title: Experimental study of mRNA from human dental pulp tissue for late postmortem interval estimation

status: Public on Nov 30 2025

city: Changsha

first: Qun

last: Tang

address: Yuelu District

country: China

institute: Hunan University of Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: This study investigates mRNA degradation in human dental pulp to explore its utility for estimating the late postmortem interval (LPMI). Morphological changes in pulp tissue at 0, 7, 14, 21 and 28 days postmortem were observed via HE staining, showing progressive cellular degradation. High-throughput sequencing of samples at 0, 7, and 21 days identified candidate mRNAs. Five mRNA biomarkers were obtained , namely SRSF5, FGFR1, ACADVL, FOS, and LRP1. Their expression levels at 0, 3, 7, 10, 14, 21 and 28 days were quantified using RT–qPCR with 18S rRNA as the reference gene. Results demonstrated a consistent decrease in all five mRNAs over time. Mathematical models correlating mRNA levels with LPMI were established. Multi-index models exhibited superior fitting accuracy and predictive performance compared to single-index models, as validated using samples from 10, 18 and 25 days postmortem intervals, indicating greater practical applicability. This approach provides a new direction for forensic LPMI estimation research and contributes to the development of forensic pathology.

first: Muxuan

last: Yin

first: Haibo

last: Gao

first: Juncai

last: Chen

first: Longqi

last: Zou

first: Xinru

last: Wang

first: Shuhan

last: Lu

first: Huan

last: Li


title: SOS components differentially regulate seed germination and seedling growth under saline condition in Arabidopsis

city: Seoul

first: DAMI

last: YANG

address: Cheonpa-ro 47 gil 100, Yongsan-gu

department: Department of Biological Sciences

country: South Korea

institute: Sookmyung Women's University

summary: Seed germination is an important process that begins new life in plant. To ensure that seedlings grow under optimal condition after germination, seed germination should be precisely regulated by endogenous and environmental factors. Salinity is the major abiotic stress that often adversely impacts plants by inhibiting seed germination, growth and development. Comparative transcriptome analyses of salt-treated seedlings and seeds revealed that although some of the well-known salt-stress marker genes, including RD29a and DREB2A were not induced under salt, genes that can be categorized in similar GO terms involving with stress responsiveness are changed both in seeds and seedlings in response to salt treatment.

overall_design: Examination of mRNA expression patterns was conducted in imbibed seeds of Arabidopsis Col-0 and the serk1-1 mutant. Col-0 and serk1-1 seeds were incubated in liquid MS medium and MS medium supplemented with 200 mM NaCl for 24 hours.

first: Dami

last: Yang

first: Yunmi

last: Ha

first: Myeong Min

last: Lee

first: Kyoung Hee

last: Nam


title: Endometrial gland secretions induce metabolic reprogramming and immunomodulatory signalling in trophoblast

city: Manchester

first: Peter

last: Ruane

state: England

address: 5th Floor Research, St Mary's Hospital, Oxford Road

country: United Kingdom

institute: University of Manchester

summary: The implanting embryo and developing placenta interface with the endometrium through a multinuclear trophoblast layer, syncytiotrophoblast (STB), which plays critical barrier, transport, immunomodulatory and endocrine roles throughout pregnancy. Understanding trophoblast and endometrial biology has recently been accelerated through sophisticated stem cell and organoid models, however few studies have combined these models to explore maternal-embryo communication. Here, we combined organoid models of secretory phase and decidual endometrial glands with trophoblast stem cell-derived STB to investigate signalling from maternal glands to the developing placenta. Luminal secretions collected from endometrial organoids by centrifugation were added to STB cultures and transcriptome analysis revealed that both secretory phase and decidual organoid secretions had profound effects on STB gene expression, inducing 3279 and 2634 differentially expressed genes (DEG), respectively (padj<0.05, >50% ≥1 log2 fold change). Gene set enrichment analysis of shared DEG (1926 genes) suggested upregulation of immune signalling and downregulation of mitochondrial respiration. Secretory and decidual secretions led to increased basal and maximal respiration (p<0.01) but reduced respiratory spare capacity (p<0.05) in STB, while glycolytic activity was also increased (p<0.05) together with increased expression of rate-limiting glycolysis enzymes HK1, HK2, PFKP and PKM (padj<0.03). Integrating cytokine array analysis of organoid secretions with upstream regulator analysis of STB DEG identified VEGFA and CSF1 as secretory products that might regulate mitochondrial and glycolytic genes, respectively, whereas secreted LCN2 and IL1A were upstream of immunomodulatory genes. Regulation of both immunomodulatory and metabolic gene sets was predicted for secreted CSF1 and EGF. The findings suggest that STB is highly responsive to endometrial gland secretions, which induce metabolic reprogramming likely to result in a more glycolytic phenotype in vivo as well as stimulating STB to modulate maternal immune responses. Endometrial gland signals thus shape trophoblast development to support successful establishment of pregnancy.

