title: CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [RNA-seq]

status: Public on May 31 2025

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

department: Dermatology

country: USA

institute: Boston University

type: Expression profiling by high throughput sequencing

summary: Epigenetic macromolecular enzyme complexes tightly regulate gene expression at the chromatin level and have recently been found to colocalize with RNA splicing machinery during active transcription1; however, the precise functional consequences of these interactions are uncertain. Here, we identify unique interactions of the CoREST repressor complex (LSD1-HDAC1-CoREST) with components of the RNA splicing machinery and their functional consequences in tumorigenesis.  Using mass spectrometry, in vivo binding assays, and cryo-EM we find that CoREST complex-splicing factor interactions are direct and perturbed by the CoREST complex selective inhibitor, corin2–5, leading to extensive changes in RNA splicing in melanoma and other malignancies. Moreover, these corin-induced splicing changes are shown to promote global effects on oncogenic and survival-associated splice variants leading to a tumor-suppressive phenotype. Using predictive machine learning models, MHC IP-MS, and ELISpot assays we identify thousands of neopeptides derived from unannotated splice sites which generate corin-induced splice neoantigens that are demonstrated to be immunogenic in vitro. Corin is further shown to reactivate the response to immune checkpoint blockade and promote dramatic expansion of cytotoxic T cells in an immune cold melanoma tumor model, effectively sensitizing them to anti-PD1 immunotherapy. These data position CoREST complex inhibition as a unique therapeutic opportunity in cancer which perturbs oncogenic splicing programs across broad tumor types while also creating tumor-associated neoantigens that enhance the immunogenicity of current therapeutics and may be readily translated to the clinic.

overall_design: Total RNA was extracted from melanoma cell lines treated with corin (2.5uM, 24h) or vehicle control (DMSO) using the Qiagen RNeasy Mini Kit. Samples were quantified using nanodrop and sequenced by Azenta Inc.

first: Kihyun

last: Park

first: Kwangwoon

last: Lee

first: Katarina

last: Pinjusic

first: Allison

last: Vanasse

first: Christina

middle: S

last: Ennis

first: Scott

last: Ficcaro

first: Jarrod

last: Marto

first: Stephanie

last: Stransky

first: Joseph

last: Duke-Cohan

first: Anupa

last: Geethadevi

first: Eric

last: Raabe

first: Simone

last: Sidoli

first: Derin

middle: B

last: Keskin

first: Chad

middle: W

last: Hicks

first: Catherine

middle: J

last: Wu

first: Philip

middle: A

last: Cole

first: Rhoda

middle: M

last: Alani


title: Gain-of-function PPM1D mutations attenuate ischemic stroke

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

summary: Identification of genetic aberrations in stroke, the second leading cause of death worldwide, is of paramount importance for understanding the disease pathogenesis and generating new therapies. Whole-genome sequencing from 10,241 ischemic stroke patients identified eight patients carrying gain-of-function mutations on coding variants in protein phosphatase magnesium-dependent 1 δ (PPM1D) gene. Patients carrying PPM1D mutations exhibit better stroke-related clinical phenotypes, including improvements in systolic blood pressure, fibrinogen level, low-density lipoprotein, and plateletcrit level. Experimental brain ischemia in Ppm1d-deficient (Ppm1d-/-) mice resulted in enlarged lesions and pronounced neurological impairments. Spatial transcriptomics revealed a distinct Ppm1d-associated gene expression pattern, indicating disrupted endothelial homeostasis during ischemic brain injury. Proteomic analysis demonstrated that differentially expressed proteins in primary brain endothelial cells from Ppm1d-/- mice were significantly enriched in the peroxisome proliferator-activated receptors (PPARs)-mediated metabolic signaling. Mechanistically, Ppm1d deficiency promoted aberrant fatty acid β-oxidation and increased oxidative stress, which impair endothelial cell function through the PPARα pathway. A small molecule, T2755, was identified to engage Trp427 and stabilize PPM1D protein, thereby mitigating ischemic brain injury in mice. Collectively, we found that PPM1D protects against ischemic brain injury and validates its pharmacological stabilizer T2755 as a promising therapy for ischemic stroke.

overall_design: To explore the impact of Ppm1d on key pathological events post-brain ischemia, spatial transcriptomics was performed on the ischemic hemisphere of Ppm1d+/+and Ppm1d-/- mice following stroke. A 30 minutes middle cerebral artery occlusion (MCAO) model was utilized to induce a controlled infarct lesion, facilitating spatial transcriptomic analysis and ensuring a comprehensive evaluation of the anatomical structures in the peri-lesion region.

first: Wenyan

last: He

first: Yan

last: Li

first: Junwan

last: Fan

first: Yang

last: Liu

first: Meng

last: Yuan

first: Si

last: Cheng

first: Xinying

last: Huang

first: Zhuoran

last: Zhang

first: Yuwen

last: Xiu

first: Huimin

last: Zhu

first: Tian

last: Lan

first: Zhilin

last: Chang

first: Yong

last: Jiang

first: Hao

first: Xia

last: Meng

first: Yilong

last: Wang

first: Luc

middle: V

last: Kaer

first: Alexei

last: Verkhratsky

first: Yongjun

first: Fu-Dong

last: Shi


title: Vagal neuroimmune axis modulates heart failure by limiting monocyte-derived inflammatory CCRL2 macrophage II

first: li

middle: guo

last: qi

state: Chaoyang

address: Anzhen number 2 road

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Autonomic neuronal dysfunction is associated with heart failure (HF). Here, we report that targeted vagal nerve stimulation (VNS) using optogenetics attenuates cardiac remodelling and HF induced by pressure overload. Unbiased approaches revealed that VNS decreased the proportion of the Ccrl2+ macrophage subset, which derived from myeloid monocytes and exhibited a distinct tumour necrosis factor-alpha (TNFα)-responsive, pro-hypertrophic, and profibrotic signature. Elimination of Ccrl2+ macrophages prevented cardiac remodelling and HF. Functional characterisation by Ccrl2+ macrophage-specific overexpression or global genetic loss of α7 nicotinic acetylcholine receptor (α7nAChR) highlighted its crucial contribution to VNS-mediated cardioprotection. Mechanistically, activation of α7nAChR inhibited the TNFα responsiveness through upregulated expression of the transcription factor NRF2. Cardiac Ccrl2+ macrophages and TNFα-responsive proteins were positively correlated with cardiac remodelling and dysfunction in humans. Finally, an α7nAChR agonist effectively blocked the development of HF. These results suggest that the vagal neuroimmune axis modulates heart failure and is a promising target for treatment.

overall_design: We performed bulk RNA-sequencing (RNA-seq) and single-cell RNA-sequencing (scRNA-seq) 8 weeks after TAC. Bulk RNA-seq analysis of heart tissues identified 873 differentially expressed genes (DEGs) between Ctrl-TAC and VNS-TAC mice, and the significant pathways in the VNS-TAC group were mapped to 16 categories, most of which were involved in the immune response

first: Guoqi

last: Li

first: Congcong

first: Yang

first: Jie

last: Yang

first: Jianing

last: Wu

first: Yihui

last: Shao

first: Yulin


title: Amygdala-liver signaling orchestrates rapid glycemic responses to stress and drives stress-induced metabolic dysfunction

city: New York

first: Sarah

last: Stanley

state: NY

address: 1230 York Avenue

department: Dept of Molecular Genetics

institute: Rockefeller University

summary: Behavioral adaptations to environmental threats are crucial for survival and necessitate rapid deployment of energy reserves. The amygdala coordinates behavioral adaptations to threats, but little is known about its involvement in underpinning metabolic adaptations. Here, we show that acute stress activates medial amygdala (MeA) neurons that innervate the ventromedial hypothalamus (MeAVMH neurons), which precipitates hyperglycemia and hypophagia. The glycemic actions of MeAVMH neurons occur independent of adrenal or pancreatic glucoregulatory hormones. Instead, using whole-body virus tracing, we identify a polysynaptic connection from MeA to the liver, which promotes the rapid synthesis of glucose by hepatic gluconeogenesis. Repeated stress exposure disrupts MeA control of blood glucose, resulting in diabetes-like dysregulation of glucose homeostasis. Our findings reveal a novel amygdala-liver axis that regulates rapid glycemic adaptations to stress and links recurrent stress to metabolic dysfunction.

overall_design: 12 sections (2 sections per mouse) of formalin-fixed & paraffin-embedded (FFPE) mouse brains with AAV hSyn-mCherry injection into the ventromedial hypothalamus.

first: Jamie

last: Carty


title: Midline Assembloids Reveal Regulators of Human Axon Guidance

city: Stanford

first: Sergiu

last: Pasca

state: California

address: 318 Campus Drive

department: Psychiatry

institute: Stanford University

summary: Organizers are specialized cell populations that orchestrate cell patterning and axon guidance in the developing nervous system. Although non-human models have led to fundamental discoveries about the organization of the nervous system midline by the floor plate, an experimental model of human floor plate would enable broader insights into regulation of human neurodevelopment and midline connectivity. Here, we have developed stem cell-derived organoids resembling human floor plate (hFpO) and assembled them with spinal cord organoids (hSpO) to generate midline assembloids (hMA). We demonstrate that hFpO promote Sonic hedgehog-dependent ventral patterning of human spinal progenitors and Netrin-dependent guidance of human commissural axons, paralleling non-human models. To investigate evolutionary-divergent midline regulators, we profiled the hFpO secretome and identified 27 evolutionarily divergent genes between human and mouse. Utilizing the hMA platform, we targeted these candidates in an arrayed CRISPR knockout screen and reveal that GALNT2, a gene involved in O-linked glycosylation, impairs floor plate-mediated guidance of commissural axons in humans. This novel platform extends prior axon guidance discoveries into human-specific neurobiology with implications for mechanisms of nervous system evolution and neurodevelopmental disorders.

overall_design: single cell RNA-sequencing of day 8 floor plate organoids (3 replicates) , day 11 spinal organoids (4 replicates), day 11 floor plate organoid-assembled spinal organoids (4 replicates), and day 35 spinal organoids (3 replicates)

first: Massimo

last: Onesto

first: Neal

middle: D

last: Amin

middle: P


title: A novel translational in-silico indication discovery framework identifies indications and predictive biomarkers for cenerimod

city: Allschwil

first: Pijus

last: Brazauskas

address: Hegenheimermattweg 91

country: Switzerland

institute: Idorsia Pharmaceuticals

summary: To fully explore a drug candidate's therapeutic potential, assessing its effectiveness across all possible diseases is essential. While traditional approaches match drug mechanisms to disease pathophysiology, they are limited by the high costs and slow progress of preclinical and clinical trials. This study introduces a novel in silico framework to identify new indications for drug candidates or repurpose approved drugs by analyzing their effects on gene expression in patients or animal models compared to controls. The framework integrate data from 13,602 patient samples across 146 diseases with drug candidate tested in preclinical models and use a neural network to reduce noise and improve sensitivity. The framework was exemplified with cenerimod, a S1P1 receptor modulator, which predicted its efficacy in immune-related diseases such as SLE, Psoriasis, and Crohn’s disease and kidney transplantation complications. Additionally, it identified six genes predictive of maximal clinical response in SLE patients, validated using RNA-seq data from a phase 2b cenerimod trial.

