title: Calcium and Cadmium Activate ESRRB to Mediate Cell Stemness and Pluripotency

city: Washington

first: Mary Beth

last: Martin

state: DC

address: 3970 Reservoir Rd. NW

department: Oncology

institute: Georgetown University

summary: Estrogen-related receptor beta (ESRRB) is thought to be an orphan receptor that functions as a transcription factor, pioneer factor, and mitotic bookmarker to regulate cell stemness, pluripotency, and differentiation. This study 1) investigates whether calcium and cadmium activation of ESRRB regulates signaling pathways of stemness and pluripotency, 2) explores the transcriptomic and biological alterations of metal activation of ESRRB, and 3) reveals the underlying mechanisms by which metals activate ESRRB. In HEK293T cells, treatment with calcium and cadmium increased the expression of ESRRB-regulated genes that was blocked by an ESRRB antagonist. In the breast cancer cell line MDA-MB-453, treatment with calcium, cadmium, or a synthetic agonist also increased expression of ESRRB-regulated genes that was blocked by the antagonist, enhanced ESRRB nuclear localization, increased the recruitment of RNA polymerase 2 to estrogen-related receptor response elements, enhanced cell stemness and proliferation pathways, and induced the expression of estrogen receptor alpha. Mutational analysis and molecular docking identified potential metal interaction sites within ESRRB’s ligand-binding domain. Together, these results suggest calcium acts as a natural ligand for ESRRB and cadmium, which mimics calcium, activate ESRRB to mediate cell stemness and pluripotency.

overall_design: RNA-seq profiling of MDA-MB-453 cells with treatment of calcium, cadmium, DES (ESRRB antagonist), DES+calcium, DES+cadmium, or GSK4716 (ESRRB agonist) for 24 hours, plus no-treatment controls.

first: Xu

last: Shi

first: Gai

last: Yan

first: Nicole

first: Qiaochu

first: Dajun

last: Lu

first: Destiny

last: Lawler

first: Reem

last: Gahtani

first: Celia

last: Byrne

first: Bassem

last: Haddad

first: Robert

middle: L

last: Copeland


title: The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function [C2C12]

status: Public on Jan 14 2026

city: Barcelona

first: Jacob

last: Smith

state: Barcelona

address: Av. Diagonal, 643

country: Spain

institute: University of Barcelona

type: Expression profiling by high throughput sequencing

summary: Circadian clocks present throughout the brain and body coordinate diverse physiological processes to support daily homeostasis, yet the specific inter-organ signalling axes involved are not well defined. We previously demonstrated that the skeletal muscle clock controls transcript oscillations of genes involved in fatty acid metabolism in the liver, yet the impact of the liver clock on the muscle remains unknown. Here, we use hepatocyte-specific Bmal1 KO mice (Bmal1hep-/-) to reveal that approximately one-third of transcript rhythms in skeletal muscle are influenced by the liver clock in vivo. Treatment of myotubes with serum harvested from Bmal1hep-/- mice inhibits expression of genes involved in metabolic pathways, including oxidative phosphorylation. Only small transcriptional changes were induced by liver clock–driven endocrine communication in vitro, leading us to surmise that the liver clock acts to fine-tune metabolic gene expression in muscle. Consistent with functional tuning, treatment of myotubes with serum collected from Bmal1hep-/- mice during the dark phase lowers mitochondrial ATP production as compared to serum from wild-type mice. Overall, our results reveal communication between the liver clock and skeletal muscle, uncovering a bidirectional endocrine communication pathway that may contribute to the metabolic phenotypes of circadian disruption.

overall_design: RNA-seq profiling of C2C12 myotubes treated for 24 hr with serum collected either during the day-time (ZT4) or night-time (ZT16) from wildtype (WT) mice or mice with liver-specific deletion of Bmal1 (Bmal1hep-/-)

first: Sica

last: Valentina

first: Sato

last: Tomoki

first: Tsialtas

last: Ioannis

first: Hernandez

last: Sophia

first: Chen

last: Siwei

first: Baldi

last: Pierre

first: Muñoz Cánoves

last: Pura

first: Sassone-Corsi

last: Paolo

first: Koronowski

last: Kevin B.

first: Smith

last: Jacob G.


title: RNA-seq analyses of citrate synthase (CS) knocked down cells

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

country: China

institute: Nanjing Agricultural University

summary: To study the effects of reduced CS expression on human cancer cell lines, we used small interfering RNAs to knockdown CS, then analyzed the RNA expression profiles of these cells.

overall_design: Total RNA was isolated from the cells, and RNA-seq was performed.


title: Analysis of gene expression in orbital tissue in thyroid-associated eye disease

city: Tongling

first: Wumei

last: Hua

state: Anhui

address: Tongguan District

institute: Tongling People's Hospital

summary: In this study, next-generation transcriptome sequencing technology and bioinformatics analysis were used to identify differentially expressed genes and signaling pathways associated with orbital adipogenesis and muscle fiber formation in thyroid-associated ophthalmopathy (TAO).

overall_design: Orbital adipose connective tissues from three cases each in the TAO and control groups were subjected to transcriptome sequencing

first: Ji

last: Zhang


title: MSLN-mediated activation of EGFR-ERK1/2 signaling drives liver metastasis in breast cancer [HCC1806-HM3]

city: Chongqing

first: boxuan

last: wang

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

summary: Introduction: Breast cancer (BC) is the most prevalent malignant disease affecting female patients globally, with triple-negative breast cancer (TNBC) being the subtype linked to the poorest clinical outcome. The liver is a frequent metastatic site of breast cancer. Therefore, elucidating the mechanism underlying liver metastasis in TNBC is crucial for identifying effective diagnostic and therapeutic targets, which holds significant potential for guiding clinical treatment. Objectives: To identify the key gene driving liver metastasis in breast cancer, investigate its mechanism of action, and advance breast cancer treatment. Methods: RNA sequencing was conducted on 4T1-HM3 and its corresponding primary tumor cell 4T1-Pri to identify and screen genes involved in liver metastasis. The enhanced MSLN, a gene encoding mesothelin, was identified in metastatic TNBC cells and tissues using qRT-PCR, Western blotting, and immunohistochemistry. Dual-luciferase reporter assays, chromatin immunoprecipitation (ChIP) analysis, and bioinformatics were employed to identify transcription factors regulating MSLN. Liquid chromatography-tandem mass spectrometry (LC-MS/MS), co-immunoprecipitation (co-IP), and immunofluorescence (IF) co-localization were utilized to investigate the mechanism of MSLN action in BC cells. Cellular viability was assessed using a colony formation assay. Cell proliferation and chemosensitivity were assessed using the CCK8 assay. Results: MSLN exhibits aberrantly overexpression in liver-metastatic cells. Elevated MSLN levels are significantly associated with liver metastasis compared to metastases in other organs. MSLN promotes cell proliferation and survival in vitro and TNBC liver metastasis in vivo. Mechanistically, MSLN binds to epidermal growth factor receptor (EGFR) and activates the EGFR-ERK1/2 signaling axis, thereby promoting TNBC cell survival and proliferation during metastasis. Notably, targeting MSLN with a paclitaxel/carboplatin combination can efficiently inhibit liver metastasis of hepatotropic TNBC in a mouse model.

overall_design: RNA-seg profiling of HCC1806-HM3 cells and their knockdown derivatives (shMSLN)

first: Jing

last: Chen

first: Zexiu

last: Lu

first: Boxuan

last: Wang

first: Die

last: Meng

first: Yubi

last: Gan

first: Chao

last: Chang

first: Peijin

last: Dai


title: Role of small extracellular-vesicle microRNA-302f in endometriosis-associated ovarian cancer

city: Kaohsiung

first: ChiaYi

last: Hsu

state: State...

address: No. 100, Shih-Chung 1

country: Taiwan

institute: Kaohsiung Medical University Hospital, Kaohsiung Medical University

summary: Background: Tumor microenvironment is well known to have a key role in tumor development. Extracellular vesicles are capable in cell signaling transduction and important in regulation of tumor microenvironment.   Objective: To investigate whether peritoneal fluid–derived extracellular vesicles help regulate the tumor microenvironment in the malignant transformation of endometriosis.  Methods: Samples of peritoneal fluid were taken from women with benign gynecological disease, endometriosis, or endometriosis-associated ovarian cancer. Small extracellular vesicles in the samples were isolated via ultracentrifugation and characterized by western blotting, transmission electron microscopy, and nanoparticle tracking. A global microRNA (miRNA) expression profile array was used to analyze miRNA abundance in peritoneal fluid–derived small extracellular vesicles. Candidate miRNAs were quantified by reverse transcription PCR to assess their potential role in cell migration.  Results: A total of 22 miRNAs were identified from the analysis of miRNAs in peritoneal fluid–derived small extracellular vesicles from patients with endometriosis or endometriosis-associated ovarian cancer. We confirmed that each miRNA was expressed in various ovarian cell lines. The miRNA miR-302f was consistently highly expressed in both clinical specimens and ovarian cell lines from patients with endometriosis, yet expression was relatively low in specimens and cell lines from patients with endometriosis-associated ovarian cancer. A bio-functional assay revealed that miR-302f regulates cell migration. Finally, the possible target mRNAs of miR-302f were identified in the Gene Expression Omnibus database.  Conclusions: These data may provide a basis for the development of novel therapeutic strategies for endometriosis-associated ovarian cancer patients by downregulating PDGFRA abundance in cancer cells via overexpression of miR-302f.

first: Hsu

last: CY

first: Tsai

last: CC

first: Lin

last: HY

first: Suen

last: JL

first: Ou

last: YC

last: EM


title: Runx1 in Postn-expressing fibroblasts exacerbates adverse cardiac remodeling post myocardial infarction

city: Milwaukee

first: Anooj

last: Arkatkar

state: WI

address: 8701 W Watertown Plank Rd.

department: Cell Biology, Neurobiology, and Anatomy

country: USA

institute: Medical College of Wisconsin

summary: Runx1 is strongly induced in the heart after acute injury and in chronic disease settings. Its expression negatively correlates with outcomes, and past work has shown a protective effect when Runx1 is inhibited through a variety of experimental means. We sought to establish the cell type(s) responsible for Runx1-dependent adverse remodeling following infarction. Using immunostaining for RUNX1 along with existing single cell RNA sequencing data sets, we established which cell types express Runx1 and prioritized two from this list – cardiomyocytes and fibroblasts. Cre drivers for the respective cell populations were paired with a Runx1 floxed allele to generate inducible, cell-type specific knockout mice. Following myocardial infarction induced by permanent ligation, mice were assessed for functional recovery by echocardiography and histological measurements, including scar size, cardiomyocyte dimension, and cell proliferation. Detailed transcriptomic analysis was used to assess mechanism of action. In contrast to existing literature, we did not observe a measurable impact of cardiomyocyte-specific loss of Runx1 on heart function or histology following myocardial infarction when compared to Cre-positive controls. On the other hand, loss of Runx1 in the Postn-expressing activated fibroblast population resulted in a protective effect on heart function seen as early as 3 days post-infarction and maintained until the 56-day experimental endpoint. These functional benefits were accompanied by smaller scars, reduced cardiomyocyte hypertrophy, and a reduction of activated fibroblasts progressing to an SMA-positive myofibroblast. Overall, we demonstrate Runx1 expression in activated fibroblasts drives adverse remodeling phenotypes following myocardial infarction.