overall_design: RNA-seq profiling of TSC and TSC-derived STB treated with Day 8 STB organoid secretions

first: Daman

middle: J

last: Adlam

first: Isabella

last: Smith

first: Sam

last: Kebbe

first: Isabel

middle: M

last: Paterson

first: Terence

last: Garner

first: Adam

last: Stevens

first: Roger

middle: G

last: Sturmey

first: John

middle: D

last: Aplin

middle: T


title: Extracellular matrix-driven antagonism: Bacillus ECM components modulate Botrytis physiology and counterdefence

city: Malaga

first: Alicia

last: Pérez Lorente

address: Av Louis Pasteur 49. IHSM

country: Spain

institute: University of Malaga

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of Bacillus subtilis growing in the presence of Botrytis cinerea. In addition, we study  the transcriptomic response of Botrytis cinerea when cocultured with Bacillus subtilis and also the transcriptomic response of Botrytis treated with purified TasA and Fengycin after 6h

sample_organism:
Bacillus subtilis
Botrytis cinerea

platform_organism:
Bacillus subtilis
Botrytis cinerea

overall_design: Botrytis-Bacillus coculture for 6h and Botrytis treated with TasA and Fengycin for 6h. All in liquid media, PDB cultured at 28 °C

first: Alicia Isabel

first: Carlos

last: Molina Santiago

first: David

last: Vela

first: Paolo

last: Stincone

first: Abzer

last: Pakkir Shah

first: Jesus

last: Hierrezuelo

first: Daniel

last: Petras

first: Diego

last: Romero


title: ZNF865 (BLST) Regulates Human Cell Senescence and DNA Damage [RNA-seq]

city: Salt Lake City

first: Jason

last: Gertz

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

country: USA

institute: University of Utah

summary: Senescence has been shown to contribute to the progression of aging related diseases including degenerative disc disease (DDD). However, the mechanisms regulating senescence in the intervertebral disc (IVD) and other tissues/diseases remain poorly understood. Recently, in a CRISPRa genome-wide screen, our lab identified a previously uncharacterized zinc finger protein, ZNF865 (BLST), that regulates a wide array of genes related to protein processing, cell senescence and DNA damage repair. Here, we demonstrate that ZNF865 expression is correlated with age and disease state in human patient IVD samples and mouse IVD.  Utilizing CRISPR-guided gene modulation, we show that ZNF865 is necessary for healthy cell function and is a critical protein in regulating senescence and DNA damage in intervertebral disc cells, with implications for a wide range of tissues and organs. We also demonstrate that downregulation of ZNF865 induces senescence and upregulation mitigates senescence and DNA damage in human nucleus pulposus (NP) cells. Importantly, upregulation of ZNF865 shifts the chromatin landscape and gene expression profile of human degenerative NP cells towards a healthy cell phenotype. Collectively, our findings establish ZNF865 as a novel modulator of genome stability and senescence and as a potential therapeutic target for mediating senescence/DNA damage in senescence related diseases and disorders.

overall_design: RNA-seq was used to identfiy differentially expressed genes in HEK 293 and ASC cell lines treated with either a non-targeting control (NTC) gRNA or CRISPRa to activate ZNF865 (VPR ZNF865) as well as healthy (hNPC), degenerative (dhNPC), and degenerative with ZNF865 activation (ZNF865 VPR dhNPC) nucleus pulposis cells obtained from human donors.

first: Christian

last: Lewis

first: Hunter

last: Levis

first: Jacob

last: T. Polaski

first: Robby

last: D. Bowles


title: Cataloguing the postnatal small intestinal transcriptome during the period of susceptibility to necrotizing enterocolitis

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary: In the first postnatal month, the developing mouse intestine shifts from an immature to a mature intestine that will sustain the organism throughout the lifespan. Here, we surveyed the mouse intestine in C57Bl/6 mice by RNA-Seq to evaluate the changes in gene expression over time from the day of birth through 1 month of age in both the duodenum and ileum. We analyzed gene expression for changes in gene families that correlated with the periods of NEC susceptibility or resistance. We highlight that increased expression of DNA processing genes and vacuolar structure genes, tissue development and morphogenesis genes, and cell migration genes all correlated with NEC susceptibility, while increases in immunity gene sets, intracellular transport genes, ATP production, and intracellular metabolism genes correlated with NEC resistance. Using trends identified in the RNA analyses, we further evaluated expression of cellular markers and epithelial regulators, immune cell markers, and adenosine metabolism components. We confirmed key changes with qRT-PCR and immunofluorescence. In addition, we compared some findings to humans using human intestinal biopsies and organoids. This dataset can serve as a reference for other groups considering the role of single molecules or molecular families in early intestinal and postnatal development.

