title: In-Depth Patient-specific Analysis of Tumor Heterogeneity in Melanoma Brain Metastasis: Insights from Spatial Transcriptomics and Multi-Region Bulk Sequencing

city: Stockholm

first: Nidhi

last: Sharma

state: Stockholm

address: Tomtebodavägen 23, Solna

department: Oncology-Pathology

institute: Science for life laboratory, Karolinska Institute

summary: Melanoma brain metastasis (MBM) response to treatment varies greatly among patients, affecting overall prognosis and survival. This study aims to provide a comprehensive multi-omics overview of MBM by investigating tumor tissue composition at spatial, proteomic and transcriptomic levels, elucidating the spatial tumor landscape, characterizing tumor tissue cell populations and identifying enriched signaling pathways in the MBM tumor tissue. We found higher inter-tumoral heterogeneity than intra-tumoral heterogeneity in MBM at the protein and transcriptional levels. The treatment-naive patient exhibited high intra-tumoral heterogeneity (ITH) compared to patient who received treatment, with ITH levels varying across neighboring regions in all patient tumors. Significant global protein and cell type enrichment associated with malignant cells, macrophages, CAFs, and immune cells was observed in MBM using cellular deconvolution and tumor microenvironment (TME) analysis. The presence of MBM cell-type specific gene signatures, and enriched pathways identified using ST and bulk-seq provide an essential framework for understanding tumor composition and potential treatment-related effects in each MBM patient tumor. Taken together, our results provide a comprehensive spatial and molecular view of intra-tumoral and inter-tumoral heterogeneity in MBM, potentially guiding personalized treatment strategies in MBM therapy.

overall_design: We obtained fresh frozen tumor tissues from four patients with MBM. The freshly frozen (FF) tissue blocks were OCT-fixed and sectioned using a cryotome. Briefly for multi-region bulk sequencing, 20 sequential sections of 20 µm were collected for four regions, starting with regions (R) 1- 4. We analyzed transcriptome of multiple regions (R1-4) in each patient tumor. Here, multiple region data for patient 1 (P1) is labeled as P1-1 (for R1), P1-2 (for R2), P1-3 (R3) and P1-4 (R4). Likewise, samples for other patients (P2, P3, P4) are also labeled in a similar way.

first: Jana

last: Rájová

first: Georgios

last: Mermelekas

first: Kim

last: Thrane

first: Joakim

last: Lundeberg

first: Alia

last: Shamikh

first: Sofi

last: Vikström

first: Haris

last: Babačić

first: Margret

last: Jensdottir

first: Janne

last: Lehtiö

first: Maria

last: Pernemalm

first: Hanna

last: Eriksson


title: HEP14 treatment improves ovarian function in aged mice through mitophagy enhancement and oxidative stress reducton

status: Public on Jul 17 2025

city: Shenzhen

first: Liming

last: Gui

address: 1120 Lianhua Street

department: Obstetrics and Gynaecology

country: China

institute: Peking University Shenzhen Hospital

type: Expression profiling by high throughput sequencing

summary: Ovarian senescence impacts reproductive health and accelerates the overall aging process. Despite extensive research in this area there is still a dearth of effective therapeutic strategies. We here report the rejuvenating effects of HEP14, a natural activator of PKC pathway, on aged ovarian function. Further, we detail a method to fabricate HEP14-loaded PLGA microspheres designed for controlled and sustained drug release in vivo. Transcriptomic analysis revealed a significant overlap between the transcriptional profiles of HEP14-treated aged ovaries and those of adult ovaries, suggesting molecular rejuvenation process. Histopathological evaluations following treatment demonstrated that HEP14 not only enhances mitophagy but also exhibits antioxidative properties and promotes follicular regeneration. As a result, ovarian endocrine function was ultimately restored in aged mice, evident in raised serum levels of E2, AMH, Inhibin A/B and lowered FSH levels. In vitro studies further showcased restorative effect of HEP14 on enhancement of mitophagy and mitochondrial function by the activation of the PKC-ERK1/2 pathway in senescent GCs, which are integral to the action mechanism of HEP14. These findings pave the way for new therapeutic approaches for developing therapeutic strategies aimed at improving reproductive health in aging individuals.

overall_design: To delve into the molecular mechanisms behind HEP14-driven ovarian function restoration in aged mice, we conducted a comparative transcriptomic analysis on ovaries from four groups of mice: young (7~8 weeks), adult (27~28 weeks), aged mice (73~74 weeks) treated with vehicle, and aged mice (73~74 weeks) treated with HEP14 (aged+HEP14 mice).

first: Jiajia

last: Sun

first: Kan

last: Liu

first: Qili

first: Yingtong

last: Di

first: Qin

last: Zhong

first: Bin

last: Tang

first: Xiaojiang

last: Hao

first: Changzhong

last: Li

first: Helen

last: Picton


title: Dasatinib Remodels the Tumor Microenvironment and Sensitizes Small Cell Lung Cancer to Immunotherapy

city: Pamplona

first: Alfonso

last: Calvo

state: Navarra

address: Avenida Pío XII 55

country: Spain

institute: CIMA Universidad de Navarra

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

overall_design: Refer to individual Series


title: Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks [RNA-seq]

city: Boston

first: Gracia

middle: M.

last: Bonilla

state: MA

address: 185 Cambridge St

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

summary: Developmental gene expression is tightly regulated by the dynamic interplay of H3K4 and H3K27 methylation associated with active and repressed genes, respectively. However, our understanding of the individual and combinatorial roles these histone modifications play in a physiological context remains incomplete. Here, we have leveraged histone mutant transgenic tools to uncover a previously unappreciated role for H3K4 methylation in adult hematopoiesis. Adult mice globally depleted for all forms of H3K4 methylation via expression of an inducible histone H3 lysine-4-to-methionine (H3K4M) mutant allele succumbed to a severe loss of all major blood cell types. Unexpectedly however, H3K4M-expressing hematopoietic stem cells (HSCs) and committed progenitors were present at normal numbers and persisted long-term when transplanted into mice alongside unperturbed bone marrow, indicating that H3K4 methylation is dispensable for the maintenance and early commitment of HSCs but essential for the maturation of downstream progenitors. Importantly, the restoration of H3K4 methylation in H3K4M animals rescued their morbidity, released progenitors from the maturation block and enabled normal blood cell production. Mechanistically, we showed that H3K4 methylation opposes the deposition of repressive H3K27 methylation at differentiation-associated genes bivalently marked by H3K4me3 and H3K27me3 in HSCs or progenitors. Indeed, by concomitantly suppressing H3K27 methylation in H3K4 methylation-depleted mice we could rescue the acute lethality, hematopoietic failure and gene dysregulation. Collectively, our results reveal that H3K4 methylation safeguards hematopoiesis by opposing repressive H3K27 methylation at fate-instructive bivalent genes, providing evidence for the functional interaction between these crucial chromatin marks in mammalian tissue homeostasis.

overall_design: RNA-seq was performed for H3WT, H3K4M, H3K27M, or H3K4M/K27M  samples in duplicate

first: Masaki

last: Yagi

first: Nikolaos

last: Tsopoulidis

first: Ruslan

last: Sadreyev

first: Konrad

last: Hochedlinger


title: Pyrazole-derived TRPC3 antagonist ameliorates synaptic dysfunctions and memory deficits in Alzheimer’s disease models

city: MEMPHIS

first: Zhengjun

last: Wang

state: TN

address: 71 S Manassas Street

institute: University of Tennessee Health Science Center

summary: Among the canonical transient receptor potential (TRPC) channels, TRPC3 expression is uniquely upregulated in brains with Alzheimer’s disease (AD) based on our recent studies. Herein, we used JW-65, a selective inhibitor for TRPC3 over TRPC6, to investigate the potentially distinct role of TRPC3 in AD. JW-65 treatment completely restored impaired synaptic plasticity and learning memory in acute and chronic experimental AD models. JW-65 treatment of symptomatic 5XFAD transgenic mice reversed the impaired LTP, correlating with their largely corrected synaptic gene expression based on hippocampal RNA-seq data analysis. JW-65 also provided synaptic protection in primary rat hippocampal neurons against soluble β-amyloid oligomers (AβOs), primarily via restoring the AβOs-impaired Ca2+/calmodulin-mediated signaling pathways. JW-65 treatment also significantly prevented  Ca2+ overload induced by AβOs. These findings suggest that aberrantly upregulated TRPC3, as a novel non-selective ion channel, significantly contributes to Ca2+ dyshomeostasis in AD. Our work identifies TRPC3 as a potential therapeutic target for treating synaptic dysfunction of AD.

overall_design: Twelve-month-old 5xFAD mice were treated with 20 mg/kg JW-65 over the course of one month (3 injections per week) via intraperitoneal (i.p.) dosing.

first: Jiaxing

first: Francesca-Fang

last: Liao


title: Gene expression dynamics before and after zygotic genome activation in Drosophila early embryogenesis

city: New York

first: Yeon

last: Choi

state: NY

address: 1470 Madison Ave

institute: Iicahn school of medicine at mount sinai

summary: Post-transcriptional gene regulatory mechanisms are fundamental for the determination of gene expression dynamics and especially crucial for the earliest stages of animal development in which transcription is nearly silent. Here we performed high-resolution gene expression level change analysis in Drosophila maternal-to-zygotic transition (MZT). Intriguingly, we found that both stable transcript expression and an increase in translation efficiency can be crucial for protein upregulation prior to zygotic gene activation (ZGA), whereas such features diminished following ZGA. The results suggested that there are distinct regulatory mechanisms for protein upregulation pre- and post-ZGA in Drosophila embryos. Further, this study is the first to report the proteome-wide quantitative changes in protein ubiquitination in Drosophila MZT. Our results indicate that timely ubiquitination of the distinct target proteins during MZT are essential for the downregulation of protein expression levels. Profiling of the RNA-associated proteome changes in Drosophila MZT suggested that RNA-binding activities can be regulated without the respective change in net protein expression levels for over 200 proteins, including Pcid2, Sym, and Cpsf73. Taken together, we report a diverse array of features that mediate post-transcriptionally regulated gene expression dynamics in Drosophila MZT.

overall_design: RNA-seq on drosophila embryos and unfertilized eggs were conducted in high-temporal resolution.

first: Yongwoo

first: Thi

middle: T

last: Nguyen

first: Hoang-Anh

last: Pham-Bui

first: Jeesoo

last: Kim

first: V

middle: N

first: Mihye

last: Lee

first: Jong-Seo


title: Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer’s disease [RNA-Seq]

city: Shanghai

first: Zixin

address: Siping Road

institute: Tongji University

summary: 5-hydroxymethylcytosine (5hmC) constitutes up to 20% of 5-methylcytosine (5mC) in mammalian cells. As conventional bisulfite sequencing is unable to distinguish 5hmC from 5mC, several methods have been proposed to detect 5hmC and infer 5mC levels by subtracting 5hmC from whole-genome bisulfite sequencing data. This subtraction approach, however, can lead to the underestimation of 5mC levels at sites with high 5hmC abundance. Here, we present two orthogonal methods: CMD1-Deaminase sequencing and CMD1-TET bisulfite sequencing, which enable the direct and independent detection of 5mC. In combination with ACE-seq or TAB-seq, these techniques facilitate an accurate distinction between 5mC and 5hmC, eliminating the need for subtraction. Using these approaches, we generated a comprehensive landscape of 5mC and 5hmC in the hippocampus of the Alzheimer's disease (AD) model mice. Notably, while 5hmC levels were substantially reduced in the AD mice, 5mC levels remained largely unchanged, suggesting a critical role for 5hmC as an independent epigenetic mark in the pathogenesis of AD.

