-frozen in liquid nitrogen and stored at -80°C for Whole Genome Bisulfate Sequencing (WGBS) DNA Methylation analysis. Portions of the remaining DC were either antibody-stained for key surface molecules, HLA-DR, CD11c, T cell costimulatory and coinhibitory molecules and CD163 (clone RM3/1, Biolegend) and flow cytometry data analyzed using Flow Jo software. DNA was extracted from frozen cell pellets and underwent bisulfite treatment. The bisulfite modified DNA-sequencing library was generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) per the manufacturer’s instructions. WGBS data were collected from 6 sDC libraries and 6 corresponding DCreg libraries from the same donors.

first: Silvia

first: Alan

last: Zahorchak

first: Diana

last: Metes

first: Angus

last: Thomson

first: Hossam

last: Abdelsamed


title: The impact of METTL14 knockdown on gene expressions and m6A modifications in breast cancer

city: Hangzhou

first: Xupeng

last: Bai

state: Zhejiang

address: No.79 Qingchun Road

department: The First Affiliated Hospital

institute: Zhejiang University

summary: We previously found that the downregulation of METTL14 played a crucial role in maintaining breast cancer stem-like properties. The present study aims to explore the impact of METTL14 knockdown on gene expressions and m6A modifications related to stemness in order to elucidate the underlying mechanisms.

overall_design: To investigate the underlying mechanism through which METTL14 governs the stemness of breast cancer, we generated MCF7-shM14 cell lines wherein the expression of METTL14 was knocked down by shRNA. We conducted MeRIP-seq (m6A-seq) and RNA-seq analyses on these cells, comparing them to the control cells (MCF7-shNC).


title: Deciphering the gut microbiota of very early systemic sclerosis (VEDOSS): the first taxonomic and functional characterization

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Comparison of the faecal microbiota in patients with very early SSc (VEDOSS) and established SSc (systemic sclerosis).

overall_design: Total DNA was extracted from the stool of healthy subjects, VEDOSS (very early systemic sclerosis) patients and SSc (systemic sclerosis) patients, 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: Edda

last: Russo


title: Post-Stroke Learning Impairment and Brain Hemorrhage are Augmented in Hypertensive Mice

city: Bundoora

first: David

middle: Edward

last: Wong Zhang

state: Victoria

address: Plenty Road and, Kingsbury Dr

department: Microbiology, Anatomy, Physiology & Pharmacology

country: Australia

institute: La Trobe University

summary: Hypertension is a major risk factor for both stroke and cognitive impairment, but it is unclear whether it may specifically affect post-stroke cognitive impairment. We assessed the effect of hypertension and/or stroke on brain injury, cognitive outcome, and the brain transcriptomic profile. C57BL/6J mice (n=117; 3-5 mo.) received s.c. infusion of either saline or angiotensin II (for 14 d or 28 d) followed by sham surgery or photothrombotic stroke targeting the prefrontal cortex seven days later. Cognitive function was assessed with the Barnes maze. RNA sequencing was used to quantify transcriptomic changes in the brain. Angiotensin II treatment produced spontaneous hemorrhaging on the stroke brain. In the Barnes maze, hypertensive mice that received stroke surgery had an increased escape latency compared to other groups (day 3: hypertensive + stroke=166.6±6.0 s vs. hypertensive + sham=122.8±13.8 s vs. normotensive + stroke=139.9±10.1 s vs. normotensive + sham=101.9±16.7 s), consistent with a greater learning impairment. RNA sequencing revealed >800 differentially expressed genes related to neuroinflammation in hypertensive + stroke vs. hypertensive + sham, which included genes associated with apoptosis, microRNAs, autophagy, anti-cognitive biomarkers and Wnt signaling. The combination of hypertension and stroke resulted in greater learning impairment and brain injury.

overall_design: To investigate the concomittant effect of hypertension and stroke on the brain, prefrontal samples of the male mice brain were used to assess transcriptomic changes related to neuroinflammation.

first: Tayla

last: Gibson Hughes

first: Sharmalee

last: Selvaraji

first: Andrew

middle: N

last: Clarkson

first: Thiruma

middle: V

last: Arumugam

first: Grant

last: Drummond

first: Christopher

middle: G

last: Sobey

first: T

last: De Silva


title: A novel regulatory axis of MSI2-AGO2/miR-30a-3p-CGRRF1 drives cancer chemoresistance by upregulating the KRAS/ERK pathway