overall_design: RNAseq profiling of  8-10 week old wildtype (CTL) and Runx1 conditional knockout (RUNX FB-KO) C57BL/6J mice at 7 days post myocardial infarction.

first: Kaelin

middle: A

last: Akins

first: Michael

last: Flinn

first: Natalie

last: Sandor

first: Alexandra

last: Purdy

first: Annabelle

last: Brusacoram

first: Samantha

middle: K

last: Swift

first: Sydney

last: Buday

first: Priyanka

last: Choudhury

first: Miao

last: Cui

first: Brian

last: Lin

first: Caitlin

middle: C

last: O'Meara

first: Michaela

last: Patterson


title: The methyltransferase N6amt1 regulates hippocampal neurogenesis through 6mA modification of Txnrd3 DNA

city: Guangzhou

first: yuanfei

last: wu

address: No. 1 Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenine (6mA), the most prevalent DNA modification in mammals and other eukaryotes, regulates DNA mismatch repair, chromosome replication, and transcription. However, its role in adult hippocampal neurogenesis remains unkown. Here we showed that the methyltransferase N6amt1 and 6mA modification were highly enriched in hippocampal neurons both in vitro and in vivo. Functionally, knockdown of N6amt1 in neural stem cells (NSCs) significantly reduced 6mA levels, neuronal genesis, and proliferation while promoting glial differentiation. Conversely, N6amt1 overexpression enhanced neuronal differentiation and proliferation. Mechanistically, N6amt1-mediated 6mA modification of Txnrd3 DNA increased its transcription, thereby promoting hippocampal neurogenesis. Furthermore, exogenous Txnrd3 overexpression rescued the defects in cell differentiation and proliferation induced by N6amt1 depletion. Notably, N6amt1 deficiency impaired hippocampal neurogenesis and spatial memory in adult mice. Our findings highlight the critical role of DNA 6mA in N6amt1-mediated neurogenesis and suggest that targeting N6amt1 may offer a novel therapeutic strategy for neurological disorders associated with cognitive impairment.

overall_design: MeDIP-seq of the DNA 6mA modification in NSCs,Neurons and Astrocytes.

first: Aiguo

last: Xuan

first: Yuanfei

last: Wu


title: Bulk RNAseq parietal bone PND9-Isotype VS aCSF1R

city: Marseille

first: Rejane

last: Rua

address: 163 Avenue de Luminy

country: France

institute: Centre d'Immunologie de Marseille Luminy

summary: Bulk RNAseq of the parietal bone of C57Bl6J pups treated transcranially at post-natal days 2, 4 and 6 with control isotype or CSF1R blocking antibody to deplete myeloid cells. Pups are perfused at PND9 and parietal bone is collected to analyze transcriptomic differences.

first: Elisa

last: Eme-Scolan

first: Michel

last: Gomes

first: Oussama

last: Kassem


title: RHOA Controls Oncogenic B-Cell Receptor Signaling in Aggressive Lymphoma

city: Frankfurt am Main

first: Sebastian

last: Scheich

address: Theodor-Stern-Kai 7

department: Hematology/Oncology

country: Germany

institute: University Hospital Frankfurt

summary: Diffuse large B cell lymphoma (DLBCL), divided into activated B-cell-like (ABC) and germinal center B-cell-like (GCB), is the most common type of aggressive lymphoma. While many studies have shown treatment response differences based on subtype, recurrently mutated proteins can further alter these responses and may require therapeutic alterations. Mutational effects in DLBCL have recently begun to be investigated, of which one mutated protein, the master cytoskeletal regulator RhoA, is here evaluated. While having been identified in previous studies, a complete investigation into the effects of this protein and its mutations in the context of DLBCL have been lacking. Through use of various methodologies, RhoA was found to play a role in the chronic active BCR signaling and NF-κB survival signal that are characteristic for the ABC DLBCL subtype. Not only was it essential in proximal BCR signaling, but additionally in the formation of the My-T-BCR super-signaling complex. Additionally, the interaction with essential surface membrane signalling proteins, and effects on internalization, emphasize the importance of this protein. Differing point mutations alter the activity of RhoA itself, along with its response to various clinically relevant inhibitors, clustering of IgM on the plasma membrane, and the actin cytoskeleton. The investigation of RhoA and its recurrent mutations are essential for deeper understanding of this malignancy.

overall_design: RNA-seq profiling of ABC DLBCL cell lines after 10hr of DMSO, Rhosin, or Ibrutinib treatment. RNA-seq profiling of TMD8 RhoA WT cells and TMD8 p.R5W cells under Copanlisib treatment.

first: Ariana

last: Jacobs

last: Wolf

first: Dominique

last: Jahn

first: Thomas

last: Oellerich

first: Louis

middle: M

last: Staudt


title: Targeting CHD1L Suppresses Prostate Cancer Progression via the FOXO3-PUMA Axis

first: Pusheng

last: Hui

address: No.1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Prostate cancer (PCa) is one of the most prevalent malignancies in men and remains a major cause of cancer-related mortality worldwide. While taxane-based chemotherapies, such as docetaxel, are standard treatment options for metastatic castration-resistant prostate cancer (mCRPC), their long-term efficacy is limited. This highlights an urgent need for new therapeutic targets and more effective treatment strategies to improve survival in advanced PCa. Here, we show that CHD1L is overexpressed in prostate cancer tissues and correlates with poor prognosis. Knockdown of CHD1L substantially inhibits PCa cell proliferation and induces apoptosis. Moreover, inhibition of CHD1L by the small molecule OTI-611 significantly suppresses PCa cell proliferation, migration, and invasion, and induces apoptosis both in vitro and in vivo. Mechanistically, inhibition of CHD1L induces the expression of FOXO3 (a classic transcription factor) and its downstream target PUMA (a key apoptosis inducer). Restricting the expression of FOXO3 substantially reverses the anti-tumor effects induced by OTI-611. Furthermore, OTI-611 synergizes with docetaxel to enhance apoptotic cell death, providing a promising strategy to overcome docetaxel resistance. These findings highlight the therapeutic potential of targeting CHD1L in combination with existing treatments, offering a novel approach for the treatment of advanced prostate cancer.

overall_design: DU145 cells were treated with vehicle (DMSO) or OTI-611 (5 μM) for 24 h. The cells were collected for RNA-seq analysis


title: TIMP1-Mediated M2 Macrophage Polarization Facilitates Liver Metastasis in Colorectal Cancer

city: Zunyi

first: lin

last: Wang

state: 贵州省遵义市新蒲新区

address: 贵州省遵义市新蒲新区学府西路6号

institute: Zunyi Medical University

summary: Colorectal cancer (CRC) remains one of the leading causes of cancer-related morbidity and mortality globally, with liver metastasis (CRLM) accounting for the majority of CRC-associated deaths. Although advances in early detection and treatment have improved outcomes, the prognosis for patients with advanced disease remains dismal. Recent studies have underscored the critical role of the hepatic pre-metastatic niche (PMN) in facilitating CRC dissemination, where M2-polarized macrophages play a central role in promoting immune suppression and metastatic colonization. However, the molecular mechanisms driving M2 polarization in this context remain incompletely understood.

overall_design: To explore the immunomodulatory effects of TIMP1 on liver macrophages, we isolated hepatic macrophages from BALB/c mice, treated them with recombinant TIMP1 (rTIMP1) protein for 48 hours, and conducted transcriptomic profiling via RNA sequencing.

first: liming

last: zhao

first: Lin

first: Zhaoxu

last: Zheng


title: Extracellular vesicles derived from pro-inflammatory M1 macrophages induce an inflammatory and invasive phenotype in melanoma cells.

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Melanoma progression and metastasis depend on intercellular communication within the tumor microenvironment (TME), where extracellular vesicles (EVs) have emerged as essential mediators through the transfer of molecular cargo. In melanoma, macrophages are enriched in the TME, and their abundance and infiltration into the tumor area are associated with poor prognosis. In this study, we examined the effects of pro-inflammatory M1 and immunosuppressive M2 macrophage-derived extracellular vesicles (EVs) on melanoma cells to gain insights into EV-mediated interactions between macrophages and tumor cells. Our results demonstrate that M1 EVs reprogram MV3 melanoma cells into a pro-inflammatory state by upregulating the expression and secretion of pro-inflammatory cytokines CXCL8, IL-6 and IL-1B. This M1 EV -induced inflammatory phenotype enhanced melanoma cell invasion, which was suppressed by CXCL8 silencing. Furthermore, M1 EV treatment activated the NF-κB signaling pathway, and its inhibition with the IKK16 inhibitor led to downregulation of inflammation-associated genes. These results suggest that M1 EVs promote tumor-associated inflammation in melanoma through NF-κB signaling, underscoring the pivotal role of EV-mediated macrophage–tumor cell communication in cancer progression.

overall_design: RNA-seq was performed on MV3 melanoma cells treated with Ctrl, M0, M1 and M2 EVs for 24 h (n=3). Macrophage-derived EVs were isolated by ultracentrifugation from conditioned media of THP-1 cells polarized to M0, M1 and M2 macrophages for 48 h.

first: Kaisa

last: Mäki-Mantila

first: Sanna

last: Pasonen-Seppänen


title: Carbonic Anhydrase 12 is a Novel Prognostic Biomarker and Therapeutic Target for High-Risk Follicular Thyroid Cancer

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Identifying high-risk follicular thyroid cancer (FTC) is critical for stratified treatment and developing targeted therapies. This study performed RNA sequencing on high-risk FTC, identifying Carbonic Anhydrase 12 (CA12) as a promising biomarker. High CA12 expression predicted poor disease-free survival, surpassing conventional markers. In vitro, CA12 knockdown reduced proliferation and invasion, while a CA12 inhibitor showed synergistic anti-proliferative effects with Lenvatinib. These findings establish CA12 as both a novel prognostic biomarker and a potential therapeutic target for FTC.

overall_design: To compare gene expression profiles between thyroid cancer tissues and adjacent normal tissues , total RNA was extracted from the FFPE tissues.