overall_design: RNA-seq in hippocampus of WT and Alzheimer's disease model mice

first: Faying

last: Chen

first: Baodan

last: He

first: Fanchen

first: Jiaxue

last: Cha

first: Yu

last: Song

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Yujun

last: Hou

first: Jiejun

last: Shi

first: Jianhuang

last: Xue


title: Unveiling the Molecular Legacy of Transient Insulin Resistance: Implications for Hepatic Metabolic Adaptability [ATAC-Seq]

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

country: France

institute: Inserm

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Metabolic flexibility (MetF) refers to an organism's capacity to adapt to changes in metabolic supplies and energy demands. MetF involves various organs, such as skeletal muscle, white adipose tissues, and the liver, and plays a critical role in altering fuel selection. Insulin acts as a central coordinator of MetF, regulated at the molecular level through various mechanisms, including signaling cascades, transcriptional responses, and circadian regulation. Insulin resistance (IR) can hinder MetF, leading to the development of type 2 diabetes and obesity. These conditions are primarily linked to long-term, chronic exposure to sedentary lifestyles, unbalanced diets, and disruptions in circadian rhythms. However, transient episodes of IR significantly elevate the risk of later-in-life development of type 2 diabetes, as seen in cases like gestational diabetes and stress-induced hyperglycemia. Despite their significance to human health, the molecular processes underlying metabolic dysregulation after these transient episodes remain poorly understood. In our study, we demonstrate that a temporary and fully reversible insulin receptor blockade in young mice results in later-in-life hepatic abnormalities that impair the PPARα-mediated response to a high-fat diet. This impairment is associated with increased histone repressive marks at PPARα-centered loci and decreased hepatic content of PPARα endogenous ligands. Transient insulin receptor blockade temporarily disrupts the liver's circadian rhythm, and this disruption specifically propagates to high-fat diet-fed animals. Our findings reveal that PPARα ligand responsiveness is critically influenced by the circadian clock, adding another layer of (dys)regulation to hepatic homeostasis due to early transient events.  In summary, our data suggest that seemingly reversible and unnoticed metabolic challenges in early adulthood may predispose the liver to exacerbated metabolic dysfunctions when confronted with chronic challenges later in life.

overall_design: ATAC-Seq on mouse Liver under high fat diet after transient insulin resistance event (IR) or not (Ctrl). Each condition has been conduced in triplicate.

first: Philippe

last: Lefebvre


title: Unveiling the Molecular Legacy of Transient Insulin Resistance: Implications for Hepatic Metabolic Adaptability [array]

overall_design: All conditions were analyzed in 5 biological replicats (exept J85_PBS_HFD: n=4)

first: Céline

last: Gheeraert


title: Unveiling the Molecular Legacy of Transient Insulin Resistance: Implications for Hepatic Metabolic Adaptability [ChIP-Seq]

overall_design: Histone marks (H3K4me1, H3K27me3 and H3K27Ac)  analysis from mouse on mouse liver under high fat diet after transient insulin resistance event (IR) or not (Ctrl). Each condition has been conduced in triplicate (exept H3K27ac IR which was a duplicate).


title: Comparative analysis of Ad5, mRNA, and protein vaccines reveals context-dependent immune responses

status: Public on Jul 16 2025

first: Pablo

last: Penaloza-MacMaster

address: 3 Blackfan Circle

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: Despite the widespread use of adenovirus, mRNA, and protein-based vaccines during the COVID-19 pandemic, their relative immunological profiles and protective efficacies remain incompletely defined. Here, we compared antigen kinetics, innate and adaptive immune responses, and protective efficacy following Ad5, mRNA, and protein vaccination in mice. Ad5 induced the most sustained antigen expression, but mRNA induced the most potent interferon responses, associated with robust antigen presentation and costimulation. Unlike Ad5 vaccines, which were hindered by pre-existing vector immunity, mRNA vaccines retained efficacy after repeated use. As a single-dose regimen, Ad5 vaccines elicited superior immune responses. However, as a prime-boost regimen, and particularly in Ad5 seropositive mice, mRNA vaccines outperformed the other vaccine platforms. These findings highlight strengths of each vaccine platform and underscore the importance of vaccination context in determining optimal vaccine performance.

overall_design: C57BL/6 mice were immunized intramuscularly with each respective vaccine (Ad5, mRNA, and protein vaccines). At day 1 post-vaccination, lymph nodes from five mice were pooled and MACS-sorted with a CD45 MACS positive selection kit (STEMCELL) and used for single-cell sequencing. A naive group with no vaccination was used as control.

first: Bakare

last: Awakoaiye

first: Shiyi

last: Li

first: Sarah

last: Sanchez

first: Tanushree

last: Dangi

first: Nahid

last: Irani

first: Laura

last: Arroyo

first: Gabriel

last: Arellano

first: Shadi

last: Mohammadabadi

first: Malika

last: Aid


title: Transcriptomic profiling of primary mediastinal liposarcoma

city: Kobe

first: Suguru

last: Mitsui

state: Hyogoken

country: Japan

institute: Kobe University Graduate School of Medicine School of Medicine: Kobe Daigaku Daigakuin Igakukei Kenkyuka Igakubu

summary: Primary mediastinal liposarcoma (MLPS) is an extremely rare tumor with unclear molecular biology. We conducted RNA sequencing in five cases of MLPS and compared gene expression between dedifferentiated liposarcoma (DDLPS) and well-differentiated liposarcoma (WDLPS). Enrichment analyses and immune cell deconvolution revealed that DDLPS showed features of dedifferentiation, cell cycle activation, Wnt signaling, and immune-cold status. This dataset provides the first transcriptomic landscape of primary MLPS and offers insight into potential therapeutic targets.

overall_design:
Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor samples from five patients with mediastinal liposarcoma. RNA-seq libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform. Processed data includes transcript per million (TPM) values and raw count matrices for downstream transcriptomic and immunologic analyses.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Yoshimasa

last: Maniwa


title: Allopregnanolone is neuroprotective in hypoxic-ischemic injury of the immature brain

city: Hempstead

first: Anthony

last: Szema

state: New York

address: 500 Hofstra Blvd,

department: Department of Occupational Medicine, Epidemiology and Prevention,

institute: Donald and Barbara Zucker School of Medicine

summary: Hypoxic-ischemic (HI) brain injury in premature infants causes major cognitive deficits and cerebral palsy (CP). Premature infants are devoid of a placental supply of Allopregnanolone (ALLO). ALLO is essential for brain growth and neuronal and glial cell survival. Goals and objectives: To assess whether ALLO supplementation mitigates hypoxic-ischemic (HI) brain injury. To conduct a comparative analysis of RNA sequencing between ALLO-treated HI mice and untreated HI mice. To elucidate the mechanism of action of ALLO in the context of HI brain injury.Methods: A neonate mouse model of HI was treated with 3 doses of ALLO (10mg/kg/dose IP) on P5, P8, and P11 or saline. Molecular, biochemical, histopathological, and transcriptome studies were done on P12-P14. Others were examined at P60 for neurobehavioral analysis. Results: ALLO-treated HI mice showed significant improvement in neuro-regeneration, myelination, motor function, coordination, learning, and memory, along with significant attenuation of neuro-inflammation. RNA sequencing analysis showed that the ALLO-treated HI group had a significant downregulation of inflammatory responsive genes, reduced glutamate excitotoxicity, improved neurogenesis, and improved neural repair, restoring neural integrity and cognitive function. Using electron microscopy, mitochondrial ultrastructure in hippocampal neurons showed small, fragmented mitochondria, with loss of mitochondrial membrane and cristae in HI group, while ALLO protected mitochondrial ultrastructure after HI exposure. Conclusion: ALLO is a unique natural neurotherapeutic steroid in HI injury through promoting neurogenesis, neurodegeneration, and oligodendrogenesis, reducing neuroinflammation and glutamate excitotoxicity, and preserving mitochondrial structure and function.

overall_design: RNA-seq profiling of a Swiss Webster pup's whole brain at neonatal day 5 post-birth after hypoxia-ischemia induced brain injury in control  and after treatment with Allopreganolone

first: Nahla

last: Zaghloul

first: Mohamed

last: Ahmed

first: Akash

last: Gupta

first: Michael

middle: D

last: Weiss

first: Tian

last: Wang

first: Fei

last: Yen

first: Roberta

last: Brinton


title: Evaluation of a novel chemokine receptor 2 (CCR2)-antagonist in painful diabetic polyneuropathy

city: Piscataway

first: Lei Yu

last: Lei Yu

state: New Jersey

address: 145 Bevier Rd

department: Genetics

institute: Rutgers University, New Brunswick: School of Arts and Sciences

summary: Background and aims: Preclinical data suggest that the chemokine receptor 2 (CCR2) is involved in the pathophysiology of neuropathic pain through modulation of neuronal excitability, synaptic transmission and activation of spinal cord microglia. CCR2-antagonists have shown to be effective in preclinical models of neuropathic pain. The aim of this study was to evaluate the analgesic efﬁcacy, safety and tolerability of a novel CCR2-antagonist, AZD2423, in patients with painful diabetic neuropathy (PDN).  Methods: This was a double-blind, randomized, parallel-group, multi-center study in patients with sym- metric distal sensory polyneuropathy due to type 1 or 2 diabetes and duration of neuropathic pain between 3 months and 5 years. Concomitant treatment with neuropathic pain medications (e.g. anticon- vulsants, tricyclic antidepressants, serotonin-noradrenaline uptake inhibitors, opioids, topical lidocaine or capsaicin) was not allowed. 134 patients with PDN were equally randomized to 28 days oral admin- istration of 20 mg AZD2423, 150 mg AZD2423, or placebo. The primary efﬁcacy variable was the change of average pain score from 5-days baseline to the last 5 days of treatment, measured with numerical rating scale (NRS, 0–10). The secondary efﬁcacy measures included NRS worst pain scores, patient global impression of change, pain interference on sleep and activity, and neuropathic pain symptom inventory (NPSI).  Results: The change of NRS average pain score was not signiﬁcantly different between treatment groups (AZD2423 20 mg: −1.50; AZD2423 150 mg: −1.35; placebo: −1.61). The NPSI total score and three out of ﬁve subscores (evoked pain, pressing/deep pain and paresthesia/dysesthesia) tended to be reduced more by AZD2423 150 mg than by placebo. No other secondary efﬁcacy variables differed between treatment groups. The frequency and type of adverse events for AZD2423 were similar to placebo. The achieved plasma levels of AZD2423 in the two dose groups were in line with predictions from pharmacokinetic data previously obtained in healthy volunteers. Dose-dependent increase of plasma levels of the ligand of CCR2 (CCL2; chemokine ligand 2) and decrease of the mean levels of monocytes (−27% by AZD2423 150 mg) suggested that the administrated doses of AZD2423 interacted with the CCR2 target.  Conclusion: The CCR2-antagonist AZD2423 showed no analgesic efﬁcacy in PDN based on NRS average pain scores and global and functional pain outcome measures. The NPSI data suggested possible effects on certain sensory components of pain. There were no major safety or tolerability concerns.