overall_design: For the lupus mouse model, 7-week-old female MRL/lpr mice were treated with vehicle or cenerimod (0.2 mg/g food) until the end of the study, which was predefined as the time point when at least 20% morbidity/mortality was reached in one group (end of treatment week 10). RNA from blood and kidney from cenerimod- and vehicle-treated mice was isolated and prepared for sequencing using NUGEN Universal Plus mRNA kit with PolyA select (and globin depletion for the blood samples) according to protocol and sequenced on Illumina NextSeq 500 mRNA-seq platform. Age matched w C57BL/6 mice were used as healthy reference.

first: Dominik

last: Hartl

first: Madeleine

last: Suffiotti

first: Daniel

last: Strasser


title: H4K20me3 erasure facilitates reprogramming to totipotent-like state by promoting DUX4 mediated transcription [RNA-Seq]

city: hangzhou

first: Danya

state: zhejiang

address: xihu

institute: zhejiang unvercitt

summary: Epigenetic remodeling following fertilization is essential for the acquisition of embryonic totipotency. The role of H4K20me3, a key component epigenetic mark, remains largely unexplored in the context of early human embryogenesis. Here, we observed a dynamic erasure of H4K20me3 modification during zygotic genome activation (ZGA), followed by a re-establishment after ZGA in human embryos. Using in vitro reprogramming of totipotent-like states, we demonstrated transient removal of H4K20me3 in human embryonic stem cells (hESCs) promotes DUX4-mediated expression of totipotent genes, the transition into a totipotent-like state.

overall_design: RNA-seq profiling of DMSO, A196, DUX4-OE, A196&DUX4-OE samples and DMSO,A196, PlaB, A196&PlaB samples.

first: Hongqing

last: Liang


title: Targeting the Survival Pathways in TH17 Cells

city: Albuquerque

first: Dandan

state: NM

address: 915 CAMINO DE SALUD  NE room 360

department: Molecular Genetics and Microbiology

institute: University of New Mexico

summary: Treated the Th17 cells with different inhibitors, RNA-seq analyzes DEG and related pathways.

first: Xuexian


title: Retinal sequencing results of glaucoma model in rats

city: Hangzhou

first: Da

last: Qian

state: Zhejiang

address: No. 158 Shangtang Road

department: Breast Surgery

institute: Zhejiang Provincial People's Hospital

summary: Detecting differential genes between glaucoma model rats and normal group rats, studying gene pathways that may cause glaucoma visual impairment, and providing possible research directions for further prevention and treatment

overall_design: Rats injected with 2uL PBS via intravitreal injection C1, C2, C3, C4, C5, C6;Rats intravitreal injection of 2ul 20mM NMDA N1, N2, N3, N4, N5, N6


title: SUL1 deficiency reduces PKA activity to increase replicative lifespan in yeast Saccharomyces cerevisiae

city: Cheng

first: Ma

last: Meng

address: University of Electronic Science and Technology Shahe Campus

institute: University of Electronic Science and Technology of China

summary: The process of sulfate uptake plays a crucial role in cellular metabolism and growth. SUL1, a plasma membrane transporter responsible for regulating the entry of extracellular sulfate in S. cerevisiae. Our previous work verified SUL1 as a fundamental gene involved in the regulation of lifespan. This study aimed to undertake a more comprehensive analysis of the role of SUL1 in regulating longevity. Our data showed that that sulfate transport is not required for the effect of SUL1 deletion on increased longevity. The SUL1 mutant demonstrates decreased functionality within the PKA signaling pathway, resulting in a variety of effects, such as increased stress-protective trehalose and glycogen, enhanced autophagy, elevated expression of stress response genes, and reduced expression of ribosomal genes. Concurrently, the observed increase in lifespan resulting from the deletion of SUL1 may be partially attributed to the stimulation of autophagy and MSN2-mediated transcriptional activity. The findings of this study provide additional evidence for the association between sulfate transporter and longevity, thereby identifying a novel potential intervention target for extending lifespan.

overall_design: To investigate the mechanism by which SUL1 mutations extend lifespan, exponential phase cells from the SUL1 mutant、SUL2 mutant、 E427 mutant and wild-type (WT) groups were harvested and subjected to total RNA extraction for the construction of mRNA libraries intended for sequencing analysis. The WT strain was utilized as a control group, with three biological replicates per group.

first: Juan

last: Long

first: Hao

first: Jing


title: Pulmonary endothelial cells endocytosis of HMGB1 promotes lung injury after renal ischemia-reperfusion injury

first: Yuxian

last: Kuai

address: No. 88 Jiefang Road, Shangcheng District

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

summary: Dysfunction of other organs is a significant contributor to the poor outcomes associated with acute kidney injury (AKI). HMGB1 is proposed to play a crucial role in the development of common extra-renal complications: acute lung injury (ALI). However, the mechanisms underlying these connections are not fully understood. Here, we established mice models of renal ischemia-reperfusion injury (IRI). HMGB1 was observed to be released from renal cell nucleus 1 hour after reperfusion. Based on mass spectrometry screening, clathrin was identified and the released HMGB1 entered pulmonary endothelial cells via clathrin-mediated endocytosis after binding to TLR4. Further investigations revealed that blocking HMGB1 with neutralizing antibodies or knocking down clathrin in lungs reversed pulmonary injury induced by renal IRI through inhibiting neutrophil recruitment and the formation and release of neutrophil extracellular traps (NETs) in lungs. Moreover, knocking down HMGB1 in TCMK-1 cells or clathrin in MPVECs in the co-culture systems in vitro obtained similar results. These findings demonstrate the effect of HMGB1 released from kidney in promoting ALI following renal IRI, disclose pulmonary endothelial cell endocytosis of HMGB1 mediated by clathrin as the potential mechanism, and identify neutralizing antibody to HMGB1 as a promising ALI mitigation strategy by inhibiting NETs formation in lungs.

overall_design: Co-cultured untreated TCMK-1 cells or the ATP repleted TCMK-1 cells after ATP depletion with untreated MPVECs for 12 h. Then the MPVECs in the lower chamber underwent gene sequencing.

first: Yueying

last: Zhou

first: Xiuxia

first: Ning

last: Liu

first: Dongping

last: Ning

first: Fang

last: Fang

first: Jian

last: Pan

first: Yanhong

last: Li


title: CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [scRNA-seq]

first: Robert

last: Fisher

overall_design: 6-10 week-old female C57BL/6 female mice (Jackson Lab) were inoculated with 2.5x105 B16F10 cells. Mice were treated with 200 µg/mice of Corin (HY-111048, MedChemExpress) or 200 µl vehicle control (5% DMSO/PBS) by daily intraperitoneal (i.p.) injections starting from day 6 after the tumor injection. For Anti-PD1 treatment, mice were treated with 150 µg/mice anti-PD1 (clone 29F.1A12, BioLegend, 135248) or isotype control (clone RTK2758, BioLegend, 400566) 3 times/week starting from day 7 post-tumor grafts. 10 mice per treatment group were used. Minced tumor biopsies were incubated with 200uL 20mg/mL collagenase, 200uL 20mg/mL hyaluronidase, and 5uL DNase for 20 minutes to 1 hour with agitation until the tumor fully dissociated. Single-cell suspension was passed through a 100um strainer and washed with 1X PBS by centrifugation. Cells were resuspended in 1ml of freezing media frozen down. Cryopreserved single-suspension tumor samples were thawed and dead cells were removed using the Dead Cell Removal Kit (Miltenyi, 130-090-101) following manufacturer instructions. Live cells from the flow-though were used for CD45+ cell isolation using CD45 mouse MicroBeads (Miltenyi, 130-052-301) following the recommendations. CD45+ cells were counted and resuspended in PBS + 0.04% BSA at 1000 cells/µL for scRNA-seq.

first: Kihyun

last: Park

first: Kwangwoon

last: Lee

first: Katarina

last: Pinjusic

first: Allison

last: Vanasse

first: Christina

last: Ennis

first: Scott

last: Ficcaro

first: Jarrod

last: Marto

first: Stephanie

last: Stransky

first: Joseph

last: Duke-Cohan

first: Anupa

last: Geethadevi

first: Eric

last: Raabe

first: Simone

last: Sidoli

first: Derin

last: Keskin

first: Chad

last: Hicks

first: Catherine

last: Wu

first: Philip

last: Cole

first: Rhoda

last: Alani


title: The effects of nintedanib combined with radiation on gene transcription in the MC38 cell line

city: Wuhan

first: Chunya

last: Li

address: No. 1095 Jiefang Dadao, Hubei Province, Jiaokou District, Wuhan City

department: Tongji Hospital

institute: Huazhong University of Science and Technology

summary: Nintedanib, a small molecule tyrosine kinase inhibitor, has been approved for patients with NSCLC who progressed following first-line chemotherapy. However, there are relatively few related studies on the treatment strategy of nintedanib combined with radiotherapy. This study aims to explore the effectiveness and mechanism of nintedanib combined with radiotherapy in both in vivo and in vitro experiments.

overall_design: The MC38 cell line was treated with 3 μ m nintedanib and 8Gy X-rays alone or in combination for 24 hours respectively. Then, RNA was extracted together with the control group cells and RNA transcriptome sequencing was performed. And this experiment was independently repeated three times.