first: Masashi

last: Tanida

last: Okuzaki

first: Eiichi

last: Morii


title: Determinants of “placental” versus “maternal” preeclampsia

city: La Jolla

first: Mariko

last: Horii

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Background: The placenta is known to be critical in the etiology of preeclampsia (PE). However, there is a subset of PE cases without identifiable placental pathology. We evaluated which clinical PE classification system best distinguishes PE with placental pathology from PE without placental pathology. Methods: We evaluated five placental pathologic features in 197 placentas from PE patients grouped by three clinical PE subclasses. 1. PE with calculated infant birthweight <10th percentile (small) for gestational age (SGA PE) versus PE with birthweight ≥10th percentile for gestational age (NSGA PE). 2. PE with delivery before 34 weeks of gestation (EDPE) versus PE with delivery at or after 34 weeks of gestation (LDPE) and 3. PE with severe features versus PE without severe features. Clinical, histologic and molecular findings in patients with PE were compared to normotensive patients, with and without SGA infants (N = 1,078 total). Results: The SGA versus NSGA PE classification system performed best (likelihood ratios (95% CI) for ≥ 3 of 5 placenta pathologic findings: 15.7 (6.5, 38.1) in SGA PE vs. NSGA PE; 6.8 (4.3, 10.8) in EDPE vs. LDPE and 5.2 (1.95, 14.1) in PE with SF vs. PE without SF; all p <.0001). SGA PE and SGA normotensive placentas were abnormal and shared alterations in hypoxia, TNF alpha, glycolysis, unfolded protein response, estrogen response, UV response, p53, TGF beta and mTORC1 signaling pathways. Conclusions: Classifying PE based on birthweight percentile for gestational age is the most useful system for consistently identifying PE associated with placenta pathology.


title: Clinical and Molecular differences of hypertensive disorders during pregnancy

summary: Background: Hypertensive disorders of pregnancy (HDP) comprise a spectrum of four subtypes: chronic hypertension (cHTN), gestational hypertension (gHTN), preeclampsia (PE), and superimposed preeclampsia (siPE). Although often characterized as a spectrum of disease severity, there have been limited comparative studies of detailed clinical and molecular characteristics of these disorders. We hereby evaluate HDP subtypes using clinical, placental histopathological and molecular data to compare the similarities and differences between HDP subtypes. Methods: We utilize data from over 10-year-long pregnancy cohort with detailed clinical and placental pathology, as well as placental tissue RNA-sequencing. Clinical diagnosis was based on current ACOG criteria, and placental gross and histologic examination was based on the Amsterdam consensus statement. Results: Clinical data analysis showed cHTN and gHTN to be more likely to have normal placental pathology, while PE and siPE were more enriched in maternal vascular malperfusion (MVM). RNA-seq showed distinct gene expression signatures and pathway activation across  our HDP subgroups. We could not identify any molecular evidence that preeclampsia (PE or siPE) was an advanced stage of hypertensive disorder (gHTN or cHTN), but rather identified distinct gene expression profiles between these entities, suggesting preeclampsia (PE or siPE) and hypertension (gHTN or cHTN) are distinct pathophysiological conditions. Finally, we found that, in the presence of MVM, siPE and PE share significant gene expression profiles and pathway activation. Conclusion: Our findings suggest that MVM specifically differentiates pregnancies that progress to PE and siPE. MVM is thought to initiate in early gestation, indicating the cascade to PE/siPE maybe differentiated from gHTN/cHTN early in pregnancy. Incorporating placental evaluation into patient care is essential, in order to probe the etiology of HDP.

overall_design:
Placental tissue RNA-seq from hypertensive disorder that includes chronic hypertension (cHTN), gestational hypertension (gHTN), preeclampsia (PE), and superimposed preeclampsia (siPE).We used previously derived (GSE186257, GSE234729, PRJNA1027377) as well as newly derived data for this study. All the data were re-mapped as described in the data processing section.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Marni

last: Jacobs

first: Robert

last: Morey

first: Jennifer

last: Chousal


title: MSLN-mediated activation of EGFR-ERK1/2 signaling drives liver metastasis in breast cancer

first: boxuan

last: wang

address: 重庆市渝中区医学院路1号

summary: To facilitate the study of organ metastasis of triple-negative breast cancer (TNBC), liver metastatic models of TNBC were developed using 4T1 cell lines via repeated fat pad injections and the selection and growth of metastatic clones in vivo . The obtained cell lines were designated based on their source organs and injection cycles. Through ex vivo bioluminescence imaging (BLI) and metastatic nodule quantification, liver metastasis potential was validated in HM3 (third-passage liver metastatic cells). These cells exhibited preferential metastasis to the liver. Metastatic burden progressively increased across serial transplantations, as evidenced by escalating nodule counts in target organs. For the liver-specific metastasis mouse model, 100 μl of PBS containing 1×10⁶  4T1 (BALB/c mice) cells was injected in situ into mammary fat pad of mice. Cells from primary tumors and liver metastases were separately isolated and cultured (cells isolated from mouse primary tumors were named 4T1-Pri, the metastatic tumor cells isolated from liver organs were named HM). After stable clones were established, liver organ metastatic cells were reinoculated into new mice to generate metastatic tumors. After at least three rounds of screening, highly liver organotropic metastasis cells were successfully established, designated as 4T1/HM3 (liver-preferential metastases). The firefly luciferase reporter gene (for bioluminescence tracking) retrovirus was infected with 4T1-derived cells and puromycin (1 μg/mL, Sigma Aldrich, USA) was selected for 14 days.

overall_design: RNA sequencing analysis of 4T1/HM3 (third-passage liver metastatic cells) in comparison with their corresponding primary tumor cells (4T1/Pri).

first: Jing

last: Chen

first: Zexiu

last: Lu

first: Boxuan

first: Die

last: Meng

first: Yubi

last: Gan

first: chao

last: chang

first: Peijin

last: Dai


title: Multi-region spatial transcriptomics reveals region specific differences in response to amyloid beta (Aβ) plaque induced changes in Alzheimer’s Disease (AD)

city: Durham

first: Amanda

middle: S

last: MacLeod

state: North Carolina

address: 40 Duke Medicine

department: Dermatology

institute: Duke University

summary: Alzheimer’s disease (AD) is the leading cause of dementia affecting 55 million people worldwide. The pathological hallmarks of AD, beta-amyloid (Aβ) plaques and neurofibrillary tangles (NFT), follow distinct stereotypical patterns of progression across brain regions and trigger a multicellular response that ultimately leads to neuronal loss and cognitive decline. Despite the uniform spread of Aβ plaque across the cortex during AD progression, different regions demonstrate varying levels of vulnerability and resilience to temporal Aβ plaque induced changes, such as NFT accumulation. There is a critical gap in our understanding of the cell types and molecular mechanisms that underlie these region-specific differences in resilience to Aβ plaque induced changes. In this study, we hypothesized that brain region and cell type specific transcriptional responses within the Aβ microenvironment, and more broadly within the grey matter, may contribute to this variation. We carried out matched multi-region spatial transcriptomics and Aβ immunofluorescence staining from the entorhinal, occipito-temporal, dorsolateral prefrontal and striate cortices from two individuals with Braak III and Thal 4 AD. Spatiotemporal comparisons of cell type proportions, gene expression, and cell-cell communication revealed differences in the vulnerability of somatostatin and somatostatin chondrolectin inhibitory neurons and the expression of endosomal and lysosomal trafficking and metallothionein genes within the Aβ plaque microenvironment. We also observed variations in blood-brain-barrier dysfunction, fibroblast growth factor signaling, and vascular impairment and repair related cell-cell communication networks within the grey matter. Our results demonstrate the value of simultaneously profiling AD-omic and spatial modalities in multiple regions to elucidate how cortical region-specific differences contribute to selective vulnerability and resilience during neurodegeneration.

overall_design: Two post-mortem brain tissue samples matched for AD disease (Thal 4, Braak III) stage were dissected to analyze sections from the entorhinal (ENT-BA28), occipito-temporal (OCCP/TEMP-BA37), dorsolateral prefrontal (DLPFC-BA46), and striate (STR-BA17) cortices using 10xVisium spatial trranscriptomics.

first: Odmaa

last: Bayaraa

first: Michael

last: Aksu

first: Evon

last: DeBose-Scarlett

first: Emily

last: Hocke

first: Vaibhav

last: Jain

first: Shih-Hsiu

middle: J

last: Wang

first: Dianne

last: Cruz

first: Simon

last: Gregory


title: Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni)

city: Escondido

first: Elena

last: Ruggeri

address: 15600 San Paqual Valley Rd.

institute: San Diego Zoo Wildlife Alliance

summary: The northern white rhinoceros (Ceratotherium simum cottoni) genome and annotation were previously published, but the annotation contained few genes, with many annotation misalignments, and nomenclature not matching HGNC/VGNC naming conventions, making transcriptional studies very difficult. We used in vivo collected granulosa cells for RNA sequencing and de novo transcript assembly through StringTie to identify all nucleotide gene sequences in our samples. Through extensive manual curation we were able to generate a greatly improved genome annotation increasing gene numbers by 81%. This will greatly enable researchers in this field to utilize the genome and annotation to complete transcriptional studies with this species.

overall_design: Transcriptomic of SWR GC from follicles in different stages of development.

first: Ruggeri

last: Elena

first: Prunier

last: Julien

first: Marc-André

last: Sirard

first: Durrant

last: Barbara

first: Klohonatz

last: Kristin


title: The LXRβ/NF-κB Axis Reprograms CAR-T Cells to Resist Exhaustion in the Tumor Microenvironment

city: Seoul

first: Hyungseok

last: Seo

address: Gwanak ro 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Liver X Receptor β (LXRβ) is a pivotal transcription factor regulating lipid metabolism and immune cell function. Although LXRβ has been implicated in T cell homeostasis, its role within the tumor microenvironment (TME) remains poorly understood. Notably, LXRβ can inhibit NF-κB target gene expression, yet the functional interplay between LXRβ and NF-κB signaling in tumor-infiltrating CD8⁺ T cells has not been fully elucidated. Here, we demonstrate that LXRβ modulates the differentiation and functional state of CAR-T cells within the TME. LXRβ overexpression reshaped the phenotypic landscape of CAR-T cells, including altered expression of the progenitor marker TCF1, proliferation marker Ki-67, and effector cytokines IFNγ and TNFα. Furthermore, perturbation of NF-κB signaling, particularly through RelB deletion, enhanced CAR-T cell cytotoxicity and mitigated exhaustion-associated features such as TOX expression. Combined modulation of LXRβ and RelB synergistically improved the functional fitness of CAR-T cells and their anti-tumor efficacy in vivo. These findings reveal a critical regulatory axis between LXRβ and NF-κB that governs CAR-T cell exhaustion and effector function in solid tumors. Targeting this pathway may provide a novel strategy to enhance CAR-T cell–based immunotherapies.

overall_design: RNA-seq profiling was performed on hCD19 CAR-T cells engineered to overexpress LXRβ (LbOE) and on control CAR-T cells transduced with an empty vector (pMIG).