overall_design: RNA-seq profiling of blood samples.

first: Thomas

last: Richardson


title: Bovine colostrum-derived extracellular vesicles  influence on Akkermansia in the gut environment

city: Seoul

first: Daye

last: Mun

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Extracellular vesicles derived from milk are known to play a significant role in regulating gut microbiota. However, few studies have focused on the effects of these vesicles on specific bacterial species. This study aimed to investigate how bovine colostrum-derived extracellular vesicles (BCEVs) affect the growth and viability of commensal bacteria, specifically Akkermansia muciniphila. BCEVs and A. muciniphila were co-cultured to measure growth rates using spectrophotometry, and cell viability was assessed at the endpoints. Additionally, to determine whether BCEVs enhance the survival of A. muciniphila in the presence of Caco-2 cells, an anaerobic co-culture experiment was conducted to determine the specific interaction between intestinal epithelial cells and gut microbiota using a Transwell system. The results showed that co-culture with BCEVs increased the growth rate and viability of A. muciniphila. Consistent with this, increased viability of A. muciniphila was observed when it was co-cultured with Caco-2 cells. Transcriptomic analysis revealed that BCEVs regulate nitrogen metabolism in A. muciniphila, enhancing the growth rate and viability. Thus, regulating beneficial gut bacteria, such as A. muciniphila, through BCEVs presents a novel biological approach that positively impacts human health.

overall_design: Analysis of transcriptomic changes in Akkermansia muciniphila KCTC 15667 co-cultured with bovine colostrum-derived extracellular vesicles or PBS


title: Photostimulation Promotes Maturation of Human Stem Cell-Derived Photoreceptors

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

country: Czech Republic

institute: Masaryk University

summary: Human retinal organoids derived from stem cells have become powerful tools to model retinal development and disease, but they often remain immature and lack key features required for full function. Light is not only the sensory target of photoreceptors but also an important developmental signal in vivo. However, light has rarely been used as a deliberate stimulus during in vitro differentiation. Here we show that exposing retinal organoids to rhythmic light flicker at a specific frequency enhances photoreceptor maturation across multiple levels.

overall_design: Bulk RNA-seq: Organoids were exposed to four distinct light conditions in a 12-hour light / 12-hour dark cycle for 7 days:      Dark (no light exposure – control),      Constant light,      Random-frequency flickering light (1–100 Hz), and      40 Hz flickering light (gamma-frequency stimulation).     The aim was to identify global transcriptional changes in response to various light stimulation paradigms.  Single-cell RNA-seq (scRNA-seq): Performed on organoids cultured under either Dark or 40 Hz flickering light conditions, using matched protocols. This allowed assessment of cell-type specific transcriptional responses and changes in cell composition. Thirty organoids were pooled per condition, with dissociation and scRNA-seq performed using the 10x Genomics Chromium platform.  Together, the samples encompass both global and cell-type resolved transcriptomic responses to photostimulation, with experimental variables including light regime and biological replication.

first: Canan

last: Celiker


title: Transcriptomic profiling of Alzheimer's disease and high-fat diet-induced exacerbation in mouse brain

city: Xiangtan

first: Shen

last: Yang

address: No.100 Shuyuan Road, Yuetang District, Xiangtan City, Hunan Province

institute: Department of Neurology, The First People's Hospital of Xiangtan City,

summary: This project investigates transcriptomic changes in the brain associated with Alzheimer's disease (AD) and the influence of a high-fat diet (HFD) on disease progression. RNA sequencing was performed on brain tissues from three groups of mice: control, AD model, and HFD-exacerbated AD model. These data provide insights into how metabolic stressors such as high-fat diet may aggravate neurodegeneration in AD.

overall_design: RNA-seq was performed on mouse brain tissues from control, AD model, and AD+HFD model groups to evaluate transcriptomic changes caused by AD and metabolic stress.

first: Duobin

last: Zhang

first: Lingyun

last: Shao

first: Min

last: He

first: Zhongwu

last: Sun


title: Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

summary: The histone methyltransferase Polycomb repressive complex 2 (PRC2) is required for specification of the neural crest, and mis-regulation of neural crest development can cause severe congenital malformations. PRC2 is necessary for neural crest induction, but the embryonic, cellular, and molecular consequences of PRC2 activity after neural crest induction are incompletely understood. Here we show that Eed, a core subunit of PRC2, is required for craniofacial osteoblast differentiation and mesenchymal proliferation after induction of the neural crest. Integrating mouse genetics with single-cell RNA sequencing and epigenomic profiling, our results reveal that conditional knockout of Eed after neural crest cell induction causes severe craniofacial hypoplasia, impaired craniofacial osteogenesis, and attenuated craniofacial mesenchymal cell proliferation that is first evident in post-migratory neural crest cell populations. We show that Eed drives mesenchymal differentiation and proliferation in vivo and in primary craniofacial cell cultures by regulating diverse transcription factor programs that are required for specification of post-migratory neural crest cells. These data enhance understanding of epigenetic mechanisms that underlie craniofacial development, and shed light on the embryonic, cellular, and molecular drivers of rare congenital syndromes in humans.

overall_design: E12.5 and E16.5 craniofacial tissue from n=3 Sox10-Cre; Eed Fl/WT (WT) and  Sox10-Cre; EedFl/Fl (KO) embryos were processed for H3K27me3 Cut & Tag and sequenced using illumina paired end sequencing.

first: Casey-Clyde

last: Tim

first: Padmanabhan

last: Arun

first: Pelonero

last: Angelo

first: Raleigh

last: David

first: Liu

middle: S

last: John

first: Camara Serrano

last: Juan

first: Teng

last: Camilla

first: Jang

last: Yoon-Gu

first: Vasudevan

last: Harish

first: Bush

last: Jeffrey


title: Neutrophil transcriptomes in blunt traumatic injury

city: Los Angeles

first: Jinyao

last: Tian

address: 3185 Wilshire Blvd

department: Keck Medicine of USC

institute: University of Southern California

summary: Trauma induces a “genomic storm” of gene expression in circulating leukocytes. We hypothesized that the neutrophil contribution to this response after blunt trauma varies with the magnitude of physiologic insult and with exposure to additional and subsequent inflammatory stimuli.

overall_design:
Bulk RNAseq on isolated CD66b+ neutrophils, sequenced with Novaseq 6000; Trauma: On admission to the trauma bay (0h), 8 hrs, 24 hrs, and 72 hrs after admission. Dates of Collection:  10/2023-6/2024

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Submitter states that missing raw files are due to file loss.
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first: Anaar

middle: E

last: Siletz

first: Kelly

last: Street

first: Jeremy

last: Yu


title: Transcriptional landscape of MYCN-driven liver tumors

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death, often diagnosed at advanced stages and characterized by high recurrence rates. While chronic liver inflammation and metabolic dysfunction are recognized contributors to tumorigenesis, the molecular mechanisms linking early microenvironmental stress to malignant transformation remain poorly understood. MYCN, a proto-oncogenic transcription factor, has emerged as a potential biomarker of cancer stemness, yet its functional role in hepatocarcinogenesis is unclear. Here, we elucidate the oncogenic role of MYCN and its dynamic regulation during metabolic liver tumorigenesis.Using a transposon system in mice and the human hepatocyte cell line Hc, we demonstrate that MYCN overexpression functionally promotes liver tumorigenesis and hepatocyte transformation. Transcriptomic profiling of MYCN-driven tumors revealed molecular features resembling human HCC subtypes enriched in stress-adaptive gene programs, highlighting MYCN's role in shaping tumor-promoting transcriptional landscapes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profiling was performed on mouse liver tissues collected at 3, 14, and 50 days following hydrodynamic tail vein injection of a transposase plasmid alone (Control, Ctl group) or in combination with MYCN (MYCN group), myristoylated AKT (AKT group), or both MYCN and myristoylated AKT (MYCN+AKT group) and on normal hepatocyte cell line Hc overexpressed with MYCN.


title: Mitochondrial One-Carbon Metabolism is Required for TGF-β-Induced Glycine Synthesis and Collagen Protein Production

city: Chicago

first: Kun Woo

last: Shin

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

summary: A hallmark of Idiopathic Pulmonary Fibrosis is the TGF-β-dependent activation of lung fibroblasts, leading to excessive deposition of collagen proteins and progressive scarring. We have previously shown that synthesis of collagen by lung fibroblasts requires de novo synthesis of glycine, the most abundant amino acid in collagen protein. TGF-β upregulates the expression of the enzymes of the de novo serine/glycine synthesis pathway in lung fibroblasts through mTORC1 and ATF4-dependent transcriptional programs. SHMT2, the final enzyme of the de novo serine/glycine synthesis pathway, transfers a one-carbon unit from serine to tetrahydrofolate (THF), producing glycine and 5,10-methylene-THF (meTHF). meTHF is converted back to THF in the mitochondrial one-carbon (1C) pathway through the sequential actions of MTHFD2 (which converts meTHF to 10-formyl-THF), and either MTHFD1L, which produces formate, or ALDH1L2, which produces CO2. It is unknown how the mitochondrial 1C pathway contributes to glycine biosynthesis or collagen protein production in fibroblasts, or fibrosis in vivo. Here, we demonstrate that TGF-β induces the expression of MTHFD2, MTHFD1L, and ALDH1L2 in human lung fibroblasts. MTHFD2 expression was required for TGF-β-induced cellular glycine accumulation and collagen protein production.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from Normal Human Lung Fibroblasts (HLFs) under TGF-beta treatment. MTHFD2 was inhibited by siRNA knock down.

first: Gokhan

last: Mutlu

first: Robert

last: Hamanaka

first: Rengul

last: Cetin-Atalay

last: Meliton


title: High-throughput sequencing of LPS-stimulated mouse macrophage Raw264.7 pretreated by Lespedeza bicolor root components

city: Wen zhou

first: haoyi

last: han

address: Ou hai Cha shan

institute: Wenzhou Medical University

summary: In this study, mouse macrophage Raw264.7 was pretreated with Lespedeza bicolor root components and then stimulated with LPS and then high-throughput sequencing technology was used to explore the expression of inflammation-related genes of Raw264.7 in mouse macrophages treated with Lespedeza bicolor root components, and to find interesting targets,NF-kappaB and p38 signaling pathway.

overall_design: RAW 264.7 cells were seeded in 100 mm dishes at a density of 1 × 107 cells per well.Three experimental groups, Control, LPS, and LB+ LPS, were set up, and 0.5 μg/mL LPS was added to stimulate for 6 h after LB was activated for 30 min. After treatment, the cells were collected, and total RNA from each group was extracted using TRIzol (TaKaRa, Japan). Paired-end sequencing was ultimately carried out on an Illumina HiSeq 4000 platform at LC-BIO Technologies (Hangzhou, China).