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South of Chongqing Road

department: Department of Biochemistry and cell biology

institute: Shanghai Jiao Tong University

summary: The KRAS/ERK pathway is crucial in cancer progression and chemotherapy resistance, yet its upstream regulatory mechanism remains elusive. We identified MSI2 as a new promoter of chemotherapy resistance in cancers. MSI2 directly binds to a specific class of mature miRNAs by recognizing the 'UAG' motif and interacts with the essential effector AGO2, highlighting MSI2 as a novel regulatory factor within the miRNA pathway. Specifically, MSI2 recruits UAG-miRNA miR-30a-3p to facilitate its loading onto AGO2, efficiently inhibiting the expression of CGRRF1. Further analysis reveals that CGRRF1 functions as a new ubiquitin E3 ligase for KRAS, mediating the ubiquitination and proteasome degradation of KRAS. Consequently, a novel regulatory axis involving MSI2-AGO2/miR-30a-3p-CGRRF1 positively regulates the KRAS/ERK pathway. Remarkably, platinum-based chemotherapy drugs significantly enhance the levels of phosphorylated ERK1/2 (p-ERK1/2) in cancer cells, and the EGFR inhibitor Gefitinib also increases p-ERK1/2 levels in Gefitinib-resistant cancer cells. Combining small-molecule inhibitors targeting MSI2, such as Ro 08-2750, efficiently alleviated chemoresistance in tumor cells exposed to Platinum and Gefitinib. These findings suggest that MSI2 could be a novel therapeutic target for developing strategies to counteract cancer resistance to treatment.

overall_design: mRNA expression profiles and miRNA expression profiles in DU145 stable cell lines.

first: Runhui

last: Lu


title: Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution (eccDNA)

first: Hanchen

last: Xu

address: No.725, South Wanping Rd

institute: Institute of Digestive, Longhua Hospital, Shanghai University of Traditional Chinese Medicine

summary: We collected 5 normal colon tissues, 5 colorectal adenomas, and 5 colorectal cancer tissues for high-throughput sequencing， Identify differential expression changes in ecDNA during disease progression

first: Lu

first: Lin

last: Zeng


title: Role of GLI-signaling in the postnatal cardiomyocyte development

city: Minneapolis

first: Bhairab

last: Singh

state: MN

address: 312 Church St SE, 7-124 Nils Hasselmo Hall

department: Biomedical Engineering

institute: University of Minnesota

summary: Developmentally, we found downregulation of GLI-signaling in adult human CM, adult murine CM, and in late-stage hiPSC-CM. To investigate the role of GLI-signaling in early-stage cardiomyocyte, we inhibited GLI-signaling and undertook bulkRNAseq analysis at two distinct levels of inhibitions.


title: Single-cell nuclear transcriptome sequencing and cross-species analysis reveal tree shrew retina Age-associated cellular profiles and specific markers

city: Chengdu

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

summary: Tree shrews (TS) possess a highly developed visual system with great potential for modelling human age-related diseases in eyes. However, the cellular and molecular characteristics of the TS retina are rarely understood. Here, we used single-nucleus RNA sequencing (snRNA-seq) to analyze the cellular map of the TS retina and determine the involvement of each cell type in retinal development during the postnatal lifespan. Intriguingly, increases in cones and retinal ganglion cells (RGCs), along with a reduction in rods and bipolar cells, were observed in the TS retina with an increase in age. Moreover, differential gene expression and histological analysis revealed retinal cell type-specific crucial genes in the developmental progression of TS. Especially, we observed that the circadian rhythm increased with age in TS from young to adult and elder stage, reflected in an increase in cone and RGC cells. Meanwhile, age-related TS-specific intercellular interactions in the retina were depicted, and these complex cell-cell communications may contribute to retinal degradation resistance and retinal homeostasis. Importantly, cross-species analysis compared the differences in retinal cell types and gene expression among TS, chicks, mice, primate macaques, and humans. TS exhibited a similar overall transcriptome expression associated with that in mice, which may be attributed to the higher complexity of retinal cell subtypes. Our findings for the first time decipher the cellular and molecular signatures in TS retina in different developmental stages, providing insights into the potential of TS as suitable animal model for studying retinal senescence and related disorders.

overall_design: We used single-nucleus RNA sequencing (snRNA-seq) to analyze the cellular map of the TS retina and determine the involvement of each cell type in retinal development during the postnatal lifespan.