title: Vagal neuroimmune axis modulates heart failure by limiting monocyte-derived inflammatory CCRL2 macrophage

first: li

last: qi

overall_design: We attempted to activate the vagal-α7nAChR axis via pharmacological tools and investigated which type of therapy, enhancing ACh contents or activating α7nAChR, was more effective for treating HF. The selective α7nAChR agonist EVP-6124 was used, as it is well tolerated and has successfully progressed to phase III clinical trials. As well, the acetylcholinesterase inhibitor donepezil was used, as it improves heart dysfunction in rats with acute myocardial infarction. To determine whether drug treatment could mitigate the progression of HF after cardiac remodelling, WT mice that underwent TAC for 4 weeks were randomised into three treatment groups administered saline, donepezil (5 mg/kg/day), or EVP-6124 (2 mg/kg/day)

first: Guoqi

first: Congcong

last: Zhang

first: Yang

first: Jie

last: Yang

first: Jianing

first: Yihui

last: Shao

first: Yulin


title: Aspiration-assisted intra-operative 3D bioprinting of scaffold-free modular units for skeletal muscle tissue regeneration

city: Palo Alto

first: Ishita

last: Jain

address: 3801 Miranda Avenue

summary: Traumatic muscle injury associated with volumetric muscle loss results in reversible muscle regeneration and function. Bottlenecks to conventional tissue engineering strategies to augment muscle regeneration are limited by low cell transplantation capacity by conventional injection of dissociated cells, the lack of customization of engineered tissues based on muscle defect geometry, as well as the feasibility of intra-operative use.  Here, we developed a facile approach to engineer modular units of scaffold-free high-density muscle tissues in customizable geometric shapes and sizes with integration potential.  For the first time, we describe aspiration-assisted intra-operative bioprinting of scaffold-free modular units for preclinical treatment of volumetric muscle loss.  We demonstrated the ability of 3D modular muscle units to be bioprinted to the site of the muscle defect, leading to improved muscle, vascular, and neuromuscular regeneration in a mouse model of volumetric muscle loss.  Transcriptional profiling revealed that the scaffold-free muscle units enable pre-formed cell-cell interactions that support myogenesis, unlike dissociated cells that lack cell-cell interactions.  This technology of intraoperative modular muscle unit implantation is promising for clinical use for precise bioprinting of scalable tissues from geometrically tunable modular units.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA Sequencing was performed on modular muscle tissue units composed of either murine C2C12 myoblasts or primary human muscle cells. For the murine muscle tissue units formed from C2C12 myoblasts, the experimental groups consisted of muscle units formed from cells with pre-differentiation treatment as were denoted as follows: Group I: C2C12 myoblasts were used to fabricate tissue strands on day 0 without prior differentiation and then maintained in the mold in differentiation media for 5 days. Group II: C2C12 cells were subjected to 2 days of pre-differentiation on tissue culture plastic before 3D tissue fabrication for an additional 3 days. Group III: C2C12 cells were subjected to 4 days of pre-differentiation on tissue culture plastic for 4 days before 3D tissue fabrication for an additional 1 day (n=4-5 per group).
To study the molecular effects by which pre-formed cellular interactions present within the modular muscle units may prime muscle myogenesis after implantation, RNA Sequencing was performed on human muscle units composed of primary human muscle cells cultured within rectangular solid-shaped molds for 2 days in differentiation media prior to RNA isolation. As a basis for comparing to pre-formed inter-cellular interactions within the modular unit in the setting of VML, an additional group consisted of primary human muscle cells cultured for 2 days in differentiation media were suspended in ultralow adhesion dishes, where there was negligible cell-cell interaction (n=3 per group).

first: Bugra

last: Ayan

first: Gaoxian

last: Chen

first: Gladys

last: Chang

first: Caroline

last: Hu

first: Beu P.

last: Oropeza

first: Ngan

last: Huang


title: H4K20me3 erasure facilitates reprogramming to totipotent-like state by promoting DUX4 mediated transcription [ChIP-Seq]

first: Danya

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic remodeling following fertilization is essential for the acquisition of embryonic totipotency. The role of H4K20me3, a key component epigenetic mark, remains largely unexplored in the context of early human embryogenesis. Here, we observed a dynamic erasure of H4K20me3 modification during zygotic genome activation (ZGA), followed by a re-establishment after ZGA in human embryos. Using in vitro reprogramming of totipotent-like states, we demonstrated transient removal of H4K20me3 in human embryonic stem cells (hESCs) promotes DUX4-mediated expression of totipotent genes, the transition into a totipotent-like state. Mechanistically, we show that H4K20me3 preferentially accumulates around genes specific to 8-cell-like (8CLC) state, which are induced by DUX4 and repressed by H4K20me3 modification. Furthermore, H4K20me3 enrichment near the pericentromeric regions may regulate satellite repeat transcripts, thereby modulating heterochromatin structure to facilitate totipotency reprogramming.

overall_design: ChIP-seq of H4K20me3 in hESCs

first: Hongqing

last: Liang


title: Transcriptional characterisation of skin tissues from photoaged mice and mice treated with alpha-ketobutyrate (α-KB).

city: KUNMING

first: LU

last: KeJin

state: YUNNAN

address: keyi Road NO.53#

institute: Yunnan Characteristic Plant Extraction Laboratory

summary: The skin is the largest organ in the human body and due to the inevitable exposure to the external environment, over time and the accumulation of various stimuli, the skin will undergo photoaging. Our study has shown that metabolite alpha-ketobutyrate (α-KB) in the transsulfuration pathway has an ameliorating effect on photoaging in mouse skin tissue. We used RNA-Seq analysis to investigate the transcriptional profiles of skin tissue from photoaged and α-KB-treated mice to elucidate the molecular mechanisms by which α-KB improves skin organisation in mice.

overall_design: RNA-seq profiling of skin tissue from Balb/c mice treated with different methods (control group, photoaging group, photoaging group with 7.5% a-kB treatment and photoaging group with 12.5% a-kB treatment) at 10 weeks.

first: Ke-Jin

last: Lu

first: Yi-Cheng

last: Ma

first: Cheng-Gang

last: Zou

first: Li

last: He


title: Gene knockout screen to identify genes involved in human neural stem/precursor cell proliferation

city: Fukuoka

first: Takumi

last: Nakagawa

address: 3-1-1, Maidashi

country: Japan

institute: Kyushu University

summary: During cortical development, neural stem/precursor cells (NS/PCs) sequentially produce neurons, astrocytes, and oligodendrocytes. Before producing these cells, human (h) NS/PCs self-renew longer-term to form a larger cortex than other mammalians, whereas the mechanisms are mostly unknown. In this study, we performed a gene knockout screen using the CRISPR/Cas9 system to identify genes having a key role in human NS/PC self-renewal.

overall_design: The gene knockout screen was conducted with the human CRISPR knockout pooled library (Brunello) in a human iPS cell-derived neural stem/progenitor cell (NS/PC) line, AF22. AF22 cells were transduced with the lentiviral library encoding sgRNAs, Cas9, and the puromycin-resistance gene. The single guide RNAs (sgRNAs) were then collected from three different fractions: (1) AF22 cells before differentiation (day 0) (2) CD133-positive undifferentiated NS/PCs after 10 days differentiation of AF22 (CD133), and (3) CD24-positive neurons after 10 days differentiation of AF22 (CD24). The enrichment of sgRNAs in these fractions was subsequently analyzed and compared.

first: Kinichi

last: Nakashima


title: CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [PRO-seq]

first: Robert

last: Fisher

overall_design: SKMEL5 cells were treated for 24h with 2.5uM corin or DMSO and permeabilized as described. All sample preparation was conducted on ice (4°C). Cells were washed in ice cold 1x PBS and resuspended in wash buffer (10 mM Tris-HCl pH 8.0, 10% glycerol, 250 mM sucrose, 10 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 1mM EGTA, Halt protease inhibitor cocktail (Thermo Scientific), and 4 u/mL RNase inhibitor [SUPERaseIN, Invitrogen]). Then cells (2x10^7) were gently permeabilized in permeabilization buffer (10 mM Tris-HCl pH 8.0, 10% glycerol, 250 mM sucrose, 10 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 0.1% Igepal, protease inhibitors cocktail (Roche), 4 u/mL RNase inhibitor [SUPERaseIN, Invitrogen]) for 5 minutes. Cells were recovered by centrifugation (400 x g for 8 minutes) and the supernatant was carefully removed. Cells were washed with 10 mL of wash buffer and then centrifuged again under the same conditions. Finally, cells were resuspended in 400uL of freeze buffer (50 mM Tris-HCl pH 8.0, 40% glycerol, 5 mM MgCl2, 0.5 mM DTT, 4 u/mL RNase inhibitor [SUPERaseIN, Invitrogen]) and stored at -80°C.

first: Kihyun

last: Park

first: Kwangwoon

last: Lee

first: Katarina

last: Pinjusic

first: Allison

last: Vanasse

first: Christina

last: Ennis

first: Scott

last: Ficcaro

first: Jarrod

last: Marto

first: Stephanie

last: Stransky

first: Joseph

last: Duke-Cohan

first: Anupa

last: Geethadevi

first: Eric

last: Raabe

first: Simone

last: Sidoli

first: Derin

last: Keskin

first: Chad

last: Hicks

first: Catherine

last: Wu

first: Philip

last: Cole

first: Rhoda

last: Alani


title: Unlocking Oocyte Potential: L-Asp's Protective Role Against Heat-Induced Meiotic Disruption

city: Guiyang

first: Qingwei

last: Wang

state: Guizhou

address: No. 515, Jiaxiu South Road, Huaxi District, Guiyang City

department: College of Animal Science

institute: Guizhou University

summary: Global warming has made heat stress (HS) an unavoidable challenge in livestock production, significantly impacting animal feed intake, growth, reproduction, and health. Germ cells, including oocytes, are particularly sensitive to HS, with impaired oocyte maturation being a primary cause of reproductive dysfunction. This study examines the effects of HS on porcine oocyte meiotic maturation and evaluates the protective role of L-aspartic acid (L-Asp) supplementation during this process. Here, we report that L-Asp supplementation improves the quality of porcine oocytes under heat stress. More specifically, we found that heat stress resulted in oocyte maturation failure by disturbing the dynamics of meiotic organelles, including the spindle assembly, chromosome structure and mitochondrial function. Moreover, heat stress triggered the overproduction of reactive oxygen species (ROS) and caused DNA damage, resulting in apoptosis in oocytes and halting embryonic development. Importantly, our findings showed that L-Asp supplementation during heat stress alleviated the meiotic defects in porcine oocyte maturation. These findings demonstrate that L-Asp supplementation is a beneficial strategy for improving oocyte quality under HS by facilitating both nuclear and cytoplasmic maturation. This approach holds promise as a practical strategy for mitigating the reproductive challenges posed by global warming in livestock production.

overall_design: After L-Asp treatment, MII oocytes were collected from the control, HS, and L-Asp-supplemented groups (25 oocytes per group). The single-cell collection mixture contained cell lysate to disrupt the cell membranes and release RNA and RNase inhibitors to prevent RNA degradation. Total RNA was isolated, and reverse transcription was performed using nucleic acids bound to Oligo dT to synthesize first-strand cDNA. PCR amplification of the first-strand cDNA enriched the nucleic acids, and the amplified products were purified for library construction. The library preparation process included DNA fragmentation, end repair, the addition of “A” splices, PCR amplification, and quality control. The constructed library was sequenced on an Illumina platform

first: Xiang

last: Chen


title: Platelet Factor 4 (PF4) Regulates Hematopoietic Stem Cell Aging

city: CHICAGO

first: Constantinos

last: chronis

state: IL

address: 900 S Ashland Ave, Mbrb 2370

department: Biochemistry and Molecular Genetics

institute: UIC

summary: Hematopoietic stem cells (HSCs) responsible for blood cell production and their bone marrow regulatory niches undergo age-related changes, impacting immune responses and predisposing individuals to hematologic malignancies. Here, we show that the age-related alterations of the megakaryocytic niche and associated downregulation of Platelet Factor 4 (PF4) are pivotal mechanisms driving HSC aging. PF4-deficient mice display several phenotypes reminiscent of accelerated HSC aging, including lymphopenia, increased myeloid output, and DNA damage, mimicking physiologically aged HSCs. Remarkably, recombinant PF4 administration restored old HSCs to youthful functional phenotypes characterized by improved cell polarity, reduced DNA damage, enhanced in vivo reconstitution capacity, and balanced lineage output. Mechanistically, we identified LDLR and CXCR3 as the HSC receptors transmitting the PF4 signal, with double knockout mice showing exacerbated HSC aging phenotypes similar to PF4-deficient mice. Furthermore, human HSCs across various age groups also respond to human youthful PF4 signaling, highlighting its potential in rejuvenating aged hematopoietic systems. These findings pave the way for targeted therapies aimed at reversing age-related HSC decline with potential implications in the prevention or improvement of the course of age-related hematopoietic diseases.