first: Haoyi

last: Han

first: Xiaohui

last: Zheng


title: Genome-wide CRISPR-Cas9 knockout screening identifies NUDCD2 depletion as sensitizer for bortezomib, carfilzomib and ixazomib in multiple myeloma.

city: Leuven

first: Sophie

last: Vlayen

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven

summary: Background/Objectives: The treatment of multiple myeloma (MM) remains a challenge as almost all patients will eventually relapse. Proteasome inhibitors are a cornerstone in the management of MM. Unfortunately, validated biomarkers predict-ing drug response are largely missing. Therefore, we aimed to identify genes associated with drug resistance or sensitization to proteasome inhibitors. Methods: We per-formed genome-wide CRISPR-Cas9 knockout (KO) screens in human KMS-28-BM my-eloma cells to identify genetic determinants associated with resistance or sensitization to proteasome inhibitors. Results: We show that KO of KLF13 and PSMC4 induces drug resistance, while NUDCD2, OSER1 and HERC1 KO cause drug sensitization. Sub-sequently, we focused on top sensitization hit, NUDCD2, which acts as a co-chaperone of Hsp90 to regulate the LIS1/dynein complex. RNA sequencing showed downregula-tion of genes involved in the ERAD pathway and in ER-associated ubiqui-tin-dependent protein catabolic processes in both untreated and carfilzomib-treated NUDCD2 KO cells, suggesting that NUDCD2 depletion alters protein degradation. Furthermore, bortezomib-treated NUDCD2 KO cells showed a decreased expression of genes that have a function in oxidative phosphorylation and the mitochondrial mem-brane, such as Carnitine Palmitoyltransferase 1A (CPT1A). CPT1A catalyzes the up-take of long chain fatty acids into mitochondria. Mitochondrial lipid metabolism has recently been reported as a possible therapeutic target for MM drug sensitivity. Con-clusions: These results contribute to the search of therapeutic targets that can sensitize MM patients to proteasome inhibitors.

overall_design: RNA-sequencing of unreated, bortezomib-treated and carfilzomib-treated NUDCD2 KO myeloma cells.

first: Tim

last: Dierckx

first: Marino

last: Caruso

first: Swell

last: Sieben

first: Kim

last: De Keersmaecker

first: Dirk

last: Daelemans

first: Michel

last: Delforge


title: Unveiling the Molecular Legacy of Transient Insulin Resistance: Implications for Hepatic Metabolic Adaptability

first: Alexandre

last: Berthier

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

overall_design: Refer to individual Series

first: Celine

last: Gheeraert

first: Philippe

last: Lefebvre


title: Genome-wide CRISPR-Cas9 knockout screening identifies NUDCD2 depletion as sensitizer for bortezomib, carfilzomib and ixazomib in multiple myeloma [CRISPR screen carfilzomib]

overall_design: CRISPR-Cas9 KO screen with carfilzomib on KMS-28-BM myeloma cells.


title: Genome-wide CRISPR-Cas9 knockout screening identifies NUDCD2 depletion as sensitizer for bortezomib, carfilzomib and ixazomib in multiple myeloma [CRISPR screen bortezomib]

overall_design: CRISPR-Cas9 KO screen with bortezomib on KMS-28-BM myeloma cells.


title: Sex modulates microglia in the aging brain

city: Freiburg im Breisgau

first: Omar

last: Mossad

address: Breisacher str 64

department: Institute of Neuropathology

country: Germany

institute: University Hospital Freiburg

summary: We found that sex influenced critical characteristics linked with aging.

overall_design: we compared microglia from young adult, middle-aged and aged mice from both sexes

first: Bérénice

last: Batut

first: Thomas

last: Blank


title: Transgenerational Epigenetic and Phenotypic Inheritance Across Five Generations in Sheep

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

type: Methylation profiling by high throughput sequencing

summary: Despite two extensive reprogramming events during early embryogenesis and game-togenesis, epigenetic information can be passed to the next generations, which consti-tutes transgenerational epigenetic inheritance of phenotypes. Considering its utmost importance, there have been few studies focused on the transgenerational effects of di-etary interventions, such as methionine supplementation, in livestock. Using whole-genome bisulfite sequencing, we implemented a single-base resolution differen-tial methylation analysis for the F3 and F4 descendants of control vs. methio-nine-supplemented F0 twin-pair rams. Based on the results of our previous study on F0, F1, and F2 generations, we compared current results of 2,981 and 1,726 differen-tially methylated cytosines (DMCs) as well as 798 and 553 unique differentially meth-ylated genes (DMGs) in F3 and F4, respectively. We identified 41 DMGs that exhibited transgenerational epigenetic inheritance (TEI-DMGs) across four generations and 11 TEI-DMGs across five generations. Finally, we estimated the effect size of F0 diet group on F3 and F4 growth and fertility-related phenotypes, providing evidence for transgenerational effects of diet group accompanying inherited differentially methyl-ated genes. Here, for the first time using gene-level and phenotypic data, we demon-strate that a moderate dietary intervention can exert long-lasting transgenerational effects on offspring phenotypes extending beyond the F2 generation in sheep.

overall_design: Experimental population of F3 (five control vs. five treatment) and F4 (five control vs. five treatment) sheep were descended from F0 (five control vs. 5 treatment) rams that were supplemented with methionine + control diet vs. control diet. Whole genome bisulfite sequencing (WGBS) was performed on sperm samples to identify five generations of differentially methylated genes. Differential methylation cytosines in each generation was identified by a beta binomial regression method. Genomic positions and genes were annotated with Oar_rambouillet v1.0 genome assembly.

first: Mehmet

last: Kizilaslan

first: Camila

middle: U

last: Braz

first: Jessica

last: Townsend

first: Todd

last: Taylor

last: Crenshaw


title: Ptbp1 is not required for retinal neurogenesis and cell fate specification [scRNA-seq]

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

summary: The RNA-binding protein Ptbp1 has been proposed as a master regulator of neuronal fate, repressing neurogenesis through its effects on alternative splicing and miRNA maturation. While prior studies using RNA interference suggested that Ptbp1 loss promotes neurogenesis, recent genetic studies have failed to replicate glia-to-neuron conversion following Ptbp1 loss of function. To evaluate the role of Ptbp1 in developmental neurogenesis in vivo, we conditionally disrupted Ptbp1 in retinal progenitors. Ptbp1 was robustly expressed in both retinal progenitors and Müller glia but absent from postmitotic neurons, and efficient loss of function in mutant animals was confirmed using immunostaining for Ptbp1. Furthermore, bulk RNA-Seq at E16 revealed accelerated expression of late-stage progenitor and photoreceptor-specific genes and altered splicing patterns in Ptbp1 mutants, including increased inclusion of neuron- and retina-specific exons. However, we observed no defects in retinal lamination, progenitor proliferation, or cell fate specification in mature retina. ScRNA-Seq of mature mutant retinas revealed only modest transcriptional changes limited to Müller glia, recapitulating alterations seen following selective deletion of Ptbp1 in mature glia. Our findings demonstrate that Ptbp1 is fully dispensable for retinal development and suggest that its proposed role as a central repressor of neurogenesis should be reevaluated

overall_design: Single cell RNA-seq was performed on Chx10-Cre control and Chx10-Cre;Ptbp1lox/lox KO retinas at P30 using 10x Genomics Chromium Single Cell 3’ Reagents Kit v3.1.

first: Haley

last: Appel

first: Rogger

middle: P

last: Carmen-Orozco

first: Thanh

last: Hoang

first: Seth

last: Blackshaw


title: Ptbp1 is not required for retinal neurogenesis and cell fate specification [RNA-seq]

overall_design: Bulk RNA-seq was performed on Chx10Cre control (WT) , Chx10Cre;Ptbp1lox/WT (HET), and Chx10Cre;Ptbp1lox/lox (KO) retinas at E16 and sequenced on the Illumina NovaSeq X platform


title: Depletion of BRD9-mediated R-loop accumulation inhibits leukemia cell growth via transcription-replication conflict

city: Chuncheon

first: JaeJin

last: Kim

state: Kangwon

address: 1 Hallymdaehak-gil

institute: Hallym University

summary: Bromodomain-containing protein 9 (BRD9) has emerged as a promising therapeutic target for blood cancers, including acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and multiple myeloma (MM). PROTAC-based BRD9 degraders effectively hamper the growth and survival of leukemia cells; however, the underlying mechanism of these BRD9 degraders remains unclear. In this study, we demonstrated that depletion of BRD9 triggers DNA damage via R-loop accumulation, leading to conflicts between transcription and replication processes. Replication stress inhibits the proliferation of leukemia cells and promotes their differentiation. Mechanistically, BRD9 plays a pivotal role in recruiting BRD2 and BRD4 to chromatin through direct interactions, which is critical for preventing R-loop formation during transcription. Depletion of BRD9 in leukemia cells reduces the occupancy of BRD2 and BRD4 at R-loop-prone sites, thus promoting R-loop accumulation, transcription-replication collision, excessive DNA damage, and ultimately, the demise of cancer cells. These findings provide valuable insights into the mechanisms by which BRD9 degraders function as effective therapies for leukemia mediated by the pathological accumulation of R-loops.

overall_design: R-loop mapping using MapR-seq in K562 cells after 48h treatment with DMSO or dBRD9

first: Seo Yun

last: Lee

first: Jae Jin


title: Cholinergic Signaling Modulates Intestinal Pathophysiology in a Drosophila Model of Cystic Fibrosis

city: Boston

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Cystic Fibrosis (CF) is a genetic disease caused by mutations in the CFTR gene, which affects cells in organs like the lungs, pancreas, and gut. Treatments aim to fix the CFTR protein, but many gut issues remain untreated. In this study, we use fruit flies (Drosophila) as a model to study the effects of losing CFTR specifically in the gut. We show that knocking down CFTR in gut cells leads to problems seen in CF, such as poor gut movement, trouble absorbing nutrients, and low energy levels. Using RNA sequencing, we find that CF guts have higher levels of the gene acetylcholine esterase (Ace), which lowers cholinergic (nerve signal) activity. Experiments confirm that CF guts are less sensitive to cholinergic signals, but reducing Ace brings back normal gut function. We also find a transcription factor called Forkhead (Fkh), similar to human FOXA1/2, that increases Ace in CF. Our study shows that the fruit fly gut is a useful model for studying CF in the gut, and suggests that boosting cholinergic signaling could help treat gut problems in CF.

overall_design: Fruit flies (Drosophila) was used to perform enterocyte-specific knockdown of CFTR gene to model CF gut pathology. Gut movement, nutrient absorption, and energy levels were assessed. Single-nuclei RNA sequencing (snRNA-seq) was performed to identify gene expression changes, revealing increased expression of acetylcholine esterase (Ace). Functional assays tested cholinergic signaling and showed that Ace knockdown could restore gut function. Finally, the role of the transcription factor Forkhead (Fkh) in regulating Ace was investigated.