first: Liu-Lin

last: Xiong

first: Yi-Fei

last: Sun

first: Rui-Ze

last: Niu

first: Li-Ren

last: Huangfu

first: Ting-Hua

last: Wang


title: Phase 1 Trial Combining Neoadjuvant Chemotherapy with Chemokine Modulatory Regimen for Triple Negative Breast Cancer

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: BACKGROUND. Pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) of triple negative breast cancer (TNBC) predicts long-term outcomes but is achieved only in 30-40% of patients. Higher CTL in the tumor microenvironment (TME) is associated with higher pCR. Combination with anti-PD1 immunotherapy increases pCR but at the cost of immune-related adverse events (irAEs). Our clinical trial using systemic chemokine-modulatory regimen (CKM; rintatolimod [selective TLR3-Ligand], interferon (IFN)-a2b and celecoxib [COX-2 inhibitor]) in patients with metastatic TNBC selectively increased CTL in the TME, providing rationale for its combination with NAC. METHODS. Phase I study NCT04081389 evaluated nine stage I-II TNBC patients who received 3 weeks of paclitaxel with CKM, followed by 9 weeks of paclitaxel alone, standard dose-dense doxorubicin and cyclophosphamide and surgery. Primary endpoint was safety and secondary endpoint included clinical efficacy. RESULTS. Combination treatment was well-tolerated with no dose-limiting toxicities or irAEs. 5/9 patients attained pCR, and 1 patient had micrometastatic disease (ypTmic). Circulating CTLs were decreased (0.12-fold average decrease) with upregulation of IFN-stimulatory and downregulation of CD8 gene signatures in all patients. This was accompanied by increase in CD8b (7.07- fold increase), CD8a/FoxP3 (2.18-fold increase), CCL5 (5.49-fold increase), and CXCL12 (6.06-fold increase) transcripts and multiplex analysis revealed decrease in epithelial and stromal markers with increase in CTL among patients with pCR. CONCLUSION: Combination paclitaxel/CKM regimen was safe, with preliminary indications of promising pCR+ypTmic of 66%.

overall_design: This is a phase I trial comibining  dose escalated IFN with paclitaxel, followed by Doxorubicin and cyclophosphamide, then followed by surgery. Blood samples were obtained pre-treatment and same day postreatment. 7 pairs of samples (3 Non-pCR and 4 pCR) pre and post treatment; 14 samples in total.

first: Shipra

last: Gandhi

first: Ronald

last: Slomba

first: Cayla

last: Janes

first: Victoria

last: Fitzpatrick

first: Janine

last: Miller

first: Kristopher

last: Attwood

first: Sacha

last: Gnajtic

first: Ioannou

last: Giorgio

first: Sinem

last: Ozbey

first: Igor

last: De Souza

first: Vladimir

last: Roudka

first: Suresh

last: Kalathil

first: Jianmin

last: Cortes Gomez

first: Kazuaki

last: Takabe

first: Stephen

last: Edge

first: Jessica

last: Young

first: Helen

last: Cappuccino

first: Mateusz

last: Opyrchal

first: Tracey

last: O’Connor

first: Ellis

last: G Levine

first: Pawel

last: Kalinski


title: Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution

first: Hanchen

last: Xu

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

overall_design: Refer to individual Series


title: Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus [4C-seq]

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: Enhancer clusters are platforms occupied at high-density by the transcription machinery to activate lineage-specific genes. However, it is not clear yet whether they are merely a collection of conventional enhancers or represent unique and new types of regulatory elements. Specifically, the question remains whether they activate additional enhancer programs in multigene loci. We addressed this issue in the mouse mammary gland, where genes are highly activated during pregnancy. We identify a 300kb multi-gene locus with twenty-one regulatory elements, including a cytokine-dependent primary enhancer cluster (PEC). Using genome editing in combination with ChIP-seq, RNA-seq and 3C-technologies, we show that the PEC initiates the activation of lineage-specific genes through contacting and activating secondary enhancers. This new framework of enhancer clusters indicates a hitherto unrecognized hierarchy of regulation by which a PEC activates genes via regulating secondary enhancers.

overall_design: 4C-seq for mammary tissues of wild type and mutant mice carrying a deletion of an enhancer cluster in the casein locus.

first: Hye

middle: K

last: Lee


title: Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus [Hi-C]

overall_design: Hi-C for mammary tissues of wild type mice.