overall_design: Examination of gene expression

last: Chronis

first: Sandra

last: Pinho

first: Sen

last: Zhang


title: RNA decay profile for eRF1 and UPF1 depletion in HCT116 cell lines

city: Kunming

first: Shimin

last: Gong

address: Wujiaying

institute: Life Sciences, Yunnan University

summary: We had found that non-optimal codon induced frameshifting translation coupled with NMD may play a crucial role in maintaining delicate need of mRNA from yeast to human. Our data suggests that NCFT also exist in human. We constructed eRF1-KD and UPF1-KD cell line and resort α-amanitin to treat cells in different time point, then transcriptionally profiled them to get the landscape of mRNA stability.

overall_design: The HCT116-AID2 cell lines were induced by 1 µg/ml of doxycycline for 24h, and wereadded or not added (as the control) to 10 µM 5-Ph-IAA (MCE, HY-134653) for several hours. Then transferring cultures to fresh medium supplemented with 10μg/mLactinomycin D (HY-17559, MCE). Samples were harvested at time points of 0, 4, 8 and 12h followingactinomycin Dtreatment. Three replicates were collected at each time point.To determine decay rate of RNA, 500ng HCT116-AID2 cellRNA and 50ngNeurospora RNA were input RT reaction. For tested genes, random RT primers were employed in RT reaction.

first: Zhanbiao

last: Li

first: Yunkun

last: Dang


title: Effects of a Non-Pharmacological Multidomain Intervention in Older Adults

city: Puncak Alam

first: Kalavathy

last: Ramasamy

state: Selangor

address: UiTM Cawangan Selangor Kampus Puncak Alam Bandar Puncak Alam

department: Faculty of Pharmacy

country: Malaysia

institute: Universiti Teknologi MARA (UiTM)

summary: This study aimed to investigate the effects of a multidomain intervention on gene expression profile of older adults with cognitive frailty in Selangor, Malaysia, using  mRNA gene sequencing. The intervention included a combination of dietary changes, exercise, and psychosocial support.  By analyzing gene expression profile in both groups, this study explores how multidomain interventions may influence mrna in older adults. The findings could provide insights into the role of lifestyle factors on the CF in aging populations.

overall_design: About 40 samples from two groups of older adult with CF  (IV0=7, IV6=6, IV12=6, C0= 8, C6=7, C12=5) was used for microarray analysis.mRNA from peripheral blood cells was extracted, purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

first: Abu Bakar

last: Abdul Majeed

first: Siong Meng

last: Lim

first: Suzana

last: Shahar


title: Epigenetic Silencing of GFRA1 Promotes Cervical Cancer Metastasis via SERPINE1

first: Weipeng

last: Liu

state: Yunnan

address: Jiao ling road

department: Institute of Medical Biology

institute: Chinese Academy of Medical Sciences

summary: Cervical cancer (CC) is the fourth most common malignancy among women worldwide. The abnormal methylation of oncogenes/tumor suppressor genes can lead to the occurrence and progression of cervical cancer. Here, we identified GFRA1 as an abnormally methylated gene in CC, with its expression levels inversely correlated with promoter methylation. GFRA1 promoter hypermethylation was consistently observed in cervical cancer cell lines and tumor tissues, accompanied by significantly reduced expression compared to normal counterparts. Functional assays demonstrated that GFRA1 overexpression suppressed cervical cancer cell migration in vitro and inhibited lung metastasis formation in vivo. Integrated RNA-Seq and network analyses revealed SERPINE1 as the key downstream effector, whose overexpression enhanced the migratory capacity of cervical cancer cells both in vitro and in vivo. In summary, this study reveals that GFRA1 promoter hypermethylation silences its expression, promoting CC metastasis via SERPINE1. Therefore, our findings contribute to the understanding of the potential role of GFRA1 methylation in cervical cancer and may serve as a potential diagnostic and therapeutic target for cervical cancer.

overall_design: Total RNA was extracted from a total of 9 samples, comprising three negative control samples, three samples infected with pSicoR-Ef1a-mCh-Puro-GFRA1-shRNA1, and three samples infected with pSicoR-Ef1a-mCh-Puro-GFRA1-shRNA2. Subsequently, a cDNA library was constructed and sequenced using the BGISEQ-500 platform. Transcriptome data analyses were conducted using an online platform.

first: Yueting

last: Yao


title: Regulation of heart regeneration by LSD1 through suppressing CEND1

city: Xi'an

first: Shaozhou

last: Ma

address: No. 76, Yanta West Road, Yanta District, Xi 'an City, Shaanxi Province

institute: Xi’an Jiaotong University

summary: Background: Improving heart regeneration through reactivating cardiomyocyte proliferation holds a great potential for repairing diseased hearts. We recently reported that LSD1-dependent epigenetic repression of Cend1 transcription is prerequisite for cardiomyocyte proliferation and mouse heart development. This study interrogates the potential role of this LSD1-CEND1 axis in heart regeneration and repair. Methods: The cardiomyocyte-specific Lsd1 knockout or overexpression mice, Cend1null mice and cardiomyocyte-specific Cend1 overexpression mice were used to determine the role of LSD1-CEND1 axis in heart regeneration after experimental injuries. Neonatal and adult mice were subjected to apical resection or left anterior descending coronary artery ligation, respectively, to establish cardiac injury models. Echocardiography and Masson staining were employed to assess cardiac function and histopathology, respectively. The molecular changes were determined using RNA sequencing, quantitative RT-PCR, Western blotting and immunostaining. Results: Cardiomyocyte-specific deletion impeded neonatal heart regeneration, while overexpression of Lsd1 had the opposite effect. RNA sequencing revealed that Cend1, a crucial suppressor of cardiomyocyte cycling, was the most significantly elevated gene induced by Lsd1 loss during heart regeneration. Cardiomyocyte-specific Cend1 overexpression hindered neonatal heart regeneration, while Cend1 loss in nullizygous mice had the opposite effect. Cend1 deletion resulted in gene expression alterations associated with enhanced cardiomyocyte proliferation, neovascularization, and macrophage activation. Furthermore, the cardiac regeneration defect caused by Lsd1 loss was not observed when experiments were performed with mice that were nullizyogus for Cend1. Moreover, we found that either Lsd1 overexpression or Cend1 deletion could promote heart regeneration and repair, and improve cardiac function following experimental myocardial infraction in adult mice.

overall_design: Heart tissues were collected from P14 control and Cend1-KO mice and subjected to RNA sequencing

first: Huahua

first: Jinling

last: Dong

first: Shuang


title: Gene expression profile at single cell level of ID8 ovarian cancer chemotherapy model

city: Guangzhou

first: Chaoyun

last: Pan

address: 74 Zhongshan Er Lu

institute: Sun Yat-sen University

summary: Chemotherapy is the first-line treatment for ovarian cancer, yet chemoresistance frequently develops at the late stage of treatment. In this study, we established the preclinical model of metastatic, syngeneic high-grade serous ovarian cancer (HGSOC) model using the ovarian cancer cell line ID8 that recapitulates the full chemotherapy course. 4-5 weeks following intraperitoneal injection, tumour grows extensively in the abdomen of the mice, which were subsequentially treated with cisplatin. Early treatment cycles significantly suppressed tumor growth, including a marked response during the first and subsequent cycles following initial relapse. Nevertheless, all tumors ultimately relapsed with chemoresistant phenotypes after two treatment cycles , mirroring the clinical course often observed in the treatment of HGSOC patients. We conducted single-cell RNA sequencing (scRNA-seq) on both parallelly debulked primary tumors and their corresponding resistant counterparts to elucidate changes in cellular composition.

overall_design: Primary tumor and chemoresistant tumor from the ID8 ovarian cancer chemotherapy model were harvested and analyzed using scRNAseq.

first: Jingyi

last: Lu

first: Jie


title: RNA proximity labeling in log phase Caulobacter crescentus NA1000

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: APEX2 RNA proximity labeling is a powerful method for determining localized RNAs in vivo.  APEX2 RNA proximity labeling was adapted to bacterial cells, using an APEX2 fusion to the core scaffold of BR-bodies, RNase E.  As a control, APEX2 was also fused to a variant of RNase E that lacks its C-terminal IDR and is unable to form BR-bodies, RNase E delta CTD.  RNA proximity labeling was performed, and we observed a similar pattern of enriched RNAs to density centrifugation isolated BR-bodies (Al-Husini et al. Mol Cell 2020).

overall_design: Duplicate cultures of RNase E-APEX2 and RNase E(delta CTD)-APEX2 strains were growth to mid-log phase, and incubated with alkyne phenol for 30 minutes.  The cells were incubated with H2O2 for 1 minute, and then harvested for RNA extraction.  An aliquot of the lysate of each biological replicate was saved for normalization, and the proximity labled RNA was isolated by attaching a biotin-azide via click chemistry followed by purificaiton on streptavidin resin.  Lysate RNA and proximity labeled RNA samples were then prepared for RNA-seq by the IU CGM core facility.

first: Hadi

last: Yassine


title: Epicardial Complement C3 Activation in Neonatal Cardiac Regeneration

city: Cambridge

first: Richard

last: Lee

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: The capacity for some neonatal mammals to regenerate damaged myocardium has a known dependency on immune signaling. By utilizing single cell RNA sequencing of the neonatal mouse heart two days following apical resection or a sham thoracotomy right after birth, we identify complement C3 signaling along an epicardial-to-fetal macrophage axis as playing a strong role in post-injury angiogenesis. Specifically, we identify differences in macrophage populations between surgical conditions, with major expansions in pro-angiogenic signaling fetal liver-derived macrophages post-injury. These results suggest a role for primordial macrophage lineages in the early injury response in the neonatal heart, which may in turn promote better recovery or regeneration.