first: Liz

last: Lane

first: Mujeeb

last: Qadiri

first: Norbert

last: Perrimon


title: Nociceptor neurons direct fibroblasts via a PACAP-VIPR2 axis to drive IL-11 production and colon healing

city: Jinan

first: Shi-chen

last: Fu

state: Shandong

address: No. 107 Wenhua West Road

department: Department of Gastroenterology

institute: Qilu Hospital of Shandong University

summary: Mucosal healing remains a pivotal therapeutic endpoint in ulcerative colitis (UC) management, yet cellular mechanisms driving tissue repair remain elusive. Here we demonstrate that Pirt+ nociceptor endings dynamically grow into the granulation tissue during colonic mucosal restitution, releasing pituitary adenylate cyclase-activating polypeptide (PACAP) to orchestrate reparative processes. Absence of PACAP signaling in Pirt+ sensory neurons resulted in delayed healing, while exogenous PACAP administration accelerated mucosal restitution in experimental colitis models. Mechanistically, PACAP exerts its pro-reparative effects through vasoactive intestinal peptide receptor 2 (VIPR2), with pituitary adenylate cyclase-activating polypeptide receptor type 1 and vasoactive intestinal peptide receptor 1 playing negligible roles in this context. Mouse and human fibroblast expressed VIPR2. VIPR2+ fibroblasts increased during mucosal healing and accumulated in granulation tissue. Conditional deletion of VIPR2 in fibroblasts abolished PACAP-mediated tissue repair. The effects of PACAP on mucosal healing are mediated via interleukin-11 released by VIPR2+ fibroblast. Our findings demonstrate a neuron-fibroblast axis that orchestrates mucosal healing, highlighting its therapeutic potential as a novel target for UC management.

overall_design: Sorted fibroblast from wild-type or Vipr2-KO mice were stimulated with PACAP(100nM) or vehicle (PBS, 0 nM PACAP) for 12 hour for RNA-seq.

first: Shichen

first: Junyan

last: Qu


title: GW8510 alleviated muscle atrophy and skeletal muscle dysfunction in mice through AMPK/PGC1α signaling

city: Beijing

first: Yutong

last: Chen

address: 38 Xueyuan Road

institute: Peking University Health Science Center

summary: Preventing and restoring muscle loss and function is essential for elderly individuals. In this study, we expect to investigate the protective effect of GW8510 on muscle atrophy. We established mouse models of muscle atrophy induced by denervation, dexamethasone, and glycerol. We assessed the muscle weight-to-body weight ratio, the cross-sectional area of various muscles, grip strength, fatigue tasks, and serum analysis. In vitro, we created dexamethasone-induced C2C12 myotube atrophy and evaluated mitochondrial function. Additionally, we utilized real-time polymerase chain reaction, immunoblotting, and siRNA transfection to explore the potential molecular mechanisms following treatment with GW8510. Results showed that Treatment with GW8510 resulted in a significant increase in the gastrocnemius and soleus muscle ratios in denervation mice (7% and 3%, respectively, P < 0.001), alongside an increase in cross-sectional area. Moreover, GW8510 notably improved grip strength and superoxide dismutase (SOD) activity (P < 0.0001), with similar protective effects observed in dexamethasone and glycerol-induced muscle atrophy and injury models. Furthermore, GW8510 reduced reactive oxygen species production (P < 0.01), increased mitochondrial DNA copy number (P < 0.01), maintained mitochondrial dynamics, and enhanced antioxidant activity in C2C12 myotubes. Mechanistically, GW8510 significantly inhibited the expression of atrophy-related markers Fbxo32 and Trim63 (P < 0.01) while activating AMPK (P < 0.01). The knockdown of small interfering RNA targeting Pgc1α negated the effects of GW8510. Overall, GW8510 mitigated muscle atrophy through the activation of the AMPK/ PGC1α pathway. Our findings suggest that GW8510 could serve as a novel therapeutic agent for the prevention of muscle atrophy.

overall_design: Gene expression profiling analysis of RNA-seq data from C2C12 myotubes stimulated with dexamethasone (10 μM) or vehicle, followed by treatment with GW8510 (2 μM) or vehicle for 24 hours  in triplicate.

first: Zurui

last: Liu

first: Chen

first: Daqian

last: Yang

first: Mengmeng

last: Xiao

first: Zhengqian

last: Li

first: Zhengwei

last: Xie


title: Liver FGF21 mediates sex-specific adaptation to juvenile protein malnutrition

city: Lyon

first: Filipe

last: De Vadder

address: 32-34 Avenue Tony Garnier

institute: Institut de Génomique Fonctionnelle, ENS de Lyon, CNRS UMR5242, Université Claude Bernard Lyon 1

summary: Dietary protein sufficiency during childhood is essential for healthy growth and tissue development. Chronic protein deficiency leads to stunting, height-for-age more than two standard deviations below the median, and affects 149 million children under five (https://www.who.int/publications/i/item/9789240073791). Linear growth is governed by the somatotropic axis, wherein pituitary growth hormone (GH) stimulates hepatic insulin-like growth factor 1 (IGF-1) to promote bone elongation1. Although boys are consistently more stunted than girls across populations (ranging from 18% to 45%)2,3, mechanisms underlying this apparent resilience remain unclear. Rodent studies suggest that the protein-to-carbohydrate ratio modulates life-history traits such as metabolism, lifespan, and reproduction, with evidence of sex-dependent sensitivity4,5. Whether such dimorphism reflects coordinated developmental adaptations in response to protein scarcity, particularly in females, has not been fully explored. Here, we show that juvenile dietary protein restriction causes sexually dimorphic adaptations with pronounced stunting in males and delayed reproductive maturation in females. Using liver-specific deletion, we identify fibroblast growth factor 21 (FGF21) as a sex-specific hepatic regulator of female somatic growth and reproductive development, revealing a dimorphic endocrine adaptation to early-life protein scarcity. Our findings position FGF21 as a critical metabolic checkpoint coordinating growth and reproductive timing in response to nutritional stress.

overall_design: To investigate the effect of low-protein diet on protein undernourished juveniles, we analyzed the liver of those mice at 8 weeks (after a 5 weeks dietary challenge with either control diet, 20% in kcal or low-protein diet, 5% in kcal). Bulk RNA sequencing was performed after RNA isolation from the tissue. For each sex (males and females) : we used control diet fed animals as the reference (5 mice), and low-protein diet fed ones as the experimental condition (5 mice). Which makes a total of 20 mice.

first: Amélie

last: Joly

first: Lucas

last: Rebiffé

first: Anne

last: Lambert

first: Estele

last: Caillon

first: Sandrine

last: Hughes

first: Benjamin

last: Gillet

first: Isabelle

last: Rahioui

first: Pedro

last: Da Silva

first: Justine

last: Bruse

last: Fougerat

first: François

last: Leulier


title: MYC regulates a DNA repair gene expression program in small cell carcinoma of the ovary, hypercalcemic type

city: Nashville

first: Jing

last: Wang

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: SCCOHT is an aggressive and often fatal cancer that belongs to the ~20% of all cancers defined by mutations to subunits of the SWI/SNF chromatin remodeling complex. In SCCOHT, mutations to the SMARCA4 gene, which encodes the SWI/SNF ATPase BRG1, is sufficient to impair SWI/SNF function. This single genetic lesion leads to a cascade of events that promote tumorigenesis, some of which may involve the intersection of SWI/SNF with oncogenic pathways such as those regulated by the MYC oncogene. In SCCOHT tumors and other cancers like it, MYC target genes are recurrently activated, pointing to a relationship between SWI/SNF, BRG1, and MYC that has yet to be fully explored.  In this study we investigate the contribution of MYC to SCCOHT biology through chromatin binding and transcriptome analysis performed in genetically engineered cell lines and patient tumor data. We find that MYC binds to thousands of active promoters in the BIN-67 cell line, and that depletion of MYC results in a broad range of gene expression changes with a notable effect on expression of genes related to DNA repair. We identify a MYC-regulated DNA repair gene expression program in BIN-67 cells that is oppositely regulated by BRG1 in an ATPase-independent manner. Finally, we uncover a DNA repair gene signature that is glaringly upregulated in SCCOHT tumors and in tumors defined by loss of the SWI/SNF subunit, SNF5. Collectively, these data implicate MYC as a robust regulator of DNA repair gene expression in SCCOHT and lay a foundation for future studies focused on interrogating the relationship between BRG1 and MYC.

overall_design: We used the SCCOHT cell line, BIN-67, to interrogate the contribution of MYC to the SCCOHT transcriptome. We engineered BIN-67 cells to express a version of MYC that can be depleted in cells using a dTAG chemical degrader called dTAGV-1. We performed chromatin binding assays (CUT&RUN) in untreated engineered cells. We performed RNA-seq on engineered cells treated with dTAGV-1, to deplete MYC, alongside  a vehicle control or negative chemical control (dTAGV-1-NEG). Cells were collected 24 hr post-treatment.  We then validated our transcriptome findings using patient tumor data.

first: April

middle: M

last: Weissmiller

first: William

last: Tansey

first: Qi

last: Liu


title: Impact of Aerobic Training on Transcriptomic Changes in Skeletal Muscle of Rats with Cardiac Cachexia

city: College Station

first: Mariana

middle: Janini

last: Gomes

state: TX

address: 2929 Research Pkwy

department: Health and Kinesiology

institute: Texas A&M University

summary: Cardiac cachexia (CC) is an advanced stage of heart failure (HF) characterized by structural and functional abnormalities in skeletal muscle, leading to muscle loss. Aerobic training provides benefits; however, the underlying molecular mechanisms remain poorly understood. This study aimed to investigate the therapeutic effects of aerobic training on transcriptomic alterations associated with disease progression in cachectic skeletal muscle. HF was induced in male Wistar rats by a single monocrotaline injection (60mg/Kg). Aerobic training consisted of treadmill running for 30min at ~55% of maximal capacity, 5x/week for 4 weeks. Assessments included body mass, right ventricle mass, skeletal muscle fiber size and exercise tolerance. RNA sequencing analysis was per-formed on the medial gastrocnemius muscle. Sedentary cachectic rats exhibited 114 differentially expressed genes (DEGs) while exercised cachectic rats had only 18 DEGs compared to their respective controls. GO enrichment, pathway enrichment, and weighted gene co-expression network analysis (WGCNA) identified key DEGs as po-tential hub genes involved in disrupted lipid metabolism and muscle remodeling in sedentary CC rats, which were not observed in the exercised CC rats. These findings suggest that aerobic training mitigates transcriptional alterations related to lipid me-tabolism and muscle remodeling in rats with CC, highlighting its therapeutic potential.

overall_design: RNA-seq profiling of medial gastrocnemius muscle from Sedentary cachectic rats, exercised cachectic rats compared to their respective controls.

first: Inoue

last: Daniela

first: Pigg

last: Quinten

first: Harris

last: Dillon

first: Zhang

last: Dongmei

first: Boland

middle: J

last: Devon

first: Gomes

last: Mariana


title: Spatialtemporal immune landscape and long-term immune memory in POLE-mutant endometrial cancer at single cell level