title: MRAP mediated adipocyte differentiation by thymic mesenchymal stromal cells contributes to thymic involution

city: Nanjing

first: Dandan

last: Wang

address: 321 Zhongshan Road

institute: Nanjin Drum Tower Hospital

summary: Adipocyte deposition is believed to be a primary characteristic of age-related thymic involution, but the underlying cellular and molecular mechanisms remain unknown. We show here that thymic mesenchymal stromal cells (tMSCs) have a higher tendency to differentiate into adipocytes and melanocortin-2 receptor accessory protein (MRAP) is a potential driver of tMSCs adipogenesis. Furthermore, we discover that thymosin-α1 promotes MRAP expression in tMSCs through FoxO1 signaling pathway. Additionally, the proportion of tMSCs increase in older mice compared to young mice. Importantly, MRAP is also necessary for human thymic MSCs to differentiate into adipocytes when exposed to thymosin-α1. Single-cell RNA-seq analysis of human thymus revealed an accumulation of tMSCs and adipocytes during aging, indicating a strong potential for adipogenic differentiation in age-related thymic involution. Thus, we have revealed MRAP as a key factor in promoting thymic MSCs adipogenesis triggered by thymosin-α1 and FoxO1 pathway, which may serve as potential target to hinder adiposity in age-related thymic involution.

overall_design: three samples from mouse thymus and three samples from mouse dental pulp

first: Xiang

last: Fang

first: Ousheng

last: Liu

first: Junji

first: Fudong

last: Fan

first: Dongjin

first: Xin

last: Wen

first: Yichen

last: Han

first: Peter

last: Zanvit

first: Sang

last: Park

first: Wenwen

last: Jin

first: Lingyun

last: Sun

first: Wanjun

last: Chen


title: Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution (mRNA)

summary: We collected 5 normal colon tissues, 5 colorectal adenomas, and 5 colorectal cancer tissues for high-throughput sequencing. Identify differential expression changes in mRNA during disease progression

first: Lu

last: Lu

first: Lin

last: Zeng


title: Temporal Dynamics of Gene and Protein Expression Follow Volumetric Muscle Loss

status: Public on Nov 26 2024

city: Palo Alto

first: Ishita

last: Jain

address: 3801 Miranda Avenue

institute: Stanford University

summary: Here, we performed time-series analysis of transcriptomic and proteomic changes associated with VML in a mouse model, focusing on the dynamics of gene and protein expression patterns at up to three weeks after muscle injury. We identified signaling pathways associated with temporal expression patterns that fail to restore within 3 weeks after VML, including those with sustained upregulation or downregulation.  Using temporal expression analysis, we identified Sp1 as a novel molecular mediator of dysregulated muscle recovery after VML as well as elucidated pro-inflammatory and extracellular matrix (ECM) remodeling pathways mediating the remodeling process.  These insights pave the way for the development of new targets that promote muscle regeneration and functional recovery of traumatically injured muscle.

overall_design: We utilized a well-established mouse partial-thickness VML model, in which 40% of the tibialis anterior muscle in C57BL/6 (8-week-old male) mice was unilaterally excised, based on our previous work .  At time points of 3, 7, 14, and 21 days after the induction of VML, the tibialis anterior muscles were explanted for RNA extraction (n=5-6 samples per time point).

first: Beu

last: Oropeza

first: Caroline

last: Hu

first: Gladys

last: Chiang

first: Ngan

last: Huang


title: An Omics approach on Marchantia polymorpha single FERONIA and MARIS homologs confirms links between cell wall integrity and abscisic acid

city: Sophia Antipolis

first: Aurélien

last: Boisson-Dernier

address: 400 route des Chappes, BP 167

department: SPE

country: France

institute: INRAE

summary: Plant cells are surrounded by an extracellular cell wall that shields them from their abiotic and biotic environment. To coordinate their growth with their cell wall status, they have developed cell wall integrity mechanisms at the center of which lies the transmembrane Malectin-like receptor kinase FERONIA (FER). FER controls a myriad of plant developmental processes including sexual reproduction, cell growth and morphogenesis, often intersecting with phytohormones-dependent pathways such as abscisic acid (ABA) or plant immunity. Interestingly, FER and its downstream receptor-like cytoplasmic kinase MARIS (MRI) were shown to cooperate similarly in the control of root hair and rhizoid integrity for the vascular model Arabidopsis and the early diverging bryophyte model Marchantia polymorpha, respectively. Here, we carried out comparative transcriptomics and proteomics approach on Mpfer-1 and Mpmri-1 knock-down mutant plants and the wild-type strains Tak-1 and Tak-2. Our -omics analyses revealed that globally, MpFER and MpMRI largely cooperate to negatively regulate transcriptional and translational networks in particular those related to plant defense and ABA responses. Moreover, Mpfer-1 plants were found to be hypersensitive to ABA-dependent growth inhibition indicating that FER’s function of negatively regulating ABA-related growth responses is conserved between bryophytes and vascular plants.