overall_design: Neonatal C57/BL6 mice of mixed-sex littermates underwent surgery at days P0-P1. 4 post-surgery (2 days) hearts per condition (sham and resected) were collected, perfused with PBS, and pooled. Ventricles were minced and 1200μL of dissociation media (RPMI 1640 media (Gibco 1187503), 0.04U/mL Dispase II in DMEM/F-12 (STEMCELL Technologies 07923), 2μg/mL Collagenase D (Roche 11088858001), 32U/mL DNase I (NEB M0303S)) were added. Samples were incubated (30min, 37°C) before deactivating the enzymes with cold 5% FBS in PBS. Samples were filtered through a 40μm cell strainer (Pluriselect 43-10040), centrifuged (300g, 5min, 4°C), resuspended in 2mL ACK lysing buffer (Gibco A10492-01), and incubated (5min, 37°C). Samples were centrifuged, washed (5% FBS in PBS), and recentrifuged. Live cells were enriched through dead cell removal (Miltenyi Biotech 130-090-101) and miniMACS separators. The suspension was washed and pelleted (400g, 5min, 4°C). Pellets were resuspended in 0.04% BSA in PBS at 1000 cells/μL and viability was determined through the LUNA-FL (Logos Biosystems).  Cells were processed using the 10x Genomics Chromium pipeline and sequenced on an Illumina NextSeq 2000. Feature matrices were generated from raw FASTQ files via the Cell Ranger pipeline.

first: Lee

middle: T

last: Richard


title: Gene expression profile of embryonic stem cell-derived TS-like cells by RNA-sequencing

city: Kyoto-shi

first: Masatoshi

last: Ohgushi

state: Kyoto

address: 53 Shogoin Kawahara-cho

institute: Kyoto University

summary: Human embryonic stem cells (ESCs) were differentiated into GATA3-expressing extraembryonic cells (GATA3+ ExE cells) by exposure to chemical inhibitors targeting ACTIVIN/NODAL (A83-01, 1uM) and FGF signaling (PD03714, 100nM). Using these GATA3-expressing cells as a starting material, we established trophoblast stem-like cells (TSLCs) following the established protocol for deriving trophoblast stem cells (TSCs) from the villous trophoblast of human first-trimester placenta. To characterize the resulting ESC-derived TSLCs, RNA sequencing was conducted, allowing comparisons with the parental ESCs and previously published TSCs.

overall_design: We profiled mRNA expression in ESC-derived TSLCs at two different passage numbers, each with two biological replicates, to comprehensively assess their cellular state.

first: Kaori

last: Honda

first: Rina

last: Takagi

first: Mototsugu

last: Eiraku


title: Evolution of response to hypoxia in the plant kingdom

city: Groningen

first: Hans

last: van Veen

address: Nijenborgh 7

department: GELIFES

country: Netherlands

institute: University of Groningen

summary: Molecular oxygen (O2) is necessary for plant metabolic and physiological processes. Land plants have successfully adapted to a range of habitats characterised by very different dynamics of O2 availability. O2 sensing has been mainly characterised in angiosperms, where it is mediated by the N-Cys branch of the N-degron pathway. We aimed to characterise the transcriptional response to limited oxygen availability (hypoxia) in non-seed plants. We set out to compare the transcriptional response to hypoxia in a range of species that recapitulate the major events in the evolution of land plants: M. polymorpha for Hepatophyta, P. patens for Bryophyta, S. moellendorffii for Lycophyta, E. hyemale and P. vittata for eusporangiate and leptosporangiate Monilophyta. Given the differences in each division’s life cycle, we selected the developmental phase that includes the main photosynthetically active organs, to enable comparability of tissues with similar metabolic features. Therefore, we treated mature sporophytes of Marchantia (n), Selaginella (2n), Equisetum (2n) and Pteris (2n) with 1% O2 in the dark for 8 h, while we subjected Physcomitrium gametophores to the same treatment. Controls were maintained under aerobic conditions (21% O2) in the dark. We extracted total mRNAs and sequenced them using the Illumina technology (cit.) to identify differentially expressed genes. We compared the effect of hypoxia on these five species with the datasets available for photosynthetic sporophytes of angiosperms, Arabidopsis thaliana and Oryza sativa . We observed a different extent of response for these species, where P. patens exhibited the mildest changes, in terms of both number of DEGs and extent of up- and down-regulation. In contrast, Arabidopsis and Rice showed a strong response to the treatment.

sample_organism:
Marchantia polymorpha
Physcomitrium patens
Equisetum hyemale
Pteris vittata
Selaginella moellendorffii

overall_design: We treated mature sporophytes of Marchantia polymorpha (n), Selaginella moellendorfii (2n), Equisetum hyemale (2n) and Pteris vittata (2n) with 1% O2 (v/v) in the dark for 8 h, while we subjected Physcomitrium patens gametophores to the same treatment. Controls were maintained under aerobic conditions (21% O2) in the dark. We extracted total mRNAs and sequenced them using the Illumina technology to identify differentially expressed genes.

first: Laura

last: dalle Carbonare

first: Vinay

last: Shukla

first: Francesco

last: Licausi


title: Gene Expression Analysis From Rat Models of Premature Ovarian Insufficiency Treated with Intraovarian Injection of Platelet Rich Plasma

city: Padang

first: Roza

last: Silvia

state: Sumatera Barat

address: Limau Manis, Pauh

department: Department of Histology

country: Indonesia

institute: Universitas Andalas

summary: Premature ovarian insufficiency (POI) has become a focus of many reproductive studies recently due to its long-life menopause-like symptoms in young women. It may affect up to three of a hundred women under 40 years. The possible causes include genetic diseases, infections, autoimmune disorders and iatrogenic events such as radiotherapy and chemotherapy. Recent studies investigating the regenerative dynamic potential of the ovaries demonstrate that follicular growth could be stimulated when an adequate ovarian environment is restored. This restoration can be achieved employing factors of known regenerative potential such as stem cells, or growth factors of platelet rich plasma (PRP), artificial ovary, ovarian transplantation, and mitochondrial replacement therapy. The emergence of autologous platelet-rich plasma (PRP) therapy reflects a break-through for POI patients, since the approach is the most ethical-friendly, the cheapest, the least invasive and limited adverse effects. Therefore, it has the highest potential to be applied in clinical routine practice. Nevertheless, the complex mechanism of PRP components’ on the ovary, especially in term of folliculogenesis, remains to be deciphered. Furthermore, it is necessary to clarify to what extent they impact the gene or protein targets that play important role in ovarian rejuvenation after POI. We report raw fastq data of Sprague Dawley rat models of POI in four treatment groups and one control to evaluate the effect of intraovarian injection of PRP on POI rat models. This report is a part of animal study regarding the effect of intraovarian injection of PRP on ovarian function recovery in POI rat models (unpublished study). The data collected from this study will be used to investigate how PRP induce the ovarian rejuvenation and to analyse transcriptomic changes after PRP treatment on chemotherapy-induced POI animal models.

overall_design: Young adult of female Sprague Dawley rats (10-12 weeks) were used as animal models. Each group consisted of 6 rats. Serial injections of  Cisplatin (3 mg/kg body weight, intraperitoneal, once a week) were performed either three- or five-time to induce mild- or severe-POI rat models, while control group was injected with NaCl 0.9%. Intraovarian injection of PRP (processed from the donor rats’ blood) was conducted on one mild- and severe-POI group a week after last injection of cisplatin, through laparotomic procedure. Post-operative infection was controlled with antibiotics (for the first three days). All samples for the study were collected two weeks after PRP treatment, and two weeks after last injection for control group. From each group, one ovarian tissue was randomly selected to involve in this transcriptomic analysis. The samples were stored in RNA Later solution (-80oC) before study procedure. Detailed research procedures were in accordance with the main study regarding the effect of intraovarian injection of PRP on ovarian function recovery in POI rat models (Roza et al, unpublished study).

first: Budi

last: Wiweko

first: Ahmad

last: Jusuf

first: Mila

last: Maidarti

first: Fadilah

last: Fadilah

first: Linda

last: Erlina

first: Mulyoto

last: Pangestu


title: Transcriptional characterization of ILC1 and different subsets of ILC3s lacking REV-ERBs. [ Bulk RNA-seq]

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

summary: Different subsets of ILC3s and ILC1 were sort purified from siLP of WT and DKO mice to study their transcriptomic profile in the tissue of 8-12 weeks old mice.

overall_design: Cells were sort-purified using FACS Aria II (BD Biosciences) from small intestine lamina propria of 8-12 weeks old  Vav1-Cre x NR1D1/NR1D2 fl/fl mice (DKO) and littermate fl/fl controls (WT). Sorted cells were used to prepare RNA-seq libraries by using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).

first: Bishan

last: Bhattarai

first: Marco

last: Colonna


title: Transcriptional characterization of ILC1 and different subsets of ILC3s lacking REV-ERBs. [scRNA]

overall_design: Cells were sort-purified using FACS Aria II (BD Biosciences) from small intestine lamina propria of 8-12 weeks old Vav1-Cre x NR1D1/NR1D2 fl/fl mice (DKO) and littermate fl/fl controls (WT). Nuclei were lysed and samples were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle.


title: Effect of DHT modeling on AGA frontal hair follicles.

first: shizhao

last: liu

address: guangzhou avenue north

institute: southern medical university

summary: In order to further explore the biological mechanisms of androgenetic alopecia and screen for effective treatment drugs, we have developed and validated a novel AGA organ culture model.

overall_design: We used 5*10^-6 mol/L of DHT to organ culture AGA frontal hair follicles.

first: Shizhao

last: Liu

first: Qian

last: Qu

first: Yong

last: Miao


title: Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers

city: London

first: Van

middle: Thuy Mai

last: Nguyen

address: 237 Fulham Rd, Chester Beatty Laboratories, third floor

department: Cancer Biology

country: United Kingdom

institute: Institute of cancer research

summary: Current treatments for KRAS-mutant colorectal cancers (CRCs) are often limited by cellular plasticity and rewiring responses. Here we describe a promising therapeutic strategy that simultaneously targets epigenetic and oncogenic signals. Specifically, we show that inhibitors of the histone methyltransferase, EZH2, synergize with various RAS pathway inhibitors and promote dramatic tumor regression in vivo. Together these agents cooperatively suppress WNT-driven transcription and drive CRCs into a more differentiated cell state by inducing the Groucho/TLE corepressor, TLE4, along with a network of WNT pathway inhibitors and intestinal differentiation proteins. However, these agents also induce the pro-apoptotic protein BMF, which subsequently kills these more differentiated cells. Accordingly, cell death can be prevented by activating β-catenin, blocking differentiation, or by ablating BMF expression. Collectively, these studies reveal a new therapeutic approach for treating KRAS-mutant CRCs and illustrate a critical convergence of EZH2 and RAS on oncogenic WNT signals, intestinal differentiation, and apoptosis.

overall_design: LOVO cells were treated with vehicle, tazemetostat (EZH2i), and/or trametinib (MEKi). Cells were pretreated with DMSO or EZH2i for 5 days, seeded into 15cm plates at 1,500,000 cells per plate, and treated with DMSO or MEKi with and without EZH2i the following day. Cells were collected 16 hours after combined treatment before onset of cell death.

first: Patrick

last: Loi

first: Kristian

last: Helin

first: Karen

last: Cichowski


title: Transcriptional characterization of ILC1 and different subsets of ILC3s lacking REV-ERBs.