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

summary: Polymerase epsilon mutant (POLE-mut) endometrial cancers (EC) are characterized by a near 100% disease-specific survival rate, even when treated by surgery alone. This spectacular survival, combined with the ultramutated genome and high level of neoantigens in these tumors, indicates a substantial degree of immune control in preventing disease spread and recurrence. Although these features are intriguing, the immune infiltration of POLE-mut EC has predominantly been confined to immunohistochemistry studies.  Here, we used state of the art single-cell RNA and TCR sequencing to characterize the immune landscape of POLE-mutant ECs. Moreover, we uniquely analyzed patient blood samples taken two to eight years after curative treatment to assess formation of long-term immune memory in circulation. We identified specialized tumor-infiltrating myeloid subsets at different stages of maturation, an array of lymphocytes ranging from immature to cytotoxic and adaptive natural killer (NK) as well as tumor-reactive exhausted and effector T cells, contributing to a highly inflammatory anti-tumor response. Remarkably, our analysis of blood samples taken years after curative treatment uncovered the presence of tumor-reactive T cell clones that matched the primary tumor. This indicates the formation of systemic long-term memory immune responses in POLE-mut EC survivors. Our study highlights the distinctive immunogenicity of POLE-mut EC and identifies key features associated with persistent anti-tumor immunity that may contribute to prolonged, relapse-free survival.

overall_design: Intratumoral immune cells of 4 patients with a POLE mutant endometrial cancer were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or abscence of CD45, CD3, CD8, CD4 and CD19 and analyzed using scRNAseq and scTCRseq.

first: Koen

last: Brummel

first: Marta

last: Requesens

first: Nienke

last: van Rooij

first: Hagma

last: Workel

first: Florine

last: Eggink

first: Annechien

last: Plat

first: René

last: Wardenaar

first: Diana

last: Spierings

first: Floris

last: Foijer

first: David

last: Church

first: Joost

last: Bart

first: Hans

middle: W

last: Nijman


title: Dual targeting of CDK6 and LSD1 is synergistic and overcomes differentiation blockade in AML [ATACseq_MV4_11]

city: Marseille

first: Sophie

last: Lopez

address: 27 Bd Lei Roure

institute: INSERM

summary: The heterogeneity of leukemic cells is the main cause of resistance to therapy in acute myeloid leukemia (AML). Consequently, innovative therapeutic approaches are critical to target a wide spectrum of leukemic clones, regardless of their genetic and non-genetic complexity. In this report, we leverage the vulnerability of AML cells to CDK6 to identify a combination therapy capable of targeting common biological processes shared by all leukemic cells, while sparing non-transformed cells. We demonstrate that the combined inhibition of CDK6 and LSD1 restores myeloid differentiation and depletes the leukemic progenitor compartment in AML samples. Mechanistically, this combination induces major changes in chromatin accessibility, leading to the transcription of differentiation genes and diminished LSC signatures. Remarkably, the combination is synergistic, induces durable changes in the cells, and is effective in PDX mouse models. While many AML samples exhibit only modest responses to LSD1 inhibition, co-targeting CDK6 restores the expected transcription response associated with LSD1 inhibition. Given the availability of clinical-grade CDK6 and LSD1 inhibitors, this combination holds significant potential for implementation in clinical settings through drug repositioning.

overall_design: ATACseq profiling of MV4-11 cells treated for 4 days with the combination (Palbociclib + TCP), the single molecule (Palbociclib or TCP) or vehicle control (DMSO)

first: Lise

last: Brault

first: Edwige

last: Voisset

first: Mathieu

last: Desaunay

first: Antonia

last: Boudet

first: Paraskevi

last: Kousteridou

first: Sébastien

last: Letard

first: Nadine

last: Carbuccia

first: Armelle

last: Goubard

first: Rémy

last: Castellano

first: Yves

last: Collette

first: Julien

last: Vernerey

first: Isabelle

last: Vigon

first: Jean-Max

last: Pasquet

first: Patrice

last: Dubreuil

first: Paulo

last: De Sepulveda


title: Dual targeting of CDK6 and LSD1 is synergistic and overcomes differentiation blockade in AML [RNAseq_patients]

overall_design: RNAseq profiling of primary AML samples treated for 4 days with the combination (Palbociclib + TCP), the single molecule (Palbociclib or TCP) or vehicle control (DMSO)


title: SRRM4 knockout helps the human mesenchymal stem cell line to intrude into decellularized bone

city: Tokyo

first: Iichiroh

last: Onishi

address: 1-5-45 Yushima, Bunkyo-ku

department: Pathology

institute: Institute of Science Tokyo

summary: Analysis of the human bone marrow microenvironment requires an in vivo model that reflects this microenvironment. We introduced a human bone marrow mesenchymal stem cell (MSC) line into decellularized bone. Using the CRISPR Knock Out library, we identified serine/arginine repetitive matrix 4 knockout in an MSC cell line, as a candidate factor for bone intruding, which may be applied to the analysis of hematological diseases such as myelodysplastic neoplasm.

overall_design: RNA-seq for Control UE7T-9 cell line(human mesenchymal stem cell line) and SRRM4 KO UE7T-9cell line. SRRM4 KO was induced using CRISPR.


title: Effect of Crotonylation in the development of glioma

city: 上海

first: 晋

last: 李

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

summary: To investigate the role of Crotonylation in the regulation of tumor progression and development, we treated T98G cell with  Crotonate.

overall_design: Comparative gene expression profiling analysis of CHIP-seq data for T98G cells treated with 10uM Crotonate for 48h.


title: Next Generation Sequencing Facilitates Quantitative Analysis of the murine macrophage cell line RAW264.7  Transcriptomes

city: Tianjin

first: Yi

last: Li

address: Nankai

institute: Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived  RAW264.7 cell  transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design:
Cell mRNA profiles of the murine macrophage cell line RAW264.7 were generated by deep sequencing, in triplicate, using Illumina GAIIx.
M: the model control group, which is treated with PBS.
MO: treated with nanoparticles containing nanoenzymes under the model condition (P-Mn@mHSA).
MOT: treated with nanoparticles containing nanoenzymes and a TRAF6 inhibitor under the model condition (P-Mn/TI@mHSA).

first: Xueping

first: Ting

last: Chen

first: Jian


title: CNS infiltration by Tet2-mutant peripheral myeloid cells protects from Alzheimer’s Disease

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Microglia play a key role in Alzheimer’s disease (AD) pathogenesis by clearing damaged cells and misfolded proteins such as b-amyloid. In a mouse transplant model of AD, we identified a population of bone marrow-derived immune cells that had infiltrated the brain and taken on microglia characteristics. The percentage of these infiltrating microglia-like cells within the brain was increased in AD mice that were transplanted with Tet2-mutant bone marrow when compared to mice transplanted with either wildtype or Dnmt3a-mutant bone marrow following LPS treatment. We explored the effect of mutation of TET2 and DNMT3A in human induced microglial-like cells (iMGLs) and found that TET2-mutant iMGLs were more phagocytic and hyperinflammatory than DNMT3A-mutant or wildtype iMGLs. Bulk RNA sequencing of iMGLs confirmed the upregulation of phagocytic pathways in TET2-mutant iMGLs compared to DNMT3A-mutant or wildtype iMGLs.

overall_design: Bulk RNA sequencing of WT, TET2-mutant, and DNMT3A-mutant human induced microglial-like cells (iMGLs) that were either untreated or treated with 100ng/mL LPS for 24 hours. iMGLs were differentiated from isogenic human induced pluripotent stem cell (iPSC) lines that were CRISPR/Cas9 edited to harbor either DNMT3AR882H/WT or TET2DelE3-E11/WT mutations.

first: Katie

middle: A

last: Matatall

first: Minh

last: Nguyen

first: Chih-Wei

last: Fan

first: Saul

last: Carcamo

first: Eirini

last: Pappapetrou

first: Samuele

middle: G

last: Marro

first: Katherine

middle: Y

last: King


title: The reprogramming impact of SMAC-mimetic on glioblastoma stem cells and the immune tumor microenvironment evolution

city: Tampa

first: Qiong

last: Wu

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: In order to comprehensively assess the impact of Xevinapant on the cellular and molecular heterogeneity of the TME, we employed 10X Genomics single-cell RNA sequencing (scRNA-seq) to investigate the modulation impact of Xevinapant on GBM TME. In this study, we sought to further investigate and characterize the anti-tumor and immune TME-modulating impacts of Xevinapant in human and murine GBM models at the single-cell level.  We also evaluated associated mechanisms of therapeutic resistance and therapeutic synergy to Xevinapant in GBM. Our study, which represents the first comprehensive characterization of the impact of Xevinapant on the GBM TME repertoire demonstrates robust anti-tumor activity and favorable immune modulation of the TME, all highly supportive for further clinical investigation of Xevinapant in GBM.

overall_design: We developed Trp53+/- and Nf1+/- mGSC orthotopic model in C57BL/6J mice and treated them with either vehicle control or Xevinapant daily. Cells for sequencing were isolated from these orthotopic tumors (4 from each group) right after treatment.

first: Arnold

middle: B

last: Etame

first: Jianan

first: Anders

last: Berglund

first: Dongliang

last: Du

first: Robert

last: Macaulay


title: HMG Box-Containing Protein 1 (HBP1) Protects Against Pancreatic Injury in Acute Pancreatitis but Promotes Neoplastic Progression

city: PORTLAND

first: JUNGSUN

last: KIM

state: OR

address: KCRB 5001.51, 2720 SW Moody Ave

institute: Oregon Health & Science University

summary:
Background & Aims Pancreatitis is an inflammatory disease of the exocrine pancreas and a known risk factor for pancreatic ductal adenocarcinoma (PDAC). Previously, we identified HMG- box transcription factor 1 (HBP1) as a potential master transcription factor (TF) in the early progression of PDAC, with its expression associated with poor patient survival, underscoring its significance in pancreatic disease. However, the functional role of HBP1 in the onset and progression of acute pancreatitis (AP) remains unknown.
Methods We examined HBP1 expression in human pancreatitis samples and a cerulein-induced AP mouse model. Pancreatic-specific conditional HBP1 knockout mice, with or without an oncogenic Kras mutation, were generated and compared to their littermate controls. Spatial transcriptomics and multiplexed protein assays, histological analysis, and immunostaining were utilized to characterize pathological changes. Findings from mouse models were validated using inducible HBP1-overexpressing human pancreatic ductal epithelial cells.
Results HBP1 was upregulated in pancreatic exocrine cells in human chronic pancreatitis and mouse acute pancreatitis, with its expression in human chronic pancreatitis correlating with cancer presence. Pancreatic HBP1 ablation disrupted acinar homeostasis by impairing autophagic flux and exacerbating inflammation following injury. In the presence of oncogenic KRAS, HBP1 ablation delayed the formation of pancreatic intraepithelial neoplasia (PanIN), the precursor to PDAC, and slowed its progression to higher-grade lesions.
Conclusions HBP1 upregulation in pancreatitis mitigates pancreatic inflammatory injury; however, in the presence of oncogenic KRAS, it facilitates PanIN progression. Thus, HBP1 serves as a critical regulator in both pancreatitis and early pancreatic neoplasia, representing a potential therapeutic target for intervening pancreatitis and PanIN progression.

overall_design: Spatial transcriptomic analysis was performed on pancreata from three HBP1 WT and three HBP1 CKO mice on days 1 and 2 post-cerulein treatment. Pancreatitis areas were mounted on 10x Genomics Visium slides, with 5000 barcoded 55 µm spots capturing 1–10 cells per spot, each containing millions of probes for 20,551 mouse genes via CytAssist28. Sequencing (25k read pairs/spot) generated FASTQ files, which were mapped to H&E images and feature-barcode matrices using Spaceranger.