first: Minji

last: Lim

first: Sangeun

last: Jung

first: Hyungwoo

last: Jeong

first: Youngchae

last: Moon


title: Three-Dimensional Bioprinted hiHeps Hepatorganoids with Improved Hepatic Functions for the Treatment of Acute / Chronic Liver failure and for the Promotion of Liver Regeneration

city: Hangzhou

first: Zhichao

last: Ye

address: Huajiachi Campus

institute: Zhejiang University

summary: The liver's intricate architectural organization and regenerative capacity have long posed challenges in developing therapeutic strategies for severe hepatic injuries and functional recovery. Three-dimensional bioprinting provides a unique platform to reconstruct biomimetic liver tissues through spatially orchestrated cellular and extracellular matrix integration. Here, we engineered three-dimensional (3D)-bioprinted hepatic units derived from human induced hepatocytes (hiHeps), which recapitulated native lobular zonation and exhibited enhanced metabolic functions, including glucose/lipid homeostasis and albumin synthesis. These bioengineered units demonstrated robust regenerative potential: they reversed chronic liver fibrosis by resolving pathological collagen deposition, rescued acute liver failure (ALF) through rapid functional compensation, and accelerated liver regeneration in partial hepatectomy models by stimulating endogenous hepatocyte proliferation. Preclinical validation in Bama minipigs revealed that implantation of hiHeps units following extensive liver resection restored coagulation profiles, improved synthetic function, and significantly enhanced survival rates compared to controls. By integrating patient-specific cells with tunable 3D microenvironments, our platform achieved superior functional integration and regenerative efficacy over conventional approaches. This work establishes a paradigm for bioengineered liver grafts that actively drive tissue repair and functional restoration. As a scalable and physiologically relevant solution, these bioprinted hepatic units pioneer a transformative strategy in regenerative hepatology, addressing critical challenges in treating liver failure and post-resection recovery while illuminating microenvironmental cues essential for organ-level regeneration.

overall_design: RNA-seq profiling of human induced hepatocytes (hiHeps) and three-dimensional (3D)-bioprinted hepatic units derived from hiHeps at Day7.


title: A combinatorial transcription factor screening platform for immune cell reprogramming [bulkRNA-seq]

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

summary: Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing Type-1 Conventional Dendritic Cells (cDC1) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode’s discovery power by inducing Natural Killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.

overall_design: TENE-transduced fibroblasts were FACS sorted for CD56 positive at day 12. Untransduced HEF and peripheral blood- derived CD56Bright CD16- and CD56dim CD16+ NK cells were included as controls

first: Inês

last: Maria Nascimento Caiado

first: Carlos-Filipe

last: Pereira


title: J-Lat 10.6 cell line treated with either DMSO, 10μM compound 4, or 10μM compound 16 for 24 h.

first: Xianyuan

last: Yang

state: Guangdong

address: No.132 East Ring Road

institute: Sun Yat-Sen University

summary: Human immunodeficiency virus (HIV) still remains a major global public health issue. Combination antiretroviral therapy (ART) is effective to reduce the morbidity and mortality of HIV infected patients. However, ART is unable to eradicate HIV due to the establishment of long-lived and proliferating HIV latently infected cells. Once ART is stopped, these cells will drive resurgence of the infection. Hence, ART in combination with HIV latency reversing agents (LRAs), which target signaling pathways involved in HIV transcription, has become an approach to target and eliminate HIV latency. Here, we identified two compounds with novel structures possessing HIV latency reversing activity. They are named compound 4 and 16, respectively. To understand their underlying mechanism, we carried out RNA-seq for J-Lat 10.6 cells treated with either DMSO, 10μM compound 4, or 10μM compound 16 for 24 h.

overall_design: RNA-seq profiling for J-Lat 10.6 cells treated with either DMSO, 10μM compound 4, or 10μM compound 16 for 24 h.

first: Yanjiang

last: Zhang

first: Qingren

last: Lu

first: Guihua

last: Tang

first: Sheng

last: Yin


title: HIF-1alpha activity affects stem cell fate in patient-derived ileum organoids

city: Heidelberg

first: CARL

last: HERRMANN

state: Baden-Wurtemberg

address: INF 364

department: Institut für Pharmazie und Molekulare Biotechnologie

institute: CRomLab

summary: The intestinal epithelium maintains tissue homeostasis through a dynamic balance of stem cell proliferation and differentiation along the crypt-villus axis. This process is spatially regulated, where intestinal stem cells in crypts proliferate and progenitor cells differentiate as they migrate toward the villus tips. An oxygen gradient is present along the crypt-villi structure setting the villi into a low-oxygen environment (physiological hypoxia) and the crypts into normoxia. Hence, during this differentiation and migration process, intestinal epithelial cells encounter distinct oxygen microenvironments throughout their life span. Inflammatory bowel diseases and other chronic inflammatory conditions disrupt this homeostatic balance and alter local oxygen dynamics, leading to dysregulated tissue repair and regeneration. To investigate how oxygen availability influences intestinal stem cell fate, we cultured patient-derived human ileum organoids under normoxic (20% oxygen) or hypoxic (1% oxygen) conditions. Under hypoxia, organoid growth was reduced and expression of the stem cell marker OLFM4 was decreased. Bulk and single-cell RNA sequencing revealed that hypoxia suppressed Wnt signaling pathways and reduced stem cell activity. Importantly, pharmacological stabilization of HIF-1α under normoxic conditions recapitulated the hypoxia-induced loss of stemness, demonstrating that HIF-1α is a key mediator of oxygen-dependent stem cell regulation. These findings establish that physiological hypoxia in the intestinal epithelium directly regulates stem cell fate through HIF-1α stabilization, providing mechanistic insight into how oxygen availability controls intestinal homeostasis.

overall_design: Single-cell RNA sequencing on human ileum-derived organoids generated from three different donors were incubated for 24 h or 48 h normoxia (20% O2) vs. hypoxia (1% O2). For each condition, organoids were seeded 3D-sheroids in Matrigel domes submerged in low Wnt media.

first: Zina

last: Uckeley

first: Carmon

last: Kee

first: Carlos

last: Ramirez

first: Ashwini

last: Sharma

first: Josmar

last: Polanco

first: Victoria

last: Karaluz

first: Carl

last: Herrmann

first: Megan

last: Stanifer

first: Steeve

last: Boulant


city: Gainesville

state: FL

address: 1200 Newell Drive

department: MGM

institute: University of Florida

overall_design: Bulk RNA sequencing on human ileum-derived organoids cultured in normoxia (20% O2) or hypoxia (1% O2) for 6 h, 12 h, 24 h or 48 h. For each condition, organoids were seeded 3D-sheroids in Matrigel domes submerged in  low Wnt media with four replicates.


title: FDX1-mediated cuproptosis promotes cholestaic liver injury exacerbated by taurocholic acid

city: Harbin

first: Qingbo

last: Cui

state: Heilongjiang, China

address: No.998 Aiying Street

institute: The Sixth Affiliated Hospital of Harbin Medical University

summary: As the primary route for copper elimination, cholestasis raises questions about the role of copper in cholestatic liver injury and its specific molecular mechanisms. Our findings reveal that cholestasis-induced copper overload drives liver injury via taurocholic acid (TCA) -exacerbated and FDX1-mediated cuproptosis.

overall_design: Mouse AML12 cells cultured in standard growth medium (Group A), or treated with CuCl₂ (300 μM)/elesclomol (ES, 40 nM; Group B), or treated with CuCl₂ (300 μM)/ES (40 nM)/TCA (1000 μM; Group C), or treated with TCA (1000 μM; Group D) for 24 h (n = 3/group).

first: Zhaozhu

last: Li

first: Yujun

last: Guo


title: Proteoglycan 4 and regorafenib synergistically reduce HCC progression in an orthotopic model

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

summary: Background: Hepatocellular carcinoma (HCC) is a major therapeutic challenge, with limited long-term benefits from treatments such as regorafenib due to their efficacy and adverse effects. Proteoglycan-4 (PRG4) has previously shown promise in enhancing anti-proliferative effects of multi-kinase inhibitors in simple in vitro two-dimensional (2D) HCC models. Objective: We evaluated the adjuvant effect of PRG4 in enhancing regorafenib’s anti-tumor efficacy in preclinical more complex in vitro three-dimensional (3D) HCC tumoroids, and in vivo HCC models. Design: HLC19 and HLF HCC cell lines were engineered to stably overexpress PRG4. Anti-proliferative effects of PRG4, either alone or in combination with regorafenib, were evaluated in 2D monolayers, 3D Matrigel embedded spheroids and orthotopic xenograft mouse models established via HCC cells intrahepatic injection. RNA sequencing was done to assess the transcriptomic profiles of PRG4 overexpressing spheroids. Results: PRG4 expression partially inhibited HCC tumor growth in vivo, but enhanced regorafenib treatment leading to a near-complete tumor regression. PRG4 expression significantly impaired cell growth in both 2D and 3D HCC models in vitro. In an angiogenesis in vitro model, PRG4 hindered endothelial tubulogenesis both alone and in combination with regorafenib. By transcriptomic analysis of matrigel-embedded HCC cell spheroids exposed to PRG4 and/or regorafenib, PDGF pathway emerged as a target of PRG4 + regorafenib, corroborating the role of PRG4 in impairing angiogenesis. G0/G1 phase of cell cycle resulted more delayed in spheroids exposed to PRG4 and regorafenib than those treated with regorafenib only, compared to untreated cells. Conclusions: PRG4 enhances the anti-tumor activity of regorafenib across various HCC models. These findings support PRG4 as a promising adjuvant candidate to improve clinical outcomes in HCC.

overall_design: HCC cells (HLC19) transduced with an empty vector (EV), and PRG4-expressing vector (PV) were pre-assembled as tumorspheres and embedded in Matrigel®. Spheroids were then treated with DMSO (vehicle) or regorafenib (5 µM) for 4 days. At the end of treatment, total RNA was isolated from spheroids and NGS was performed to profile differential expressed genes (DEGs) as a result of exposure to regorafenib, PRG4, and combined PRG4 + regorafenib.

first: Emanuele

last: Piccinno

first: Dituri

last: Francesco

first: Carrieri

last: Livianna

first: Giannelli

last: Gianluigi


title: Plasma of COVID-19 patients and healthy subjects

city: Turin

first: Martina

last: Schiavello

address: Via Genova 3

institute: University of Turin

summary:
Blood samples were purified in plasma from healthy volunteers' blood and COVID-19 patients for miRNA analysis.
qPCR gene expression profiling.  Plasma from eight controls and patients were used. Equal amount total RNA from each controls and patients was pooled prior to gene expression analysis.

overall_design: TaqMan™ Advanced miRNA Human Cards A and B in plasma of COVID-19 patients and healthy subjects


title: Microglia transcriptome systematic scoring to evaluate the efficacy of human cord derived mesenchymal stem cells treatment protocols in a rat model of inflammation associated preterm infant brain injury.

city: Paris

first: Andrée

last: Delahaye-Duriez

address: 48, boulevard serurier

institute: INSERM

summary: In this study, we undertook comprehensive dose, timing, and route of administration testing integrating multimodal data from preclinical models of brain injury common in preterm-born infants to validate the most effective therapeutic option for cord-derived mesenchymal stem cell product (HuMSC). We developed a scoring protocol based on microglia transcriptome analyses and myelin protein expression to evaluate the efficacy of the HuMSC product in a rat model of inflammation-associated preterm infant brain injury. We identified the superiority of treatment delivered in the tertiary phase of injury over treatments in the acute or subacute stages and the superiority of intranasal over intravenous HuMSC delivery.

overall_design: We define the control (Ctrl) uninjured group as the PBS-treated (sham treatment) animals not subjected to injury, the injured group as IL-1β-exposed that did not receive human umbilical cord-derived mesenchymal stromal cells (HuMSCs) injection but received PBS (sham treatment), and the treated group as IL-1β-exposed which received a HuMSCs treatment (diluted in PBS). Eighteen treatment protocols were tested: three different doses (dose1: 20 M cells/kg, dose2: 50 M cells/kg, and dose3: 125 M cells/kg); three different time points (acute phase at P5, the subacute phase at P10 and the tertiary phase at P20); and two routes of administration (intranasal versus intravenous) and results were compared to injured and sham-treated.