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

overall_design: Refer to individual Series


title: Establishing the conditions required to initiate a cold-shock response in Streptomyces coelicolor

city: Brighton

first: Ruslan

last: Evans

state: East Sussex

address: Lewes Road

department: School of Applied Science

institute: University of Brighton

summary: RNA-seq analysis of wild type Streptomyces coelicolor A3(2) MT1110 to examine global transcriptional profile change when exposed to cold shock from 30°C to 10°C in rich liquid medium and from 30°C to 4°C on minimal solid medium.

overall_design: Comparative transcriptome analysis using RNA-seq data for wild type Streptomyces coelicolor A3(2) MT1110 exposed to cold-shock stress

first: Giselda

last: Bucca

first: Andrew

last: Hesketh

first: Colin

last: Smith


title: Single cell RNA sequencing reveals the aging associated change of ovarian macrophage populations

city: LITTLE ROCK

first: Zijing

last: Zhang

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

summary: Macrophages are important modulators of the ovarian tissue microenvironment, and are associated with the ovarian aging process. To dissect the changes of macrophages during ovarian aging, we used a combination of single cell RNA sequencing (scRNAseq) and flow cytometry to inspect the CD45+ CD11b+ myeloid cells in young (3 months old) and aged (15 months old) murine ovaries, which mainly consists of macrophages, monocytes and dendritic cells.

overall_design: CD45+Cd11b+ cells were isolated from 3 months old or 15 months old murine ovarian tissue using fluorescence assisted cell sorting (FACS). For the each age group, 3 biological replicates were included, each consists of cells harvested from two virgin C57BL/6J mice and was tagged with TotalSeq B series hashtag. The replicates from each age group were pooled before sorting and library preparation.

first: Lu

last: Huang

first: Lynae

last: Brayboy

first: Michael

last: Birrer


title: Translatome analysis by Ribosome profiling of Streptomyces coelicolor A3(2) cold-shock response

summary: Ribosome profiling analysis of wild type prototrophic Streptomyces coelicolor A3(2) MT1110 strain to examine global translational vs transcriptional profile change when exposed to cold shock from 30°C to 10°C in minimal liquid medium.

overall_design: Comparative transcriptome vs translatome analysis using RNAseq and ribosome profiling data for wild type Streptomyces coelicolor A3(2) MT1110 exposed to cold-shock stress.


title: Epigenetic array data of saliva samples in individiduals with Crohn's Disease and Ulcerative Colitis with controls

first: Laurence

middle: Bruce

last: Lovat

address: 43-45 Foley Street

department: Division of Surgery & Interventional Science

institute: University College London

type: Methylation profiling by genome tiling array

summary: We took saliva samples from 227 people with Crohn's Disease,  75 people with Ulcerative Colitis and 250 control.

overall_design: The principle design was a two group case-control study

first: Timothy

middle: C

last: Stone

first: Laurece


title: Circular Slc17a5 regulated by VLDLR/QKI pathway inhibits ocular neovascularization

city: shantou

first: xiaoqiang

last: xiao

state: Guangdong

address: North dongxia road

institute: Joint Shantou International Eye Center,Shantou University and the Chinese University of Hong Kong

overall_design: Bend.3 cells stably expressing circular Slc17a5 or empty vector (negative control) were used for RNA sequencing

first: Xiaoqiang

last: Xiao

first: Fang

last: Deng


title: Ufl1 deficiency causes skin pigmentation by u-pregulation of Endothelin-1

city: Hangzhou

first: Jian

last: Mao

address: 2318 Yuhangtang Rd

institute: Hangzhou Normal University

summary: Ufmylation (UFM1 modification) is a newly identified ubiquitin-like modification system involved in numerous cellular processes. However, the regulatory mechanisms and biological functions of this modification remain mostly unknown. We have recently reported that Ufmylation family genes have frequent somatic copy number alterations in human cancer including melanoma, suggesting involvement of Ufmylation in skin function and disease. UFL1 is the only known Ufmylation E3-like ligase. In this study, we generated the skin-specific Ufl1 knockout mice and show that ablation of Ufl1 caused epidermal thickening, pigmentation and shortened life span. RNA-Seq analysis indicated that Ufl1 deletion resulted in upregulation of the genes involved in melanin biosynthesis. Mechanistically, we found that Endothelin-1 (ET-1) is a novel substrate of Ufmylation and this modification regulates ET-1 stability, and thereby deletion of Ufl1 upregulates the expression and secretion of ET-1, which in turn results in up-regulation of genes in melanin biosynthesis and skin pigmentation. Our findings establish the role of Ufl1 in skin pigmentation through Ufmylation modification of ET-1 and provide opportunities for therapeutic intervention of skin diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Wild Type(WT) mice and skin-specific Ufl1 knockout mice ears at 3-months of age.

first: Ke

last: Wang

first: Huning

last: Xu

first: Da

last: Liu


title: GBM-37 (post-treatment tumor): control siRNA vs. NUPR1v.1 siRNA Transfected

city: Seoul

first: Sun Ha

last: Paek

address: 101, Daehak-ro, Jongno-gu

department: Neurosurgery

country: South Korea

institute: Seoul National University College of Medicine

summary: Comparing the transcriptomic profiles of GBM-37 cells treated with control and NUPR1 v.1 siRNA. Goal was to examine the effects of NUPR1 v.1 on malignant mesenchymal transformation of GBM tumor after conventional treatment

overall_design: Primary cells of GBM-37 treated with control siRNA and NUPR1v.1 siRNA were subjected for cDNA microarray analysis to examine the role of NURP1v.1 in the malignant mesenchymal transformation of GBM tumor

first: Yona

last: Kim


title: Circular Slc17a5 regulated by VLDLR/QKI pathway inhibits neovascularization

type: Non-coding RNA profiling by high throughput sequencing

summary: Investigate whether VLDLR can mediate the biogenesis of circular RNA, and whether an adaptor that bridges the VLDLR signal and the biogenesis of circular RNA .

overall_design: Bone macrophages derived from Wild type (WT),VLDLR Knockout (VLDLR-/-,KO) and ROBO4 knockout (ROBO4-/-,KO) mice ,respectively were cultured in vitro with 20ng/ml M-CSF for 14 days. Then, those cells were used for total RNA extraction with TRIZol reagent and for high throughput RNA sequencing


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [BiSulfite-seq]

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: Recent breakthroughs in single-cell genomics allow probing molecular states of cells with unprecedented detail along the sequence of the DNA. Biological function relies, however, on emergent processes in the three-dimensional space of the nucleus, such as droplet formation through phase separation. Here, we use single-cell multi-omics sequencing to develop a theoretical framework to rigorously map epigenome profiling along the DNA sequence onto a description of the emergent spatial dynamics in the nucleus. Drawing on scNMT-seq multi-omics sequencing in vitro and in vivo we exemplify our approach in the context of exit from pluripotency and global de novo methylation of the genome. We show how DNA methylation patterns of the embryonic genome are established through the interplay between spatially correlated DNA methylation and topological changes to the DNA. This feedback leads to the predicted formation of 30-40nm sized condensates of methylated DNA and determines genome-scale DNA methylation rates. We verify these findings with orthogonal single cell multi-omics data that combine the methylome with HiC measurements. Notably, this scale of chromatin organization has recently been described by super-resolution microscopy. Using this framework, we identify local methylation correlations in gene bodies that precede transcriptional changes at the exit from pluripotency. Our work provides a general framework of how mechanistic insights into emergent processes underlying   cell fate decisions can be gained by the combination of single-cell multi-omics and methods from theoretical physics that have not been applied in the context of genomics before.

overall_design: E14 mESC were cultured in 2i+LIF media. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium. 0h, 24h, and 48h after induction of 2i-release single cells were distracted and sc-NMT sequencing was performed.

first: Fabrizio

last: Olmeda

first: Tim

last: Lohoff

first: Stephen

last: Clark

first: Laura

last: Benson

first: Wolf

last: Reik

first: Steffen

last: Rulands


title: Hierarchical ZIF-8@Au cluster Nanocarriers for In Situ CAR-M programming and Immunotherapy in Prostate Cancer

status: Public on May 30 2025

city: nanjing

first: zichen

last: liang

state: jiangsu

address: Xianlin campus, Nanjing University, Qixia District

institute: nanjing university

summary: Here, we have successfully constructed a novel nano-delivery system based on the Zeolitic Imidazolate Framework-8 (ZIF-8), which revealed high CAR gene encapsulation efficiency, reduced non-specific hepatic accumulation, targeted delivery of tumor-associated macrophages (TAM) and efficient intracellular gene transfection efficiency enable the in-situ construction of CAR-M cells. Meanwhile, the co-delivery of the IFN-γ and CAR genes not only maintains the specific killing and phagocytic activity of CAR-M against tumor cells but also activates the adaptive immunity, inducing excellent anti-tumor efficacy in a prostate cancer mouse model. In summary, this strategy provides a novel approach for the systematic in vivo editing of CAR-M.

overall_design: The obtained bone marrow-derived macrophages were transfected with PCI plasmid and PC plasmid via our nanocarriers, respectively, and then incubated with the cell incubator at 37 ° C for 48h and then collect these cells. There were two parallel experimental groups in each group.The RNA was extracted by Trizol method, and the library was constructed using Fast Rna-Seq Lib Prep Kit V2 (Cat.No.RK20306). Transcriptome related data of these macrophages were generated by deep sequencing, in triplicate, using Illumina NovaSeq X Plus. RNA samples were subjected to rigorous quality control through an Agilent 2100 bioanalyzer. PCI plasmid structure include PSMA-CAR-IFN-γ, while PCI plasmid structure just include PSMA-CAR. PSMA is the abbreviation of prostate cancer-specific antigen, CAR is the abbreviation of chimeric antigen receptor, IFN-γ is the abbreviation of interferon-γ.

first: Zichen

last: Liang

first: Rui

first: Yihan

last: Chen

first: Zehui

last: Zhang

first: Mengyuan

last: He

first: Luchen

last: Sun

first: Pingping

last: Shen

first: Nanfei

last: Yang


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates


title: RNA Sequencing Analysis of Osteoclast Precursor Cells under Dexamethasone Stimulation

city: Jinan

first: Tao

last: Yuan

address: Central District: No. 324, Jingwu Weiqi Road, Huaiyin District

institute: Shandong University

summary: Glucocorticoid-induced osteonecrosis of the femoral head (GIONFH) is a refractory joint disease caused by prolonged and excessive use of glucocorticoids (GCs). Excessive osteoclast activation has been implicated in the pathological bone erosion of GIONFH. Our previous study found that dexamethasone (10-8M) stimulation significantly enhances osteoclast formation in vitro. To identify therapeutic targets for GIONFH by characterizing glucocorticoid-driven transcriptional alterations in osteoclastogenesis, we performed RNA sequencing on osteoclast precursor cells (OPCs) under RANKL (25ng/ml) and Dex condition (treated with RANKL (25ng/ml) and Dex(10-8M) ) for 24 hours.