first: Seung-Won

last: Lee

first: Taelor

last: Ekstrom

first: Elise C

last: Manalo

first: Dmytro

last: Grygoryev

first: Jungsun

last: Kim


title: Coactivator SAGA plays a crucial role in TBP recruitment for the Gcn4 transcriptome via subunits Spt3/Spt8 [RNA-seq]

city: Rockville

first: SAKSHI

last: SINGH

state: Maryland

address: 6 center drive , Bldg 6

department: NICHD-DIR

institute: NIH

summary: Transcription initiation by RNA polymerase II is facilitated by coactivators that recruit general initiation factors to promoters. Coactivator complexes TFIID and SAGA recruit TATA-binding protein (TBP), while SAGA also enhances transcription by histone acetylation via the HAT Gcn5. It was proposed that most yeast genes depend exclusively on TFIID, with only ~10% requiring cumulative contributions by SAGA and TFIID for efficient transcription. It was further suggested that genes induced by Gcn4, transcriptional activator of amino acid biosynthetic genes induced by amino acid starvation, depend on the HAT but not the TBP-recruitment function of SAGA. At odds with this model, ChIP-sequencing of TBP and Pol II subunit Rpb1 revealed that deleting SPT3 or SPT8, but not GCN5, reduced TBP binding at many Gcn4 target genes. In contrast, deleting GCN5 but not SPT3 or SPT8 impaired promoter histone eviction at the highly remodeled subset of induced genes, whereas transcription was broadly reduced by all three SAGA mutations. Nuclear depletion of TFIID subunit Taf1 generally reduced TBP recruitment at these and most other SAGA-dependent genes only in cells lacking Spt3 or Spt8. We conclude that SAGA is crucial for TBP recruitment via Spt3/Spt8, beyond its role in histone acetylation, and functions non-redundantly with TFIID in the Gcn4 transcriptome of amino acid-starved cells.

overall_design: Total RNA isolation was carried out using Hot-Phenol Method.Followed by RNA-sequencing libraries preparation using the Illumina TrueSeq stranded mRNA Library Prep Kit. Ribo-depletion was performed to remove the rRNA using Qiagen FastSelect Yeast rRNA Depletion Kit, followed by paired-end sequencing using the Novaseq-X platform.

first: Sakshi

last: Singh

first: Alan

last: G. Hinnebusch


title: EFFECTS OF AGED GARLIC EXTRACT MAY DIFFER BETWEEN NORMAL CELLS AND CANCER CELLS

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

summary: Aged garlic extract (AGE) is one of the widely used garlic-based products that are extensively studied and are commercially available. However, there are no reports that compare the effects of AGE on normal cells and oral cancer cells. In the present study, we tried to investigate the effects of AGE on normal healthy cells and cancer cells. The effect of AGE on the proliferation of normal cell lines HaCaT and fibroblast, in addition to cancer cell lines SCC7, HSC2, HSC3 and Ca9-22 were evaluated by MTT assay. By contrast, the effects of AGE on cell migration were examined using wound healing and migration assays. Whole transcriptome analysis, Ingenuity Pathways Analysis (IPA) and western blot analysis were used to investigate the mechanism of action of AGE in HaCaT and SCC7 cells. Data from the aforementioned assays were then evaluated and compared to assess if AGE affects normal cells differently compared with cancer cells. AGE was found to promote the proliferation and migration of normal cells, especially HaCaT, in the absence of FBS more significantly compared with those of cancer cells. However, AGE could not promote wound healing in fibroblast cells at the same rate as in HaCaT cells. In normal cells, sequential or combination AGE treatment with 5-fluorouracil (5-FU), cisplatin (CDDP) and docetaxel (DOC) somewhat counteracted the proliferation-limiting effects of anti-cancer agents. However, in cancer cells, AGE treatments enhanced the inhibitory effects of anti-cancer agents when used in combination with 5-FU, CDDP or DOC. This observation was more evident in case of pre-treatment with anticancer agents followed by AGE sequential treatment. Subsequently, whole transcriptome analysis and IPA data suggested that AGE facilitated the proliferation and survival of normal cells through the induction of Akt and brain-derived neurotrophic factor pathways, whilst suppressing ferroptosis These data were also confirmed by western blotting to see if the genetic changes shown in whole transcriptome analysis and IPA are also induced at the protein level. In addition, AGE may reduce cancer cell proliferation through the suppression of cancer metastasis signaling and enhancement of phagocytic activity according to whole transcriptome analysis and IPA data. Taken together, these findings suggest that AGE may prompt the proliferation of normal cells and suppress the that of cancer cells through different cellular processes and signaling pathways.

overall_design: To investigate the mechanism of action of AGE in HaCaT and SCC7 cells, we performed mRNA-Seq using total RNA extracted from HaCaT and SCC7 cells.

first: Koji

last: Harada

first: Tarannum

last: Ferdous

first: Keisuke

last: Kawasaki

first: Kenji

last: Watanabe


title: Wumei Wan Remodels the Tumor Immune Microenvironment via the IDO1-KYN-AHR Axis in AOM/DSS-Induced Colorectal Cancer Model.

city: Shaanxi

first: Yilin

last: Zhang

address: 8P8R+27G, Shiji Blvd, Qindu District, Xianyang, Shaanxi, China

institute: Shaanxi University of Chinese Medicine

summary: Abstract Background:Colorectal Cancer (CRC) is a common malignant tumor of the digestive tract, with poor prognosis in advanced stages due to metastasis and immune evasion.Chronic intestinal inflammation may promote CRC progression by inducing an imbalance in the immune microenvironment, thus therapeutic strategies targeting immune regulation urgently need to be explored.Wumei Wan (WMW), a traditional Chinese herbal formula, has shown marked anti-inflammatory activity in ulcerative colitis (UC).However, whether it can inhibit CRC progression remains unclear. Aim:This study aims to investigate whether WMW can ameliorate CRC and to explore its underlying mechanisms. Methods:An AOM/DSS-induced CRC mouse model was established, and transcriptomicss, metabolomics, and network pharmacology analyses were integrated to investigate and validate the mechanisms of WMW. Results:WMW ameliorated CRC progression by improving colonic pathological conditions, lowering Disease Activity Index (DAI) scores, enhancing survival, and suppressing tumor growth in CRC mice. Specifically, the WMW group’s DAI score decreased by approximately 34.36% compared to the model group. Additionally, by day 70, the survival rate in the WMW-treated group was 22.806% higher than that of the model group. Multi-omics and network pharmacology analyses indicated that WMW inhibited the IDO-Kyn-AHR signaling pathway, decreased Th17 and Treg cell proliferation and differentiation, restored CD8+T cell function, and enhanced antitumor immunity. Conclusion：This research demonstrates for the first time that WMW suppresses CRC progression by rebalancing Th17/Treg immunity through modulation of the IDO1-Kyn-AHR pathway.

overall_design: The RNA-seq analysis of mouse colorectal cancer tissues includes three experimental groups: the blank control group (Group K), the colorectal cancer model group (Group M), and the WMW-H treatment group (Group G), with 5 replicates in each group, to observe the therapeutic effect of WMW-H.

first: Mingjie

last: Yang

first: Shusen

first: Yushan

last: Liu

first: Rui

last: Jia

first: Xinyue

first: Jingtao

last: Li

first: Shuguang

last: Yan


title: Transcriptional Regulation of Microglial Metabolic and Activation States by P2RY12

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Microglia are the resident immune cells of the CNS and integral to maintaining homeostasis. They rapidly respond to injury or infection within the CNS by altering their morphology, proliferating, and releasing cytokines and other signaling molecules. Microglia also play critical roles in development, regulating synaptic pruning and debris clearance. In disease, they are powerful mediators of neuroinflammation. Understanding the molecular pathways involved in microglial function is pivotal for advancing neurobiological research and developing effective strategies for CNS disorders. In this context, P2RY12 is a G protein-coupled receptor (GPCR) that is enriched in microglia in the brain parenchyma and is part of the transcriptional signature of homeostatic, ramified microglia. However, P2RY12 is downregulated in activated microglia and in neurological conditions. The downstream effects of P2RY12 downregulation in disease-associated microglia and how they influence microglial activation remain inadequately understood. In this study, we apply transcriptional and histological methods to explore the changes to microglia upon a genetic P2RY12 loss. Our findings reveal that P2RY12-deficient microglia experience alterations in distinct metabolic pathways while preserving overall homeostatic microglial transcriptional identity. P2RY12 deficiency dysregulates signature genes involved in homeostatic iron metabolism. Importantly, the Glutathione Peroxidase 4 (GPX4)-Glutathione (GSH) antioxidant pathway related to ferroptosis susceptibility is impaired upon microglial activation with LPS treatment. These results highlight the critical role of P2RY12 in regulating microglial immune and metabolic responses under both homeostatic and inflammatory conditions, providing insights into its involvement in CNS pathophysiology.

overall_design: Bulk RNA-seq of isolated microglia from adult male and female wild-type and P2RY12 knockout (KO) littermate mice.

first: Lopez

last: Aida

first: Coburn

last: Morgan

first: Okojie

last: Akhabue

first: Eyo

last: Ukpong


title: Effects of ZFA-demethylase chimeras in vivo

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

summary: Gene expression profiling of transcriptional response to interferon stimulation after zinc finger -based demethylases.

overall_design: Mice were treated with ZFA demethylases followed by gamma-interferon exposure. Lung epithelial cells were isolated and total RNA was obtained for profiling.

first: Naohiro

last: Yano


title: Dual targeting of CDK6 and LSD1 is synergistic and overcomes differentiation blockade in AML [RNAseq_MV4_11]

first: Sophie

last: Lopez

first: Lise

last: Brault

first: Edwige

last: Voisset

first: Mathieu

last: Desaunay

first: Antonia

last: Boudet

first: Paraskevi

last: Kousteridou

first: Sébastien

last: Letard

first: Nadine

last: Carbuccia

first: Armelle

last: Goubard

first: Rémy

last: Castellano

first: Yves

last: Collette

first: Julien

last: Vernerey

first: Isabelle

last: Vigon

first: Jean-Max

last: Pasquet

first: Patrice

last: Dubreuil

first: Paulo

last: De Sepulveda


title: LncRNA ASH1L-AS1 Encodes the Microprotein APPLE to Drive HCC Tumorigenesis

city: Guangzhou

first: Lei

last: Zhao

address: Xinzao Road

institute: Guangzhou Medical University

summary: RNA sequencing of HepG2 was performed to explore the molecular basis of microprotein APPLE encoded by LncRNA ASH1L-AS1 in hepatocellular carcinoma (HCC). In order to overexpress microprotein APPLE in HepG2, we constructed the overexpression plasmid containing open reading frame (ORF) of LncRNA ASH1L-AS1.

overall_design: 6 transcriptomes including 3 negative control (NC) groups and 3 ORF-Flag groups. In the NC groups, HepG2 was transfected with vector plasmids, and ORF-Flag (with Flag‐tag fusion) overexpreesion plasmids was transfected into HepG2 in ORF-Flag groups.