first: Clémence

last: Réda

first: Sophie

last: Lemoine

first: Cindy

last: Bokobza

first: Pierre

last: Gressens


title: Protein C-Terminal Variations Impact Proteostasis

city: Taipei

first: Hsueh-Chi

last: Yen

address: No. 128, Sec. 2, Academia Rd.

department: Institute of Molecular Biology

institute: Academia Sinica

summary: Protein C-termini can vary due to errors or programmed regulation, contributing to proteome diversity, yet their impact on the proteome remains poorly understood. Although aberrant C-termini are often liked to protein degradation, it is unclear if this holds true universally. In this study, we examine how C-terminal variations--arising from disease-associated nonstop mutations, alternative splicing, and translational readthrough--affect protein half-lives. Our findings indicate that, contrary to previous studies, erroneous C-termini can either stabilize or destabilize proteins. We have identified multiple oncoproteins and tumor suppressors whose protein stability is altered by disease-relevant nonstop mutations. Notably, we have found that C-terminal variations commonly influence the stability of canonical proteins, extending beyond their role in protein quality control. Furthermore, we have uncovered C-terminal features that distinguish erroneous from wild-type proteins and reveal that hydrophobic C-termini are targeted by a complex ubiquitin ligase network. Overall, our work broadens the understanding of C-terminal-dependent protein degradation and supports that C-terminal variation is a widespread strategy for generating protein forms with distinct half-lives to exert diverse biological functions.

overall_design: For the GPS peptidomic screen, amplicon sequencing was performed on GPS reporter library cells sorted into eight bins by fluorescence-activated cell sorting (FACS). Only reads that perfectly matched the designed sequences were retained. Two biological replicates were performed. For the CRISPR/Cas9 screen targeting proteostasis pathways, sgRNA sequences were amplified from reporter cells representing the top 5% of GFP/BFP ratios, while the total population was used as a control. The CRISPR screening results were analyzed using casTLE algorithm.

first: Ching-Yu

last: Chu

first: Shu-Yu

last: Hsu


title: BRRIAR lncRNA alters breast cancer risk by modulating interferon signaling in cis and in trans through BHLHE40 and RIG-I [RNA-Seq]

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

summary: Interferons (IFNs) are key regulators of cell proliferation and anti-tumor immunity. We identified a breast cancer-associated long noncoding RNA (lncRNA), BRRIAR, that modulates IFN signaling in estrogen receptor-positive (ER+) breast cancer. BRRIAR is transcribed from an 11 kb enhancer cluster at 3p26, and its reduced expression is linked to breast cancer GWAS risk variants. Primarily expressed in ER+ breast tumors, BRRIAR exhibits dual functionality, acting both in cis and in trans. Nuclear BRRIAR regulates BHLHE40 expression through its enhancer, while cytoplasmic BRRIAR binds to the pattern recognition receptor RIG-I, modulating its activation. BRRIAR RNA overexpression activates RIG-I signaling, inducing IFN responses that selectively trigger apoptosis in ER+ breast tumor cells in vitro and in vivo, while promoting immune activation in human peripheral blood mononuclear cells. These findings emphasize the complex regulatory mechanisms at GWAS risk regions, reveal the critical role of lncRNAs as modulators of tumor immunity and identify BRRIAR as a promising RNA-based therapeutic for ER+ breast cancer.

overall_design: For RNAseq: Total RNA was extracted from T47D cells using the RNeasy Plus mini kit (Qiagen). Libraries were prepared using the TruSeq stranded mRNA library prep kit (Illumina) as per the manufacturer’s protocol. Samples were barcoded and run on a NextSeq 550 (PE75; 20M reads per sample). The quality of sequencing data was confirmed with FastQC both before and after trimming. Paired-end reads were independently trimmed with Trimmomatic and aligned to the human reference genome (hg38) using STAR. SAMtools and NovoSort were respectively used to filter reads with proper mapping and sort the read pairs by name. RSEM was used to estimate read counts per transcript and generate transcript per million (TPM) counts.

first: Maina

last: Bitar

first: Stacey

last: Edwards


title: MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by SWI/SNF-mediated aberrant activation of cell fate-determining bivalent genes

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

institute: San Raffaele Scientific Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: MT-targeted MT1/2 orchestrates mitochondrial fusion dynamics-mediated WNT/β-catenin signaling to promote DA neuronal differentiation of human iPS and nerve regeneration in PD mice

city: Shen Zhen

first: Peng

last: Cui

state: Guang Dong

address: Futian District, Lianhua Street

institute: Peking University Shenzhen Hospital

summary: Parkinson's disease (PD) is a challenging neurodegenerative disorder. Recently, therapy of neural stem cells (NSCs) derived from human induced pluripotent stem cells (hiPSCs) has emerged as a significant advancement in regenerative medicine. Melatonin (MT), acting as a mitochondrial targeting hormone, exhibits neuroprotective properties in neurodegenerative diseases and modulates stem cell differentiation through mitochondrial dynamics. However, the precise mechanism by which MT influences dopaminergic (DA) neuronal differentiation in hiPSCs through regulating mitochondrial dynamics remains unclear. In this study, we developed and optimized a technical protocol for the in vitro functional neuronal differentiation of hiPSCs. Our findings demonstrate that MT enhances the differentiation potential of hiPSCs toward neuroectoderm and significantly improves the efficiency of NSCs differentiation into DA neurons within hiPSCs. Using the specific MT receptor inhibitor, Luzindole, we confirmed its inhibitory effect on MT-mediated promotion of neural differentiation. Mechanistically, we propose that MT enhances functional DA neuron differentiation from hiPSCs by activating mitochondrial dynamics-mediated WNT/β-catenin signaling pathways. Additionally, we elucidated the critical role of mitofusin2 (MFN2) in enhancing the directed differentiation of DA neurons from hiPSCs. In vivo studies validated the efficacy of MT-treated hiPSC-derived DA progenitor cells in regenerating tyrosine hydroxylase (TH)-positive DA neurons and improving motor function in PD mouse models. In conclusion, this study highlights the potential clinical relevance of MT-enhanced differentiation of hiPSCs into DA neurons, offering promising implications for the treatment of PD.

overall_design: RNA-Seq profiling of NSC and DAPC cells with different concentrations of MT treatment detected the effects of MT on neurodifferentiation and neuroplasticity.

first: Ping

last: Zhang

last: Huang

first: Qiongye

last: Dong

first: Juan

last: Luo

first: Guanghui

first: Minghua

last: Li

first: Xin

last: Guo

first: Xia

last: Long

first: Hongyu

first: Wei V.

last: Zheng


title: Synaptic effects of interleukin-6 on human iPSC-derived dopaminergic neurons

city: Atlanta

first: Zhexing

last: Wen

state: GA

address: 615 Michael Street

institute: Emory University

summary: Increased inﬂammation has been linked to behavioral pathogenesis in depression. Previous studies have shown that administration of inﬂammatory stimuli induces motivational deﬁcits associated with reduced activation of the ventral striatum in association with reduced dopamine (DA) availability and release. However, the underlying mechanisms of inﬂammation-induced DA dysfunction remain largely unknown. Here, we investigated the in vitro effects of the inﬂammatory cytokine interleukin (IL)-6 on female and male human induced pluripotent stem cell (iPSC)-derived DAergic neurons from healthy volunteers. We identiﬁed inhibitory effects of IL-6 on female DA neurons, including reduced DA release, neuronal ﬁring, velocity of synaptic vesicle (SV) transport, and density of docked SV, which was further supported by transcriptomic analyses. In contrast, male DA neurons exhibited an IL-6-induced compensatory phenotype, including increased velocity and density of SV and increased presynaptic terminal density. The long noncoding RNA (lncRNA) MIAT mediated these differences in male DA neurons, potentially via interaction with genes involved in the IL-6 signaling pathway and DA regulation. Moreover, by knocking out MIAT expression in male DA neurons, IL-6-induced deﬁcits emerged, including reduced DA release, neuronal ﬁring, and SV docking. Lastly, we found that the Janus kinase (JAK) inhibitor baricitinib reversed the inhibitory effects of IL-6 on female DA neurons. This work extends our understanding of the impact of inﬂammation on DA neurons, while identifying important sex differences and pharmacologic targets, ultimately laying the foundation for anti-inﬂammatory treatments of depressed patients with increased inﬂammation.

overall_design: RNA-seq profiling of eight-week-old human iPSC-derived dopaminergic neurons treated with vehicle or 5 ng/mL interleukin-6 for 24hrs

first: Yiqi


title: Protocol for 3D direct reprogramming of human glia into dopaminergic neurons with gene expression and immunocytochemistry validation

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

summary: Direct reprogramming of somatic cells into neurons offers a promising strategy for studying neurological disorders and developing cell-based therapies. This protocol describes the 3D direct reprogramming of human glial progenitor cells into subtype-specific dopaminergic neurons. It includes spheroid formation combined with lentiviral transduction, neuronal induction using doxycycline, and validation via gene expression and immunocytochemistry. This versatile approach enables rapid and efficient reprogramming of human cells into specific neuronal subtypes.

overall_design: Bulk RNA-seq of human glia progenitors, reprogrammed DA neurons in 3D

first: Mette

last: Habekost

first: Jessica

last: Giacomoni


title: Gene expression profile of tumour-infiltrating immune cells in murine PDAC

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

summary: We established an organoid-based murine pancreatic cancer model that closely resembles human PDAC. To characterize the tumor-infiltrating immune cell states following combination therapy with immune checkpoint inhibitors (ICIs) targeting PD-1 and CTLA-4, along with agonistic CD40 antibodies (aCD40), we performed RNA sequencing (RNA-seq) on tumor-infiltrating CD45+ cells from our model.

overall_design: Tumor-infiltrating CD45+ cells were isolated by FACS from tumor-bearing mice treated with either control antibodies or a combination of ICIs and aCD40. These cells were then subjected to RNA-seq analysis, with biological tetraplicates for each group.

first: Juri

last: Ichikawa

first: Hiroshi

last: Okuda


title: A combinatorial transcription factor screening platform for immune cell reprogramming [scRNA-seq]

first: Ilia

last: Kurochkin

overall_design: 9 TF, 22 TF, 42 TF and 48TF-transduced fibroblasts were FACS sorted for CD45+HLA-DRA+ or CD45+, and CD45-HLA-DRA-day9 (d9) and profiled by single cell RNA sequencing.  Cells were sorted live at day 2 (d2) to capture TF representation.

first: Abigail

last: Altman

first: Olga

last: Zimmermannova

first: Carlos-Filipe

last: Pereira


title: microRNA profiles of human breast milk derived extracellular vesicles

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

institute: Morinaga Milk Industry Co., Ltd.

summary: We investigated the expression changes of miRNAs contained in human breast milk derived extracellular vesicles over the course of lactation.