overall_design: In this study, OPCs derived from bone marrow of six-month-old male C57BL/6J mice were treated under RANKL and Dex conditions for 24 hours, with 6 biological replicates per group.


title: COMMD4, a novel driver for skin cutaneous melanoma progression via targeting p85 to activate PI3K/Akt signaling

city: Lanzhou

first: Xiaoqiang

last: Liu

address: No. 82, Cuiyingmen, Linxia Road, Chengguan District

institute: The Second Clinical Medical College of Lanzhou University

summary: Skin cutaneous melanoma (SKCM), the most aggressive form of cutaneous malignancy globally, remains poorly understood in terms of its molecular drivers. Although the copper metabolism MURR1 domain (COMMD) protein family has been associated with oncogenesis, its functional relevance in SKCM is undefined.

overall_design: In this study, we identified COMMD4 as a prognostic biomarker upregulated in SKCM tissues and correlated with adverse clinical outcomes. COMMD4 knockout (COMMD4-KO) impaired proliferative, migratory, and invasive capacities of SKCM cells in vitro and suppressed xenograft tumor growth in vivo. Mechanistically, COMMD4 deficiency induced G2/M phase arrest by disrupting the p21-CDK1/cyclin B1 axis and impeded epithelial-mesenchymal transition (EMT). We further demonstrated that COMMD4 directly interacts with the p85 regulatory subunit to activate PI3K/Akt signaling to drive G2/M transition and EMT. Reconstitution of PI3K/Akt signaling in COMMD4-KO cells rescued these oncogenic phenotypes. Through integrative Connectivity Map analysis and functional validation, we identified triamterene as a pharmacological inhibitor targeting the COMMD4-PI3K/Akt axis, which effectively suppressed SKCM progression in vitro and vivo. Our findings establish the COMMD4-PI3K/Akt axis as a critical regulator of SKCM progression and propose triamterene repurposing as a promising therapeutic strategy against SKCM


title: Transcriptional responses to Prevnar-13 vaccination in humans

city: Palo Alto

first: Dmitri

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: Thus dataset includes transcriptional profiling data at the pre-vaccination baseline and day 7 post vaccination.

overall_design: Double center, mechanistic study of immune responses to Prevnar-13 vaccination in humans

first: B

last: Pulendran

first: D


title: Transcriptional profiling of yeast to hyphae and hyphae to yeast transitions for Histoplasma strains differing in chromosome copy number.

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary: Heritable phenotypic switches are fundamental to the ability of cells to respond to specific conditions. Such switches are key to the success of environmental pathogens, which encounter disparate conditions as they transition between the environment and host. We determine that the copy number of chromosome seven in the thermally dimorphic fungus Histoplasma dramatically affects the rate of transition. Though Histoplasma is haploid, a second copy of this chromosome is present in natural isolates of multiple Histoplasma species and is gained and lost at a high rate. Cells carrying two copies of this chromosome exhibit aspects of the environmental transcriptome even under host-like conditions and have a competitive advantage in the transition to the environmental form. Conversely, these cells are considerably less virulent than euploid cells and have a competitive disadvantage in the mouse model of infection. Chromosome seven contains a previously unstudied transcription factor that, when overexpressed in euploid Histoplasma, is sufficient to promote some of the key phenotypes of aneuploidy. We hypothesize that rapid gain and loss of this chromosome benefits Histoplasma by increasing phenotypic variation, thus helping populations of cells survive abrupt transitions between environment and host.  This series contains expression profiling of yeast to hyphae and hyphae to yeast transitions for strains differing in chromosome seven copy number.

overall_design: Three time points were collected for three replicates of two genotypes for transitions in two directions for a total of 36 samples.

first: Sarah

last: Heater

first: Anita

last: Sil


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq]

first: Felix

last: Krueger

first: Fabrizio

last: Olmeda

first: Tim

last: Lohoff

first: Stephen

last: Clark

first: Laura

last: Benson

first: Wolf

last: Reik

first: Steffen


title: Transcriptome profiling of RHD6-regulated genes under Al stress

city: Qingdao

first: Zhong-Bao

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

summary: To further better understand the downstream responsive transcriptome networks of RHD6 in response to Al stress, the transcriptional profile of WT and rhd6-1 mutant in the absence or presence of Al stress was examined using RNAseq.

overall_design: Six day old wild-type plants and rhd6-1 mutant were treated with and without Al treatment for 6 h.


title: Contrasting functions of CD73 and adenosine in CD8+ T cell exhaustion

city: SANTIAGO

first: Daniela

last: Sauma

state: Región Metropolitana

address: Las Palmeras 3425

department: Facultad de Ciencias

country: Chile

institute: Universidad de Chile

summary: T cell exhaustion is a state of functional decline in T cells, driven by chronic antigen exposure and inhibitory signals within the tumor microenvironment. Exhausted CD8+ T cells (Tex) derive from precursor exhausted T cells (Tpex), a self-renewing population responsible for the proliferative burst observed in anti-PD-1 therapies. Exhausted cells are exposed to adenosine in the tumor, yet the role of the CD73/adenosine axis and Tpex/Tex differentiation remains unclear. Using an in vitro model for CD8+ T cell exhaustion, we found that CD73 expression increased during Tpex formation and that its expression is negatively correlated with Tex generation. CD73-deficient (CD73KO) CD8⁺ T cells showed impaired activation and reduced progression to Tex. Moreover, we demonstrated that CD73 promotes transcriptional expression of the adenosine receptor A2A (A2AR) and the differentiation into IFNγ/TNFα-producing Tex cells. RNAseq analysis of exhausted CD73KO CD8+ T cells showed a more stem-like transcriptomic profile and enrichment in genes associated with the immune response than their WT counterpart. In vivo, co-transfer of naïve CD73 KO and WT tumor antigen-specific CD8⁺ T cells into tumor-bearing mice showed increased Tpex frequency and numbers among CD73KO cells in tumors. Conversely, in vitro exhaustion in the presence of A2AR agonists decreased Tex frequency and activation/exhaustion markers, while increasing CD73 and CD62L, markers associated with stemness. Supporting this, A2AR blockade with SYN115 in tumor-bearing mice reduced Tpex markers and increased Tex differentiation. Altogether, our data suggest CD73 promotes Tpex-to-Tex differentiation, whereas adenosine-A2AR signaling supports Tpex maintenance in the tumor microenvironment.

overall_design: RNA-seq profiling of wild-type and CD73 KO OT-I cells after 5 days of stimulation with the SIINFEKL peptide (10 ng/mL) in the presence of IL-7 (5 ng/mL) and IL-15 (5 ng/mL) to induce in vitro exhaustion. Live in vitro-exhausted OT-I cells were sorted before RNA extraction.

first: Juan

last: Saavedra-Almarza

first: Solange

last: Gouët

first: Felipe

last: Malgue

first: Catalina

last: Bascuñan

first: Camilo

last: Villaman

first: Moira

last: García-Gómez

first: Andrés

last: Hernández-Oliveras

first: Javiera

last: Reyes-Alvarez

first: José

last: Corrales-Bermúdez

first: Joaquín

last: De la Rosa

first: Alberto

last: Martin

first: Álvaro

last: Lladser

first: Mario

last: Rosemblatt

first: María Rosa

last: Bono


title: Distinct Characteristics of Brain Metastasis in Lung Adenocarcinoma: Development of High-Confidence Cell Lines

city: Sapporo

first: Jintao

last: He

state: Hokkaido

address: N15, W7, Kita-ku

department: Department of Cancer Pathology

institute: HOKKAIDO UNIVERSITY

summary: Lung cancer is a leading cause of cancer-related deaths worldwide, with brain metastasis occurring in approximately 30-55% of patients, particularly in lung adenocarcinoma. Due to the challenges in obtaining genuine brain metastasis tumor cells, researchers commonly use nude mouse models to establish brain metastasis cell lines, though traditional methods have limitations such as high costs, lengthy timeframes, and the need for specialized imaging equipment. To address these issues, we developed an improved approach by performing low cell number circulating intracranial injections (500-4000 cells) in nude mice, successfully establishing the H1975-BM1, BM2, and BM3 cell lines. Through RNA sequencing and bioinformatics analyses, we identified transcriptomic differences among these cell lines, revealing that H1975-BM1 cells primarily exhibit stem cell function and migration characteristics, while H1975-BM3 cells display enhanced chemotaxis, cell adhesion, and cytokine secretion associated with interactions. Experimental validation, including Transwell assays, CCK8, cell adhesion assays, and subcutaneous tumor implantation in nude mice, further confirmed these findings, with H1975-BM3 forming larger tumors and a more pronounced secretion cystic cavity. In conclusion, our improved methodology successfully established high-confidence brain metastasis lung adenocarcinoma cell lines, elucidating distinct transcriptomic and functional characteristics at different stages of brain metastasis progression.

overall_design: Based on the EGFR-mutant lung adenocarcinoma cell line H1975, this study established new cell lines with brain metastasis characteristics. Tumor cells were injected intracranially into nude mice, and when the mice experienced a body weight loss of more than 20%, it was considered the endpoint. Tumor tissues were then extracted and cultured in vitro, followed by another round of intracranial injection. This process was repeated three times, with injections of 500, 4000, and 4000 cells, respectively, to establish the H1975-BM1, H1975-BM2, and H1975-BM3 cell lines.

first: Zen-ichi

last: Tanei

first: Shinya

last: Tanaka


title: Inhibiting FOXM1 Promotes Polyploidization and Metabolic Maturation in Human iPSC-Derived Hepatocytes by Modulating the Wnt/β-Catenin Pathway

city: Sao Paulo

first: Kayque

last: Alves Telles Silva

address: 106 Matao St.

country: Brazil

institute: University of Sao Paulo

summary: Differentiating induced pluripotent stem cells (iPSCs) into hepatocytes represents a key advancement in regenerative medicine and disease modeling. However, existing protocols mainly produce fetal cells, limiting accurate replication of liver functionality. Topoisomerase II (TOP2) and its transcription factor, forkhead box M1 (FOXM1), are silenced during late liver embryonic development; however, their roles in hepatocyte differentiation remain unexplored. We examined the effects of TOP2 and FOXM1 inhibition on hepatocyte differentiation. Subtoxic TOP2 inhibition reduces nuclear chromatin condensation without causing DNA damage. RNA-seq analysis showed that TOP2 inhibition induced cell cycle arrest in a TOP2A-selective manner with FOXM1 downregulation. ATAC-seq validation demonstrated that TOP2A inhibition decreases chromatin accessibility and modulates the Wnt/β-catenin pathway. Proteomic analysis revealed that FOXM1 inhibition modulated TOP2A expression, replicated TOP2A-mediated cell cycle arrest, and reduced the levels of fetal hepatocyte proteins (HBG1/2, UGT2B7, and AFP). Prolonged FOXM1 inhibition leads to hepatocyte polyploidization, increased CYP450 activity, and improved lipid metabolism. We demonstrated that FOXM1 inhibition is necessary for terminal differentiation of human iPSC-derived hepatocytes. This study suggests a role for FOXM1 and TOP2A in liver development, regeneration, and disease.