title: Transcriptomic Profiling of Zebrafish Mutant for cdkl5 Reveals Dysregulated Gene Expression Associated with Neuronal and Skeletal Development

city: Faro

first: Tatiana

last: Varela

email: tatianacdv@gmail.com, a44770@ualg.pt

address: Campus de Gambelas

country: Portugal

institute: Universidade do Algarve

summary: Zebrafish has been recognized as a robust model organism in biomedical research for the investigation of human genetic disorders. Recently, we proposed the homozygous cdkl5sa21938 mutant zebrafish as a model of CDKL5 deficiency disorder (CDD), a rare developmental epileptic encephalopathy associated with broad range of symptoms.  Since neurological phenotypes are the primary focus of investigations, the understanding of CDKL5 function beyond the brain remains limited. Therefore, the aim of this study was to expand the knowledge about Cdkl5-associated molecular mechanisms using the proposed cdkl5 zebrafish model and to evaluate their similarity to findings in mammalian systems. For this purpose, we conducted RNA-sequencing of whole cdkl5-/- mutant zebrafish and compare it to their wild-type siblings at two different stages of development (5 and 35 dpf). Most significant DEGs were related to muscle, neuronal and visual systems which are affected in CDD. Gene Ontology (GO) analysis revealed that at both stages the downregulated DEGs were mainly enriched in muscle development, extracellular matrix and actin cytoskeleton functions while at 35 dpf the upregulated DEGs were mainly enriched in eye development functions. KEGG pathway analysis showed the enrichment of downregulated DEGs in focal adhesion and ECM-receptor interaction pathways at both stages. Additionally, we found that DEGs related to neuronal development were mainly downregulated at both stages while several upregulated DEGs were enriched in synaptic signaling at 35dpf. Moreover, we identified many downregulated key DEGs of cartilage development at both stages and bone development at 35 dpf, potential explaining the impaired cdkl5-/- mutant craniofacial cartilage and bone mineralization defects and the CDD skeletal phenotypes. In conclusion, this study shows that Cdkl5 loss in the cdkl5-/- mutant zebrafish lead to the dysregulation of several genes involved in functions known to be associated with CDKL5 in mammalian systems and provide novel insights into the less studied CDKL5 functions and phenotypes.

overall_design: RNAseq of homozigous cdkl5sa21938 zebrafish and their WT siblings at 5 and 35 days post-fertilization. Five biological replicates were performed for each condition.

first: Débora

first: Natércia

last: Conceição

first: M

middle: L

last: Cancela


title: GADD45G operates as a pathological sensor orchestrating reactive gliosis and neurodegeneration [ChIP-seq]

city: Dallas

first: tianjin

last: shen

state: Texas

address: 5323 Harry Hines Boulevard, Dallas, TX 75390

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: GADD45G functions as stress sensors and plays critical roles in the regulation of cell cycles, DNA repair, apoptosis and inflammation. They are localized in both the nucleus and the cytoplasm and carry out their specific functions through protein-protein interactions, the demethylase activity, and regulation of intracellular signaling pathways. The role of GADD45G in astrocytes is completely unknown. On the other hand, GADD45G is consistently upregulated under different pathological stimuli in astrocytes. Therefore, we decided to assess the function of GADD45G in astrocytes. In this study, we showed the GADD45G signaling in astrocytes drives a distinct pathogenic reactivity state both in vitro and in vivo. We also explore the communication between GADD45G-driven astrocytes and other cells in the CNS, including microglia and neurons, and discuss how this crosstalk regulates CNS inflammation and pathological outcomes.

overall_design: ChIP-seq of in vitro culture astrocytes expressing FLAG or FLAG-GADD45G. Primary WT astrocytes were cultured with serum-free medium, transduced with lentivirus (LV-hGFAP-FLAG or LV-hGFAP-FLAG-GADD45G).

first: Tianjin

first: Dongfang

last: Jiang

first: Chun-li

last: Zhang


title: Hypotaurine reduces glucose-mediated vascular calcification

city: Dresden

first: Claudia

last: Goettsch

state: SA

address: Fetsherstr. 74

institute: TU Dresden Faculty of Medicine Carl Gustav Carus

summary: To study the underlying molecular mechanisms driving vascular calcification, we analyzed the transcriptome of calcium-phosphate calcified human coronary aortic smooth muscle cells cultured with zero, low, and high glucose for 3 days.

overall_design: Human primary coronary artery smooth muscle cells from three independent donors were cultured in a control medium (5.5 mM glucose) or calcified in a calcium-phosphate medium (CaP) with 0 mM, 5.5 mM and 25 mM glucose.

first: Marina

last: Heuschkel

first: Steffen

last: Gräber

first: Anna

last: Artati

first: Jerzy

last: Adamski

first: Joachim

last: Jankoswksi

first: Keon

last: Schurgers

first: Nikolaus

last: Marx

first: Willi

last: Jahnen-Dechent


title: Comprehensive Analysis of tsRNA Expression in Endometriosis using PANDORA-seq technology

city: naning

first: Jingyao

last: Huang

state: Guangxi Autonomous

address: No. 6 Taoyuan Road, Qingxiu District, Nanning City, Guangxi Zhuang Autonomous Region

institute: People´s Hospital of Guangxi Autonomous Region

type: Non-coding RNA profiling by high throughput sequencing

summary: Endometriosis is a common gynecological disease and there is no reliable non-invasive biomarker for its unknown pathogenesis. TsRNA is differentially expressed in a variety of cancers and is a new non-invasive biomarker. The aim of this study was to reveal the full landscape of tsRNA expression profile in endometriosis using PANDORA-seq, which will provide strong target support for early diagnosis and treatment.

overall_design: PANDORA seq of Eutopic Endometric Tisses (EUs) and Ectopic Endometric Tisses (ECs) from the same patient with ovarian Endometriosis, as well as Eutopic Endometric Tisses (ENs) from control group patients.

first: Junping

last: Cheng

first: Dandan

first: Ying

last: Wang

first: Huanying

last: Liang

first: Liling

last: Liu


title: Protein Kinase R regulates pancreatic ductal adenocarcinoma progression by modulating the cell cycle via GADD45A

city: Toon

first: Mitsuhito

last: Koizumi

state: Ehime

address: Shitsukawa

institute: Ehime University Graduate School

summary: Protein kinase R (PKR) functions both as a promoter and inhibitor in various cancers, yet its role in pancreatic ductal adenocarcinoma (PDAC) remains unclear. This study aimed to investigate the role of PKR in PDAC. PKR expression in PDAC cell lines was assessed using real-time reverse transcriptase polymerase chain reaction and western blot analysis. The MTS assay was employed to evaluate the effect of PKR on cell proliferation. To elucidate the underlying mechanisms of PKR's action on PDAC, RNA-sequencing (RNA-seq) analysis was performed, and flow cytometry was used to examine the effects of PKR knockdown on cell cycle progression and apoptosis in PDAC cells.　The results indicated that PDAC cell lines exhibited significantly reduced proliferation when transfected with PKR-targeting siRNAs or treated with PKR inhibitors. RNA-seq analysis revealed a substantial upregulation of GADD45A expression upon inhibition of PKR expression. Following PKR silencing, cell cycle analysis showed a marked accumulation of cells in the G1 phase, which is consistent with GADD45A's known role as a cell cycle regulator. Furthermore, the inhibition of proliferation caused by PKR knockdown was reversed by the downregulation of GADD45A, suggesting an interactive effect between PKR and GADD45A in regulating PDAC cell growth.　In conclusion, PKR promotes PDAC cell proliferation by modulating the cell cycle through the regulation of GADD45A expression. These findings suggest that PKR may serve as a potential novel therapeutic target for PDAC.

overall_design: RNA-seq profiling of PANC-1 cells 72 hours after transfection with control, PKR siRNA 1, or PKR siRNA 2, and 72 hours after treatment with DMSO or C16

first: Yuki

last: Numata


title: Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks

city: Boston

first: Gracia

middle: M.

last: Bonilla

state: MA

address: 185 Cambridge St

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Tiki2 maintains articular cartilage homeostasis and protects against osteoarthritis by inhibiting Wnt/β-catenin signaling

status: Public on Jul 20 2025

city: Chengdu

first: Hengye

last: Zhang

state: Sichuan

address: No.4,Section 2,North Jianshe Road

institute: University of Electronic Science and Technology of China

summary: Osteoarthritis (OA) is a serious degenerative joint disease with high morbidity and is currently incurable because of its poorly defined underlying molecular basis. Here, we demonstrated that Tiki2, a membrane-tethered proteolytic Wnt inhibitor, is highly expressed in the articular chondrocytes of hyaline cartilage and that its expression negatively correlates with osteoarthritis. Tiki2 haploinsufficiency in mice causes spontaneous articular cartilage degeneration. Tiki2 deletion in chondrocytes accelerates instability-induced knee joint osteoarthritis progression in mice. Mechanistically, Tiki2 antagonizes Wnt signaling in chondrocytes and maintains chondrocyte anabolic gene expression. Moreover, intra-articular administration of a TIKI2-expressing adeno-associated virus significantly alleviated OA progression in mice, and expressing TIKI2 promoted chondrogenesis and chondrocyte redifferentiation and inhibited hypertrophic differentiation in vitro. Our results reveal the function of Tiki2 in articular cartilage homeostasis and osteoarthritis and suggest that Tiki2 is a potential target for osteoarthritis therapy.

overall_design: RNA-seq profiling of primary chondrocytes from Tiki2 fl/fl (control) and Tiki2 fl/fl; Col2a1-Cre/ERT (cKO) mice treated with 4-hydroxytamoxifen (4-OHT) to induce Tiki2 depletion in Cre/ERT-expressing cells.

first: Xinjun


title: A molecular switch at the yeast mitoribosomal tunnel exit controls cytochrome b synthesis

first: Mary

middle: T

last: Couvillion

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Mitochondrial gene expression needs to be balanced with cytosolic translation to produce oxidative phosphorylation complexes. In yeast, translational feedback loops involving lowly expressed proteins called translational activators help to achieve this balance. Synthesis of cytochrome b (Cytb or COB), a core subunit of complex III in the respiratory chain, is controlled by three translational activators and the assembly factor Cbp3-Cbp6. However, the molecular interface between the COB translational feedback loop and complex III assembly are yet unknown. Here, using protein-proximity mapping combined with selective mitoribosome profiling, we reveal the components and dynamic interaction of the molecular switch controlling COB translation. Specifically, we demonstrate that Mrx4, a previously uncharacterized ligand of the mitoribosomal polypeptide tunnel exit, interacts with either the assembly factor Cbp3-Cbp6 or with the translational activator Cbs2. These reciprocal interactions determine whether the translational activator complex with bound COB mRNA can interact with the mRNA channel exit on the small ribosomal subunit for translation initiation. Organization of the feedback loop at the tunnel exit therefore orchestrates mitochondrial translation regulation with respiratory chain biogenesis.

overall_design: Mitochondrial selective ribosome profiling of Mrx4 and related factors in S. cerevisiae cells

first: Andreas

last: Carlström

first: Joseph B.

last: Bridgers

last: Couvllion

first: Abeer

last: Singh

first: Axel

last: Imhof

first: L Stirling

last: Churchman

first: Martin

last: Ott