overall_design: To reveal pathways that could be regulated by the ancestral MpFER/MpMRI module or alternative compensatory ones that are up-regulated in the absence of the module in Marchantia, comparative transcriptomic (RNA-seq)  analyses of Mpfer-1 (male) and Mpmri-1 (female) lines with short bursting rhizoids and their respective wild-type male (Tak-1) and female (Tak-2) strains with intact rhizoids were carried out. For this purpose, 3-week-old Marchantia thalli grown on cellophane membranes were collected and RNA were extracted and submited to RNAseq.

first: Timothy

last: Jobe


title: Novel Immune Response Evasion Strategy to Redose Adeno-Associated Viral Vectors and Prolong Survival in Surfactant Protein-B Deficient Mice

city: Charleston

first: Martin

last: Kang

state: SC

address: 173 Ashley Avenue CR405D

department: Pediatrics

institute: Medical University of South Carolina

summary: The goals and objectives for this study are to determine whether AAV containing TLR9 inhibitory oligonucleotide sequences (AAV-hSPBTLR9i) can mitigate the immune response sufficiently to redose AAV in the lungs and prolong the survival of SP-B deficient mice.

overall_design:
24 samples were analyzed for 773 murine genes plus 12 internal reference genes. There were 6 treatment groups: (1) no treatment - on doxycycline (positive control), (2) no treatment - off doxycycline (negative control), (3) AAV-hSPB single, (4) AAV-hSPBTLR9i single, (5) AAV-hSPB repeat, (6) AAV-hSPBTLR9i repeat. Groups 3-6 were administered their corresponding treatment via intratracheal delivery on Day 0. Doxycyline feed was removed from groups 3-6 on Day 7. Ninety days after the first AAV dose, groups 5 & 6 were given their second AAV dose via intratracheal delivery. Doxycycline feed was removed from group 2 on Day 94. On Day 97, the lungs were harvested from the mice and flash frozen. Then RNA was extracted from the lungs for gene expression analysis and interferon gene expression (nCounter).
9 samples were analyzed for 773 murine genes plus 12 internal reference genes. There were 3 treatment groups: (1) 1xPBS (positive control), (2) AAV-hSPB single, (3) AAV-hSPBTLR9i single. Mice were given their corresponding AAV treatment via intratracheal delivery on Day 0. Three hours later, the lungs of the mice were harvested and flash frozen. RNA was extracted from the lungs for gene expression analysis (nCounter).

middle: H

first: Sylvia

last: Thomas

first: Caralyn

last: Westley

first: Thomas

last: Blouin

first: Liqun

last: Xu

first: Ying

last: Chan

first: Erin

last: Lisk

first: Sarah

last: Allen

first: Arul

last: Vadivel

first: Kennedy

last: Nangle

first: Janani

last: Ramamurthy

first: Yanlong

last: Pei

first: Lunndon

last: Lewis

first: Jessica

first: Marty

last: Romeo

first: Silvia

last: Vaena

first: Elizabeth

middle: C

last: O'Quinn

first: Henry

middle: D

last: Schrecker

first: Casey

last: Langdon

first: Paul

last: Nietert

first: George

last: Church

first: Jeffrey

last: Whitsett

last: Wootton

first: Bernard

last: Thébaud


title: Investigation on molecular mechanism underlying the dynamic evolution from preneoplasia to invasive lung adenocarcinoma