overall_design: RNA-seq profiling of iPSC-derived hepatocytes (control and etoposide-treated) and primary human hepatocytes at day 5 of etoposide treatment.

first: Kayque Alves

last: Telles-Silva


title: TRMT10A associated RNA targets

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

summary: Dynamic regulation of modifications in mRNA and tRNA is a significant regulatory mechanism in gene expression. Among those RNA species, transfer RNA (tRNA) is the most extensively modified. tRNA modifications are known to be critical for the stability and translation fidelity of tRNA molecules. TRMT10A is tRNA modifying enzymes and is a S-adenosylmethionine (SAM)-dependent methyltransferases that installs N1-methylguanosine (m1G) in tRNAs at the ninth position. Previous efforts in characterizing the tRNA substrates of TRMT10A were done in yeast. The entire substrate repertoire of TRMT10A in human cells has not been fully revealed, although tRNAGln and tRNAGly are confirmed as substrates of human TRMT10A. Mutations in TRMT10A have been observed in patients with young-onset diabetes syndrome and primary microcephaly-mild intellectual disability, and recent studies suggested that deficiency of TRMT10A can induce apoptosis in pancreatic cells, consistent with the correlation with diabetes. However, the mechanism by which deficiency of TRMT10A is linked to the disease phenotype remains enigmatic. Here, we identified the modifications on RNA species influenced by TRMT10A by using a combination of sequencing and biochemical tools.

overall_design: m6A IP seq and CLIP seq

first: Kathy

middle: F


title: Transcriptomic analysis of pre- and post-treatment GBM tumors (GBM-28 vs. GBM-37)

first: Sun Ha

last: Paek

summary: Finding a novel prognostic marker and therapeutic target for aggressive GBM is necessary. By analyzing pre- and post-treatment tumors from a GBM patient who experienced a very aggressive tumor recurrence after receiving concurrent chemoradiotherapy with temozolomide, we discovered a novel prognostic marker for aggressive mesenchymal GBM

overall_design: Primary cell cultures (< 5 passages) derived from brain tumor tissues were subjected for cDNA microarray analysis to analyze the transcriptomic alteration upon conventional treatment and to discover a novel key regulator responsible for such an aggressive tumor progression

first: Yona

last: Kim


title: Cold-induced suppression of myogenesis in skeletal muscle stem cells contributes to delayed muscle regeneration during hibernation

city: Hiroshima

first: Mitsunori

last: Miyazaki

state: Hiroshima

address: 1-2-3 Kasumi, Minami-Ku

department: Graduate School of Biomedical and Health Sciences

institute: Hiroshima University

summary: Mammalian hibernators experience profound cold stress and prolonged physical inactivity during torpor periods; however, it is unclear how skeletal muscle stem cells (satellite cells; SCs) respond to these challenges. In this study, we demonstrate that SCs from a mammalian hibernator, Syrian hamster exhibit remarkable resistance to cold-induced cell death, which is associated with intrinsically higher expression of the antioxidant enzyme GPX4, which likely contributes to the suppression of ferroptosis. RNA-seq analysis revealed widespread downregulation of myogenesis-related genes following cold exposure, which suggests suppression of the myogenic program. Consistently, SCs exposed to cold stress exhibited reduced activation and differentiation capacities upon subsequent rewarming, with an increased number of quiescent Pax7-positive/MyoD-negative cells. Muscle regeneration was markedly delayed during hibernation, accompanied by decreased SC activation and macrophage infiltration, suggesting that cold-induced suppression of SC function underlies limited regenerative capacity in hibernating hamsters. Our results provide insight into the unique physiology of mammalian hibernators: SC viability is preserved, whereas regenerative activity is selectively suppressed during hibernation.

overall_design: Satellite cells (SCs) isolated from Syrian hamsters were cultured at 37°C for 48 hours after plating, followed by 24-hour incubation in GM-HEPES at 37°C, and then exposed to 4°C for 24 hours. Total RNA was extracted before and after cold exposure for RNA sequencing.

first: Tatsuya

last: Miyaji


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [shsy5y-curve-kd-075-vs-ctl]

city: Leuven

first: Sam

last: Bryce-Smith

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: KU Leuven

summary: Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3’ end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a bioinformatic pipeline to reliably identify distinct APA event types: alternative last exons (ALE), 3’UTR extensions (3’Ext) and ‘ composite ’ intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3’Exts occur in multiple transcription factors, such as ELK1 , SIX3, and TLX1, and lead to an increase in RNA stability. 3’Exts are localised to the cytoplasm and neurites and translated leading to an increase in wild-type protein levels. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.

overall_design: short-read bulk RNA-sequencing of the SH-SY5Y neuroblastoma cell line with and without TDP-43 knockdown (3 controls, 3 KD samples)

first: Matteo

last: Zanovello

first: Matthew

last: Keuss

first: Anna-Leigh

last: Brown

first: Alla

last: Mikheenko


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [shsy5y-chx-tdpkd-vs-ctl]

overall_design: short-read bulk RNA-sequencing of the SH-SY5Y neuroblastoma cell line with and without TDP-43 knockdown (4 controls, 4 knockdowns)


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [humphrey-i3-cortical]

overall_design: short-read bulk RNA-sequencing of day 30 IPSC-derived cortical neurons with and without TDP-43 knockdown (6 controls, 6 TDP-43 knockdowns)

first: Jack

last: Humphrey


title: RNA-seq analysis of MLO-Y4 cells under hypoxic conditions

city: Sendai

first: Kohei

last: Narita

state: Miyagi

address: 4-1 Seiryo-machi, Aoba-ku

department: Dentistry

institute: Tohoku University

summary: To investigate the effects of hypoxia on osteocytes, we cultured MLO-Y4 osteocytic cells under normoxic (20% O₂) and hypoxic (2% O₂) conditions. We then performed gene expression profiling analysis using RNA-seq data obtained from these cells. Differential expression analysis revealed that Lipocalin 2 (LCN2) was one of the most significantly upregulated genes under hypoxic conditions.The dataset provides insights into the transcriptional response of osteocytes to hypoxic stress.

overall_design: RNA-seq profiling of MLO-Y4 osteocytic cells cultured under normoxic (20% O₂) and hypoxic (2% O₂) conditions for 24 hours. Differential gene expression analysis was performed to identify hypoxia-responsive genes in osteocytes.

first: Fumitoshi

last: Ohori

first: Aseel

last: Marahleh

first: Jinghan

last: Ma

first: Jiayi

last: Ren

first: Angyi

last: Lin

first: Ziqiu

last: Fan

first: Kou

last: Murakami

first: Hideki

last: Kitaura


title: Polysome profiling of mRNA translation in neuroblastoma cells in response to asparagine/alanine supplement

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma, the most common extracranial solid malignancy in infants and young children, originates from aberrant neural crest cells and accounts for 10-15% of childhood cancer deaths. However, the underlying mechanisms regulating neuroblastoma progression remain to be determined. To investigate the mechanisms regulating tumorigenesis and aggressiveness, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the polysome profiling of mRNA translation in neuroblastoma cells in response to asparagine/alanine (Asn/Ala) supplement. The results showed that 618 and 566 translating mRNAs were respectively elevated or reduced in SK-N-BE(2) after Asn/Ala treatment. Furthermore, we validated the polysome profiling results by western blot with high identity. Overall, our results provided fundamental information about the mRNA translation changes in response to Asn/Ala treatment in human neuroblastoma cells, and these findings will help us understand the pathogenesis of neuroblastoma progression.

overall_design: Total RNA of cells treated with asparagine/alanine (Asn/Ala) supplement or deprivation was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Wuhan SeqHealth Technology Co., Ltd. (Wuhan, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Liduan

last: Zheng


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [sknbe2-curve-kd-1-vs-ctl]

first: Sam

last: Bryce-Smith

overall_design: short-read bulk RNA-sequencing of IPSC-derived cortical neurons and neuroblastoma cell lines (SH-SY5Y and SK-N-BE(2)) with and without TDP-43 knockdown


title: Transcriptional profiling of HYF1 and HYF2 increased copy number strains.

first: Mark

last: Voorhies

summary: Heritable phenotypic switches are fundamental to the ability of cells to respond to specific conditions. Such switches are key to the success of environmental pathogens, which encounter disparate conditions as they transition between the environment and host. We determine that the copy number of chromosome seven in the thermally dimorphic fungus Histoplasma dramatically affects the rate of transition. Though Histoplasma is haploid, a second copy of this chromosome is present in natural isolates of multiple Histoplasma species and is gained and lost at a high rate. Cells carrying two copies of this chromosome exhibit aspects of the environmental transcriptome even under host-like conditions and have a competitive advantage in the transition to the environmental form. Conversely, these cells are considerably less virulent than euploid cells and have a competitive disadvantage in the mouse model of infection. Chromosome seven contains a previously unstudied transcription factor that, when overexpressed in euploid Histoplasma, is sufficient to promote some of the key phenotypes of aneuploidy. We hypothesize that rapid gain and loss of this chromosome benefits Histoplasma by increasing phenotypic variation, thus helping populations of cells survive abrupt transitions between environment and host.  This series contains expression profiling of increased copy number constructs for the HYF1 and HYF2 transcription factors.

overall_design: Three yeast culture replicates for each of three genotypes for a total of 9 samples.

first: Sarah

last: Heater

first: Anita

last: Sil


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [zanovello-i3-cortical-tdpkd-vs-tdpctl]

overall_design: short-read bulk RNA-sequencing of IPSC-derived cortical neurons with and without TDP-43 knockdown

first: Matteo

last: Zanovello

first: Matthew

last: Keuss

first: Anna-Leigh

last: Brown

first: Alla

last: Mikheenko


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [slamseq-i3-cortical]

overall_design: SLAM-seq of IPSC-derived cortical neurons with and without TDP-43 knockdown. Day 7 neurons were cultured with a uridine analogue 4sU to label newly synthesised RNA over a time course (sampled at 0, 1, 4, 8, 12 and 24hrs). Isolated RNA is treated with iodoacetamide to alkylate the incorporated 4sU (to mimic a cytosine) and then standard bulk short-read RNA-seq library preparation is performed.

last: Hill