overall_design: Human breast milk samples were obtained within a few days (colostrum) to ten days (transition milk) and at 1, 2, 3, 4-5 mo.

first: Mai

last: Morozumi


title: Lipid metabolism reprograming by SREBP1-PCSK9 targeting sensitizes pancreatic cancer to immunochemotherapy [CUT&Tag]

first: Mengyi

last: Lao

state: Zhejiang

address: Qingchun 79 road

institute: Zhejiang university

summary: Pancreatic ductal adenocarcinoma (PDAC) treatment is challenging. Determining the metabolic pathways that regulate lipids will provide new insights into PDAC therapeutic strategies. Sterol regulatory element binding transcription factor 1 (SREBP-1) regulates multiple cancer pathways; however, its role in the tumor immune microenvironment and cancer immunotherapy is unknown. Herein, we integrated our large PDAC cohort data and identified that SREBP-1, as a master transcriptional regulator of lipogenesis, aggravated lipid metabolism reprogramming in PDAC. Furthermore, interrupting lipid metabolism by targeting SREBP-1 suppressed PDAC cell growth and enhanced antitumor immunity in vitro and in vivo. We demonstrated that SREBP-1 binds to the PD-L1 (programmed cell death 1 ligand 1) promoter to suppress its transcription. Importantly, SREBP-1 binds to the PCSK9 (proprotein convertase subtilisin/kexin type 9) promoter, which regulated PD-L1 levels via lysosome-mediated degradation and aggravated tumor microenvironment immunosuppression. Targeting the SREBP-1- PCSK9 axis using available drugs sustained the remission of aggressive PDAC by synergizing with anti-PD-1 and gemcitabine. In summary, targeting lipid metabolism suppressed tumor growth and relieved tumor immunosuppression in PDAC.

overall_design: After inducing overexpression of SREBP1 in SW1990 cells using an SREBP1 overexpression plasmid, Cut&Tag analysis was performed.


title: Influenza A virus modulation of Streptococcus pneumoniae infection using ex vivo transcriptomics in a human primary lung epithelial cell [AEIC and AHFJ]

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

summary: Nanostring quantification of 76 pneumococcal probes representing 72 genes, for Streptococcus pneumoniae EF3030 (wildtype and mutants) bacteria during infection of normalized human broncial epithelial cells (nHBEC), together, or after coincubation with Influenza A virus pH1N1.

overall_design: HBECs isolated from human lung tissue of 2 donors [AEIC and AHFJ] were infected/mock infected with Influenza A [pH1N1, 72 hours] followed by Streptococcus pneumoniae EF3030 infection [wildtype WT, operon mutants EF3030_RS00905, EF3030_RS02325, EF3030_RS07890, EF3030_RS07920, 6 hours].

first: Erin

middle: Y

last: Earnhardt

first: Hervé

last: Tettelin

first: Kevin

last: Harrod


title: REV-ERB-alpha and -beta coordinately regulate astrocyte reactivity and proteostatic function

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: The molecular circadian clock is a ubiquitous transcriptional-translational feedback loop that regulates CNS function, glial responses, and neurodegenerative pathology. The druggable nuclear receptors REV-ERB-ɑ (gene: Nr1d1) and REV-ERB-.Beta. (gene: Nr1d2) are components of the core circadian clock. REV-ERB proteins regulate neuroinflammatory responses, synaptic pruning, and protein aggregation, though the cell type-specific effects and relative compensatory effects of REV-ERB-ɑ AND -.Beta. in the brain are unknown. To study the CNS functions of REV-ERBs, we developed mouse lines with global or astrocyte-specific, conditional knockout of both REV-ERB-ɑ and -.Beta.. We demonstrate that inducible post-natal global deletion of REV-ERB-ɑ and -.Beta. in vivo results in robust spontaneous astrocyte activation and increases gene expression of disease-relevant pathways such as protein catabolism, complement, and oxidative stress. Furthermore, in vivo astrocyte-specific deletion of REV-ERB-ɑ/-.Beta. recapitulates the spontaneous astrocyte activation phenotype seen in global REV-ERB-ɑ/-.Beta. KO mice, as well as in mice with deletion of key core clock gene Bmal1, indicating that REV-ERBs regulate astrocyte activation in a cell-autonomous manner downstream of the core circadian clock. REV-ERB-ɑ/-.Beta. repress transcription of Stat3 in the brain, and deletion of REV-ERBs in astrocytes induces increased astrocytic STAT3 expression and downstream STAT3-mediated gene changes, a mechanistic link to the astrocyte reactivity shift. This astrocyte activation phenotype decreases alpha-synuclein pathology in an in vivo model of Parkinson’s Disease-related alpha-synucleinopathy and increases astrocytic protein uptake and degradation in vitro. This study therefore provides insight into astrocyte function and could elucidate novel regulatory mechanisms that are candidates for therapeutic manipulation through modulating REV-ERB activity.

overall_design: To investigate the role of REV-ERB-ɑ, REV-ERB-ɑ/-.Beta., or the DNA-binding domain (DBD) of REV-ERB-ɑ in the brain. We generated inducible global knockouts of REV-ERB-ɑ, REV-ERB-ɑ/-.Beta., or REV-ERB-ɑ DBD. Genes were knocked out at 2 months of age and mice were aged to 8-9 months before sacrifice. Brains were removed and RNA was extracted from the cortices and bulk RNA sequencing was performed to determine differentially expressed genes.

first: Collin

last: Nadarajah

first: Michelle

last: Li

first: Ibrahim

middle: O

last: Saliu

first: Elsa

middle: I

last: Quillin

last: Boyer

first: Julie

last: Dimitry

first: Yinying (Cynthia

last: Chen

first: Melvin

middle: W

last: King

first: Jiyeon

last: Lee

first: Patrick

last: Sheehan

first: Albert

last: Davis

first: Mitchell

last: Lazar

first: Guoyan

last: Zhao

first: Erik

last: Musiek


title: A conserved function of EZH2-PRC2 in the repression of primitive endoderm cell fate [RNA-Seq - mouse]

city: Guangzhou

first: Man

last: Zhang

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

summary: In early blastocyst, inner cell mass (ICM) initiates the second wave of cell fate decisions to generate epiblast and primitive endoderm (PrE), crucial for proper embryo development. However, the epigenetic mechanisms underlying this segregation remain incompletely understood. Here, we reveal that treatment of embryonic stem cells (ESCs) with the EZH2 inhibitor EPZ-6438 significantly enhances transdifferentiation efficiency from ESCs to primitive endoderm stem cells (PrESCs). EZH2 knockout in ESCs markedly reduces H3K27me3 modification near the promoter regions of PrE-specific genes, upregulating their expression and promoting transition to PrESCs. Overexpression of wildtype EZH2, but not catalytic site or EED-binding motif mutants, prevents this transition. Notably, the ICM of mouse blastocysts treated with EPZ6438 at 8-cell stage contain almost no epiblast but only GATA6 positive cells. Finally, EPZ6438 treatment in human naïve ESCs upregulates hypoblast-associated genes. These findings demonstrated the conserved function of EZH2-PRC2 in protecting the pluripotency from primitive endoderm cell fate.

overall_design: We aim to investigate the conserved function of EZH2-PRC2 in protecting the pluripotency from primitive endoderm cell fate. We established two EPZ-6438-induced PrESCs (EPZ-iPrESCs-1 and EPZ-iPrESCs-2) from wild-type (WT) mouse embryonic stem cells (mESCs). Duplicate RNA-seq samples of WT mESCs, EPZ-iPrESCs-1, EPZ-iPrESCs-2, and C57-PrESCs were analyzed to characterize the transcriptomic profiles of iPrESCs. Subsequently, we generated two Ezh2 knockout lines (Ezh2KO-10 and Ezh2KO-12) and their rescued counterparts (Ezh2KO-10-OE and Ezh2KO-12-OE). These cell lines were cultured in either serum/LIF (SL) or serum/2i/LIF (S2iL) medium. Duplicate RNA-seq samples were collected from WT mESCs (SL and S2iL), Ezh2KO-10 (SL and S2iL), and Ezh2KO-10-OE. For histone modification analysis, CUT&Tag profiling of H3K27me3 was performed on WT mESCs, C57-PrESCs, Ezh2KO-10, Ezh2KO-12, Ezh2KO-10-OE, and Ezh2KO-12-OE. Additionally, triplicate samples of PXGL-H1 human ESCs maintained in N2B27 basal medium (PXGL-H1 N2B27) were treated with 5 μM EPZ-6438 (PXGL-H1 N2B27+EPZ) for 3 days, followed by duplicate RNA-seq analyses.

first: Junyu


title: A conserved function of EZH2-PRC2 in the repression of primitive endoderm cell fate [RNA-Seq - human]


title: REV-ERB-alpha and -beta coordinately regulate astrocyte reactivity and proteostatic function [II]

overall_design: To investigate the cell-autonomous role of REV-ERB-ɑ/-.Beta. in astrocytes, we generated inducible astrocyte-specific REV-ERB-ɑ/-.Beta. knockouts. REV-ERB-ɑ/-.Beta. was knocked out at 2 months of age and mice were aged a further two months before sacrifice. Brains were removed and RNA was extracted from the cortices and bulk RNA sequencing was performed to determine differentially expressed genes.

first: Kevin

first: Yinying Cynthia


title: To study the underlying molecular mechanisms causing the defect in megakaryocyte development by FLI1 p.Met100*

city: Amsterdam

first: Emile

last: van den Akker

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research Amsterdam

summary: In this study, we investigated the role of the transcription factor FLI1 in megakaryopoiesis and examined how the newly identified pathological variant, FLI1 p.Met100*, disrupts megakaryocyte and platelet development. We hypothesized that FLI1 p.Met100* would generate a truncated peptide with a dominant negative effect. To test this, we ectopically expressed both wild-type FLI1 and FLI1 p.Met100* in Meg01 cells. Following succeful detection of the truncated peptide, RNA sequencing revealed that FLI1 p.Met100* upregulated erythroid genes, including KLF1, CD235a, and CD36, whereas wild-type FLI1 suppressed their expression.

overall_design: To explore this, we lentivirally transduced Meg01 cells with an empty vector (EV), wild-type FLI1, or FLI1 p.Met100* and collected them 3 days after transduction for RNA sequecing analysis. We had four replicates for each condition.

first: Huan

first: Elise J

last: Huisman

first: Roel

last: van Rhijn

first: Arthur F

last: Svendsen

first: Hans

last: Jansen

first: Nicole

last: van der Wel

first: Carmen

last: van der Zwaan

first: Nynke

last: Gillemans

first: Wilfred F.J.

last: van IJcken

first: Marten

last: Hansen

first: Sjaak

last: Philipesen

first: Marjon H

last: Cnossen

first: Arie J

last: Hoogendijk


title: Unraveling the role of TCF7L2 in self-renewal and differentiation of trophoblast stem cells (TSCs) [ChIP-Seq]