city: Xi'an

first: Yanlu

last: Xiong

address: 569 Xinsi Road, Baqiao District

department: Tangdu Hospital

institute: Air Force Medical University

summary: The cell ecology and spatial niche implicated in the dynamic and sequential process of lung adenocarcinoma (LUAD) from adenocarcinoma in situ (AIS) to minimally invasive adenocarcinoma (MIA) and subsequent invasive adenocarcinoma (IAC) have not yet been elucidated. Here, we performed an integrative analysis of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to characterize the cell atlas of the invasion trajectory of LUAD. We found that the UBE2C + cancer cell subpopulation constantly increased during the invasive process of LUAD with remarkable elevation in IAC, and its spatial distribution was in the peripheral cancer region of the IAC, representing a more malignant phenotype. Furthermore, analysis of the TME cell type subpopulation showed a constant decrease in mast cells, monocytes, and lymphatic endothelial cells, which were implicated in the whole process of invasive LUAD, accompanied by an increase in NK cells and MALT B cells from AIS to MIA and an increase in Tregs and secretory B cells from MIA to IAC. Notably, for AIS, cancer cells, NK cells, and mast cells were colocalized in the cancer region; however, for IAC, Tregs colocalized with cancer cells. Finally, communication and interaction between cancer cells and TME cell-induced constitutive activation of TGF-β signaling were involved in the invasion of IAC. Therefore, our results reveal the specific cellular information and spatial architecture of cancer cells and TME subpopulations, as well as the cellular interaction between them, which will facilitate the identification and development of precision medicine in the invasive process of LUAD from AIS to IAC.

overall_design:
RNA-seq profiling of normal tissue, AIS, MIA and IAC
The samples were grouped according to different pathological types:
FLA representing lung squamous cell carcinoma group,
JRX representing invasive lung adenocarcinoma,
WJR representing lung minimally invasive adenocarcinoma,
YWA representing lung adenocarcinoma in situ,
ZCF representing normal lung tissue.


title: Targeting the vulnerability of arachidonic acid metabolism to enhance immunotherapy efficacy in ARID1A-deficient colorectal cancer [ChIP-Seq]

city: Harbin

first: Yanqiao

last: Zhang

address: No.150 Haping Road, Nangang District, Harbin, Heilongjiang, 150081, China

institute: Third Affiliated Hospital of Harbin Medical University

summary: ARID1A, a core constituent of SWI/SNF complex, is mutated in about 10% of colorectal cancer (CRC). This study demonstrates a synergistic effect of arachidonic acid metabolism inhibitors with immune checkpoint inhibitors (ICIs) by regulating functionality of CD8+ T cells and vasculogenic mimicry (VM) formation in ARID1A-deficient CRC. Mechanistically, ATAC-seq and ChIP-qPCR demonstrated that the lack of ARID1A results in reduced levels of the key enzymes PTGS1 and PTGS2, which control the arachidonic acid pathway. This reduction generated a reliance on the remaining functionality of arachidonic acid pathway in ARID1A-deficient cells.

overall_design: This study conducted CHIP-seq analysis on ARID1A wild-type and mutant cell lines, and further visualized gene expression

first: Chao

last: Liu

first: Shuijie

last: Li

first: Luying

last: Cui


title: Evolutionarily guided transcription factor design programs novel T cell states [scRNA-seq, MULTI-seq]

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Dr.

institute: Stanford

summary: Protein-coding genes in the human genome evolved via modular rearrangement of domains from ancestral genes. Here, we develop a scalable, evolutionarily guided method to assemble novel protein-coding genes from constituent domains within a protein family, termed DESynR (Domain Engineered via Synthesis and Recombination) factors. Using primary human chimeric antigen receptor-T cells as a model system, we find that the expression of DESynR Activator Protein-1 (AP-1) transcription factors (TFs) significantly outperforms the expression of natural AP-1 TFs in multiple functional assays in vitro and in vivo. Top DESynR AP-1 TFs exhibit non-intuitive architectures of constituent domains, including from TFs that are not canonically expressed in T cells. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming of T cells and in some cases, lead to the development of non-natural T cell states, engaging gene modules from disparate human cell types. Taken together, we demonstrate that novel configurations of existing protein domains may uncover non-evolved genes that program cell states with therapeutically-relevant functions.

overall_design: Live-sorted and MULTI-seq-barcoded human CD19-28z CAR T cells overexpressing various natural and engineered AP-1 transcription factors were analyzed using 5’ scRNA-seq (10x Genomics) following repetitive stimulation with Nalm6 targets in vitro.

first: Oliver

last: Takacsi-Nagy

first: Austin

last: Hartman

middle: Y


title: Decreased estrogen level in ovariectomized mice causes an increase in oxidative stress in osteal macrophages leading to development of cellular senescence

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

summary: Osteal macrophages were isolated from ovariectomized and control mice 4 weeks after surgery. Oeritoneal macrophages collected from ovariectomized mice exhibited gene signature of NADPH oxidase activation which is known as key modulator in aging and cell senescence.

overall_design: RNA-seq for osteal macrophages isolated from ovariectomized and control mice

first: Mohamad

first: Yoshio

last: Nishida

first: Gen

last: Matsumae

first: Norimasa

last: Iwasaki