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary: Extravillous trophoblasts (EVTs) are essential for placental development, anchoring the placenta, invading the maternal decidua, and remodeling spiral arteries. It has been reported that TCF7L2, expressed in human placental tissues and EVTs, controls EVT motility. However, its targets and role in early trophoblast differentiation are not well understood. Using trophoblast stem cells (TSCs) as a model system, we investigated the roles of TCF7L2 in self-renewal and differentiation of trophoblasts using RNA-seq and ChIP-seq.

overall_design: ChIP-seq were performed forTCF7L2 in TSC and extravillous trophoblast(EVTs). Input was sequenced for a control.


title: Transcriptomic Insights into the effect of Mesenchymal Stromal Cells Culture Medium on the Hematopoietic Stem/Progenitor Cells Co-culture

city: Lisbon

first: Ana

last: Fernandes-Platzgummer

address: Av. Prof. Dr. Cavaco Silva

department: Department of Bioengineering - Instituto Superior Técnico, University of Lisbon

country: Portugal

institute: Institute for Bioengineering and Biosciences (iBB)

summary: To investigate the molecular mechanisms underlying the altered hematopoietic support of mesenchymal stromal cells (MSC) expanded in human platelet lysate (hPL)-supplemented medium, we performed a comprehensive transcriptomic analysis comparing hPL-MSC and fetal bovine serum (FBS)-expanded MSC. MSC from three bone marrow donors were cultured under different adaptation regimens and co-cultured with hematopoietic stem and progenitor cells (HSPC). Transcriptomic analysis revealed distinct gene expression profiles, with 13% of genes differentially expressed between hPL-MSC and FBS-MSC, impacting cell signaling, extracellular matrix, and chemotaxis. Key pathways, including TGF-beta, PI3K-Akt, and Wnt signaling, were altered, affecting MSC-mediated HSPC expansion. hPL-MSC exhibited increased expression of inhibitory factors and reduced expression of promoters of HSPC proliferation, influencing Notch, TGF-β, JAK/STAT, and Wnt regulation. These findings highlight critical molecular interactions in MSC-HSPC co-culture and provide insights for optimizing xeno-free MSC expansion for hematopoietic applications.

overall_design: This study analyzed mesenchymal stromal cells (MSC) from three bone marrow donors (50, 86, 99) expanded in fetal bovine serum (FBS)- or human platelet lysate (hPL)-supplemented medium under different adaptation regimens over four passages. "F" denotes one passage in FBS, and "H" one passage in hPL. The conditions included Direct (continuous expansion in the same medium: F, FF, FFF, FFFF or H, HH, HHH, HHHH), Adapted (medium switch: HF, HHF, HFF, HHFF, or FH, FFH, FHH, FFHH), and Re-adapted (returned to the original medium: FHHF or HFFH). Bulk RNA sequencing was performed after RNA extraction using the High Pure RNA Isolation Kit (Roche). Library preparation and paired-end 150 bp sequencing were conducted by Novogene on an Illumina NovaSeq 6000 platform.

first: Maria Catarina

last: Carreira

first: André

last: Branco

first: Miguel

last: Casanova

first: Carolina

last: Smet

first: Cláudia

last: Lobato da Silva


title: Unraveling the role of TCF7L2 in self-renewal and differentiation of trophoblast stem cells (TSCs) [RNA-Seq]

summary: Extravillous trophoblasts (EVTs) are essential for placental development, anchoring the placenta, invading the maternal decidua, and remodeling spiral arteries. TCF7L2, expressed in human placental tissues and EVTs, controls EVT motility. However, its targets and role in early trophoblast differentiation are not well understood. Using trophoblast stem cells (TSCs) as model system, we investigated roles of TCF7L2 in self-renewal and differentiation of trophoblasts using RNA-seq and ChIP-seq.

overall_design: We explored the role of TCF7L2 in the differentiation of trophoblast stem cells (TSCs) into extravillous trophoblasts (EVTs) by depleting TCF7L2 using shRNAs. After knocking down TCF7L2, we extracted total RNA from the TSC-derived EVTs and performed RNA sequencing (RNA-seq) to analyze global gene expression changes.


title: A Transcriptome-wise Atlas of Human Prostate as a Function of Postmortem Interval Time

city: Montgomery

first: Gulnaz

last: Javan

state: AL

address: 915 S Jackson Street

department: Physical and Forensic Sciences

institute: Alabama State University

summary: The prostate gland is one of the last internal organs to deteriorate during human decomposition. However, the effect of postmortem interval (PMI) on the mRNA and lncRNA expression and splicing is yet to be investigated in detail. The current study aims to identify the functional role of postmortem gene induction and pathway activation in prostate tissues with respect to the PMI gradient. The cadaver samples that were used in this study were collected during forensic autopsies and preserved at -20°C within the morgue at the University of Pavia (Pavia, Italy).  After RNA extraction, total RNA sequencing was performed on Illumina’s NovaSeq 6000 using paired-ended sequencing approach. StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM. Additionally, mRNAs/lncRNAs differential expression analysis was performed by DESeq2. rMATS (version 4.1.1) was used to identify alternative splicing events and analyze differential alternative splicing events between samples having high and low PMI. Pathway analysis of the differentially expressed genes demonstrated the enrichment of FoxO signaling, aldosterone-regulated sodium reabsorption and adipocytokine signaling pathways in prostate tissue with high PMI. Gene Set Enrichment Analysis (GSEA) indicated the positive enrichment of genes belonging from protein export, proteasome, ferroptosis, and citric acid cycle in high PMI group. A comprehensive detection of alternative splicing events (ASEs) at the cellular level in postmortem prostate tissue was performed to reveal skipped exon events to be most prominent ASE in high PMI group followed by retained intron events.   Our study implies that the transcription machinery remains active in prostate tissue even after five days postmortem.

overall_design: Prostate Tissue samples were removed from the prostate of five males with different causes of death. RNA was extracted using QIAGEN RNeasy Mini Kit (cat. no. 74104, Qiagen) from the prostate tissues (~ 30 mg). RNA extracts were quantitated using the Nanodrop 2000 (Thermo Scientific, Waltham, MA, USA).For Total RNA sequencing service, RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Ribosomal RNA was removed, followed by fragmentation with divalent cation buffers in elevated temperature. The sequencing library was prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

first: Kanhaiya

last: Singh

first: Joshua

last: Bethea

first: Giovanni

last: Cecchetto

first: Silvia

middle: D

last: Visonà

middle: T


title: A conserved function of EZH2-PRC2 in the repression of primitive endoderm cell fate [CUT&Tag]

first: Man

last: Zhang

first: Junyu

last: Chen


title: Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION [RNA-Seq]

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Immunoreceptor gene recombination requires complementary 12 bp and 23 bp recombination signal sequences (RSSs). In addition, the RSSs that assemble the RAG proteins, recombination centers, must be accessible yet flanked by a 5’ nucleosome decorated with H3K4me3. In Drosophila, DNA GAGA motifs play an important role in nucleosome positioning. Herein, we report that 5’ to each functional Jk RSS is a DNA GAGA motif conserved across mammalian species. In mice, the GAGA motif 5’ to Jk1 regulated local RSS accessibility and 5’ nucleosome placement. Furthermore, it was required for Vk-Jk1 recombination. Murine Jk3 is nonfunctional, having mutations in both RSS and GAGA motifs. Restoring both GAGA and RSS motifs rescued Vk-Jk3 recombination. In contrast, restoring the RSS alone did not. Genome-wide, strong cryptic 23 RSSs were preferentially bound to nucleosomes. Furthermore, evolutionary selection against cRSS only occurred in the A Compartment of B lymphocytes, not embryonic stem cells. These data indicate that in developing B cells, nucleosome positioning both enables and restricts recombination to Jk. Furthermore, our data suggest an expanded definition of recombination center-associated RSSs to include a 5’ GAGA sequence that dictates the local epigenetic state required for gene recombination.

overall_design: RNA-seq of flow-sorted small pre-b cells from WT and Jk1-GAGAmut mice.

first: Margaret

last: Veselits

first: Kaitlin

last: McLean

first: Nathaniel

middle: E

last: Wright

first: Michael

last: Okoreeh

first: Jacob

last: Maienshein-Cline

first: Malay

last: Mandal

first: Marcus

last: Clark


title: Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION

overall_design: Refer to individual Series


title: Cumulative developmental perturbations alter adult male behaviour associated with epigenetic, ribosomal and immune dysregulation in the blood and brain of C57bl/6 mice

city: Westmead

first: Brian

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

institute: Westmead Institute of Medical Research

summary: Environmental exposures across critical developmental windows can significantly influence brain development and contribute to the risk of neurodevelopmental disorders (NDDs). Importantly, emerging clinical evidence suggests that multiple environmental factors during early development synergise and result in more pronounced disease phenotypes in offspring. To expand upon this existing notion, we developed a ‘triple-hit’ mouse model to examine the combined effects of maternal social stress, chronic high-fat diet consumption, and early life poly(I:C) exposure on long-term developmental outcomes in offspring. We observed that ‘triple-hit’ male offspring displayed autism-like social deficits and an overall increased susceptibility to NDD-like behavioural alterations in adulthood. Single-cell RNA (scRNA) transcriptomic and bulk proteomic analyses were performed in male triple hit offspring across both brain tissue and peripheral blood leukocytes. scRNA sequencing revealed consistent dysregulation in critical glial cell processes, ribosomal functions and chromatin remodelling across all brain glial cell types. Similar themes were observed across peripheral blood leukocytes - displaying immune and ribosomal dysregulation at the transcriptional level. However, innate and adaptive immune cells displayed variations in directional expression of change. Proteomics analyses revealed significant reductions in proteins associated with ribosomal biogenesis, translation and chromatin remodelling pathways between brain and peripheral blood cells. Furthermore, significantly upregulated proteins associated with synaptic structure and function were observed between both compartments. Overall, using our unique triple hit model and by harnessing a systems-level approach, we demonstrate that early life environmental perturbations synergistically drive NDD-associated behaviours and complimentary transcriptional reprogramming between the central nervous system (CNS) and periphery in male offspring

overall_design: Single Cell RNA profiling of ‘triple-hit’ mouse model to examine the combined effects of maternal social stress, chronic high-fat diet consumption, and early life poly(I:C) exposure on brain and leukocytes

first: Morgan

last: Bucknor

first: Brooke

last: Keating

first: Velda

middle: X

last: Han

first: Pinki

last: Dey

first: Nader

last: Aryamanesh

first: Lee

last: Marshall

last: Graham

first: Ruwani

last: Dissanayake

first: Shrujna

last: Patel

first: Stela

middle: P

last: Petkova

first: Anand

last: Gururajan

first: Russell

last: Dale

first: Markus

last: Hofer


title: A conserved function of EZH2-PRC2 in the repression of primitive endoderm cell fate

first: Man

last: Zhang

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


title: Loss of BCL7A Permits IRF4 Transcriptional Activity and Cellular Growth in Multiple Myeloma

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: RNA-seq was performed in control NCI-H929 cells and BCL7A knock-out NCI-H929 cells (Doxycycline inducible 24 hour) to understand the transcriptomic changes after BCL7A loss in myeloma cells.

overall_design: RNA-seq profiling of wildtype H929 cells and their knockout derivatives at 24 hours.

first: Chakraborty

last: Chandraditya

first: Fulciniti

last: Mariateresa

first: Munshi

last: Nikhil


title: Cutaneous adipose tissue has a strong inflammatory signature in psoriasis patients, and it is partly IL-17 dependent.

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: Background: Psoriasis is an inflammatory skin disease associated with systemic inflammation and comorbidities such as diabetes and cardiovascular disease. Although the association between psoriasis and obesity has been studied extensively, the role of cutaneous adipose tissue (CAT) in pathogenesis of psoriasis remains unclear. Objectives This study aimed to provide a comprehensive evaluation of the CAT transcriptome in psoriasis patients and investigate the effects of IL-17 pathway blockade on adipose tissue inflammation. Methods: In this randomized, double-blind, placebo-controlled phase 4 study (ObePso study), CAT biopsies were obtained from lesional (LS-CAT) and non-lesional skin (NL-CAT) of 82 psoriasis patients and 15 healthy controls. Patients were randomized to receive either secukinumab or placebo for 12 weeks. RNA sequencing and subsequent analyses were performed to identify differentially expressed genes and pathways. Results: Psoriatic CAT showed significant gene expression differences compared to controls, with 2132 differentially expressed transcripts identified. Both LS-CAT and NL-CAT exhibited activation of IL-17-induced, antimicrobial peptides-related, and neutrophil degranulation-related pathways. Obesity expanded differential gene expression in psoriasis by more than 100%, suggesting an additive or synergistic interaction between psoriasis and adiposity. Obese psoriasis patients showed activation of pathways related to collagen metabolism, cytokine storm signaling, and IL-17A signaling. Secukinumab treatment significantly improved inflammation in psoriatic CAT, with obese patients showing greater improvement than non-obese patients. Conclusions: This study provides the first comprehensive evaluation of the adipose tissue transcriptome in psoriasis patients. The findings reveal a strong inflammatory signature in psoriatic CAT, which is partly IL-17 dependent. The study also demonstrates that obesity amplifies the inflammatory response in psoriatic adipose tissue. IL-17 blockade with secukinumab significantly improved CAT inflammation, with enhanced benefits observed in obese individuals. These results highlight the potential role of adipose tissue in psoriasis pathogenesis and suggest that targeting adipose tissue inflammation may be a valuable therapeutic approach, particularly in obese psoriasis patients.

overall_design: Cutaneous adipose tissue biopsies were taken from lesional and non-lesional skin of 82 psoriasis patients. Samples were also collected from 15 healthy subjects using the same procedure. RNA was isolated from adipose tissue samples using the RNeasy Lipid Tissue Mini Kit (Qiagen)

middle: G

first: Naomi

last: Shishido-Takahashi

first: Sandra

last: Garcet


title: Decoding the Retn-Cap1 Pathway in Intermediate Monocytes Mediating Liver Allograft Rejection

city: Xi’an

first: Xudan

last: Wang

address: Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, 127 West Changle Street, Xi’an, 710032, China.

institute: Xijing Hospital

summary: Lymphocytes are widely recognized as the primary mediators of cellular rejection post-liver transplantation. However, conventional immunosuppressive regimens that target lymphocytes, such as calcineurin phosphatase inhibitors, corticosteroids, or lymphocyte-depleting antibodies, can only partially mitigate rejection while inducing severe adverse effects. This necessitates the search for novel immunotherapeutic targets. Here, by creating the largest single-cell multi-omics database of liver transplantation to date and employing a souporcell-based strategy to distinguish between donor and recipient cells, we delineate the dynamic landscape of immune cells during allograft rejection and their spatial distributions across donors and recipients. Our findings underscore the pivotal role of recipient derived intermediate monocytes in cellular rejection. Using CellChat ligand-receptor analysis, we identify the Resistin-Cap1 pathway as a key mechanism by which intermediate monocytes participate in T cell-mediated rejection reactions. We confirm that Resistin knockdown significantly alleviates acute rejection after rat liver transplantation, markedly extending the survival of recipients using innovative nanogold technology. These findings offer insights into the dynamic changes in the alloimmune microenvironment, pinpointing intermediate monocytes as potential diagnostic and immunotherapeutic targets during allograft rejection. This study holds significant importance in advancing non-invasive diagnostic technologies and immunotherapeutic strategies for allogeneic rejection.

overall_design: Liver transplantation was conducted from Lewis rats to BN rats to create a post-transplant rejection model, and from BN rats to BN rats to establish a syngeneic control model. Liver tissues and peripheral blood mononuclear cells (PBMCs) from both groups were collected on days 0, 1, 7, and 14 post-transplantation for single-cell sequencing.

first: Peijun

last: Yang

first: Weikang

last: Wu

first: Juzheng

last: Yuan

first: Xinrui

first: Rui

last: Ding

first: Weiwei

last: Cao

first: Cong

last: Li

first: Yinjie

first: Zihan

last: Xi

first: Kefeng

last: Dou

first: Xiao

first: Kaishan

last: Tao


title: Divergent Mechanisms of Tissue Remodeling In Acute and Chronic Models of Allergic Airway Inflammation

city: Bialystok

first: Andrzej

last: Eljaszewicz

state: Podlaskie

address: Jana Kilinskiego 1

department: Centre for Regenerative Medicine

country: Poland

institute: Medical University of Bialystok

summary: Inadequately controlled chronic airway inflammation may result in a series of irreversible changes within lung tissue, referred to as lung remodeling. The increased activation of airway fibroblasts and their differentiation towards myofibroblasts leads to the deposition of extracellular matrix (ECM) components, including collagens. The disrupted balance between the activity and concentration of matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) secreted by structural lung cells and infiltrating immune cells may lead to excessive ECM remodeling. Here, we aimed to utilize HDM-induced experimental acute (mixed and neutrophilic) and chronic (neutrophilic) experimental asthma models to assess differences in lower airway remodeling. First, we confirmed increased total collagen deposition within the lung in all analyzed models. Additionally, we found an elevated frequency of IFN-producing T cells in acute neutrophilic inflammation, while an elevated frequency of IL-4 and IL-10-producing T cells was observed in mixed airway inflammation. Transcriptomic analysis revealed Th2- and Th17- -related signaling pathways, while specifically in the chronic model, we noted Th17-driven fibrosis. Moreover, transcriptomic profiling showed the dysregulation in genes associated with ECM morphology, collagens, MMPs, and TIMPs. Targeted protein analysis confirmed the increased deposition of Collagen I, III, IV, and VI. Finally, multiplexing analysis of bronchoalveolar lavage indicated an increase in MMP-2 and TIMP-4 levels among all investigated models, whereas MMP-8 and MMP-9 appeared to be increased explicitly in chronic inflammation. In summary, we confirmed that various inflammatory profiles in experimental asthma models may differentially influence the development of airway remodeling changes.

overall_design: Female C57BL/6cmdb mice were divided into five groups. Mice were sacrificed after 2 weeks (models with 10 μg, 100  μg of HDM extract and control) and 12 weeks (models with 100  μg of HDM extract and control). Biological material was collected and biobanked for further analysis.

first: Tynecka

last: Marlena

first: Tarasik

last: Agnieszka

first: Hanczaruk

last: Bartosz

first: Janucik

last: Adrian

first: Czolpinski

last: Krystian

first: Walewska

last: Alicja

first: Zbikowski

last: Arkadiusz

first: Zeller

last: Anna

first: Kulczynska-Przybik

first: Niemira

last: Magdalena

first: Reszec-Gielazyn

last: Joanna

first: Mroczko

last: Barbara

first: Kretowski

last: Adam

first: A. Akdis

last: Cezmi

first: Sokolowska

last: Milena

first: Moniuszko

last: Marcin

first: Karaaslan

last: Cagatay

first: Eljaszewicz

last: Andrzej


title: Necessity of Notch3 signaling in myofiber maturation in a pluripotent stem cell transplant model

city: Minneapolis

first: Aline Miyoko

last: Sakaguchi Yamashita

state: Minnesota

address: 2231 6th St SE

department: Department of Medicine

institute: University of Minnesota

summary: This study investigates the role of Notch3 signaling in muscle regeneration using iPax3-derived myogenic progenitors. We generated iPax3-N3KO (Notch3-deficient) and iPax3-N3OE (Notch3-overexpressing) progenitors to assess how Notch3 influences muscle regeneration and myofiber maturation. In vivo transplantation of iPax3-N3KO progenitors showed normal myofiber engraftment but increased expression of embryonic myosin heavy chain (eMHC), suggesting delayed myofiber maturation. Conversely, iPax3-N3OE progenitors exhibited reduced myofiber engraftment and decreased eMHC expression, indicating that Notch3 activation inhibits myogenic progenitors differentiation and myofiber maturation. Secondary transplantation experiments showed similar engraftment rates between iPax3 (empty vector control, “EV”) and iPax3-N3KO satellite cells, but significantly reduced engraftment from iPax3-N3OE satellite cells. Additionally, fiber type composition analysis revealed increased eMHC expression in Pax3-N3KO grafts and no differences in iPax3-N3OE grafts compared to control. These findings suggest that Notch3 signaling plays a critical role in myofiber maturation and differentiation. Absence of Notch3 results in less mature fibers, while its activation impairs differentiation. Transcriptional profiling of iPax3-N3OE donor-derived satellite cells indicates that these effects may be driven by alterations in cell cycle regulation.

overall_design:
To investigated the effect of Notch3 GOF in iPax3 myogenic progenitors, we overexpress NICD3 (iPax3-N3OE) in PSC-derived iPax3 myogenic progenitors.
To determine the molecular changes underlying Notch3 GOF in iPax3 myogenic progenitors in an unbiased manner, we next performed RNA sequencing.
To elucidate the molecular determinants underlining the differences in satellite cell engraftment between iPax3-N3OE and iPax3 cohorts, we performed RNA sequencing analysis in donor-derived satellite cells.

first: Yamashita

last: Aline MS

first: Crist

last: Sarah

first: Garay

last: Bayardo I

first: Kim

last: Hyunkee

first: Azzag

last: Karim

first: Bosnakovski

last: Darko

first: H.D.M. Faria

last: Sergio

first: Abrahante

last: Juan E

first: Abreu

last: Phablo

first: Ahlquist

last: Aaron

first: Perlingeiro

last: Rita RC


title: Disruption of jejunal and ileum homeostasis by malnutrition in systemic jejunal and ileum microbiota-host interactions in a pregnant sheep model [miRNA-Seq]

city: Hefei

first: Peng

last: Jiao

address: No. 130, Changjiang West Road, Hefei, Anhui Province, Anhui Agricultural University

institute: Anhui Agricultural University College of Animal Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: In the current study, five late gestation multiparous ewes were restricted to a 30% feeding level to create a model of malnutrition, while five other ewes were fed normally as controls. All ewes were sacrificed and jejunal and ileal samples were collected for transcriptome sequencing to study metabolic changes.

overall_design: Compare the differences in transcriptome profiles between the jejunal and ileal sample from CON and TR ovis aries.

first: Weibin

last: Wu

first: Shengyong

last: Mao

first: Yanfeng

last: Xue