overall_design: Small intestinal samples were collected from 0 day, 2d, 4d, 6d, 8d, 2 week, 3wk, 4wk old C57Bl6/J mice. For the purposes of RNA-Seq, 2cm of proximal intestine immediately after the pylorus was collected for the “duodenum” sample and 2cm of distal intestine immediately before the ileocecal junction was collected for the “ileum” sample. The library was prepared by the Dana Farber Next Generation Sequencing Core Facility using a KAPA library quantification kit (Roche). Sequencing was done on an Illumina NovaSeq 6000 with total RNA.

first: Amy E.

last: O'Connell

first: Radhika

last: Khetani


title: Intestinal epithelial cell EphB4 deficiency on high fat diet-induced obesity

city: Beijing

first: Xiaowei

last: Xing

state: Beijing

address: No.1 Xian Nong Tan St. Xi Cheng District

department: Institute of Materia Medica

institute: Peking Union Medical College

summary: High-fat diets (HFD) exacerbate excessive lipid absorption by compelling the small intestine (SI) to take in redundant calories, yet host-encoded mechanisms are not fully explored. Previous research demonstrated that intestinal group 3 innate lymphoid cell (ILC3)–interleukin-22 (IL-22)–phosphorylated signal transducer and activator of transcription 3 (pSTAT3) axis fluctuates with feeding rhythms and engages in nutrient absorption. We found that prolonged HFD feeding enhances this axis in the proximal SI, leading to adaptively increased lipid absorption. Notably, we identified Eph receptor B4 (EphB4), an intestinal epithelial regulator that interacts with ILC3s microbiota-independently, thereby boosting pre-meal IL-22 secretion and subsequent lipid absorption, elucidating its crucial role in the interplay between diet, immune axis, and metabolism. In HFD-induced obesed mice, deleting EphB4 in intestinal epithelial cells (IECs) reduced proximal intestinal lipid absorption, improved obesity and metabolic disorders.

overall_design: To determine the relevance of intestinal epithelial cell EphB4 deficiency in obesity, we generated EphB4 flox/flox (F) mice and conditional IECs EphB4 knockout (KO) mice. 9 of EphB4 flox/flox (F) mice and 7 of EphB4 IEC-knockout (KO) mice, both 8 weeks old, were under a 19-week regimen of high fat diet (HFD). Proximal small intestine tissue from these mice were collected and subjected to RNA sequencing.

first: Xingfeng

last: Liu

first: Yibing

last: Chen

first: Shaocong

last: Hou

first: Zhenhe

last: Wang

first: Caiyi

first: Jingwen

first: Wenjia

last: Fan

first: Caihong

first: Chunxiao

last: Ma

first: Yanjun

last: Wan

first: Bing

last: Cui

first: Pingping

last: Li


title: Comprehensive transcriptome analysis of the skin in epidermis-specific Nampt cKO mice.

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: Nicotinamide adenine dinucleotide (NAD⁺) is essential for cellular metabolism, DNA repair, and stress response. NAD+ is synthesized from nicotinamide, nicotinic acid (collectively termed niacin), and tryptophan. In humans, deficiencies in these nutrients result in pellagra, marked by dermatitis, diarrhea, and dementia. The dermatitis associated with pellagra typically manifests as photodermatosis in sun-exposed areas. This study examined the effects of NAD+ deficiency on skin homeostasis using epidermis-specific Nampt conditional knockout (cKO) mice. These mice displayed substantial NAD⁺ depletion, reduced poly (ADP-ribose) polymerase (PARP) activity, and increased DNA damage, indicated by γH2AX accumulation. Nampt cKO mice also developed spontaneous skin inflammation and epidermal hyperplasia. Here, we provide gene expression profiling of skin tissues using the RNA sequencing for identifying changes in gene expression of Nampt-cKO mice.

overall_design: The mRNA profile of  skin tissues was generated by RNA sequencing using the Illumina NovaSeq 6000  (Illumina).

first: Taiki

last: Seki

first: Takashi

last: Nakagawa


title: Intestinal Microbiome in Response to Air Pollutant Exposure in Pregestational and Gestational Murine Females and their Offspring

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary: This study aimed to examine the impact of intranasal exposure to air pollutants during eight weeks of preconception, periconception, and gestation (days 0 to 18) on the intestinal microbial composition, diversity, and metagenomically inferred functional pathways. The investigation focused on adult female mice during pregestational and late gestational periods (G19), as well as male and female postnatal suckling offspring (PN21), comparing the results with age- and sex-matched control groups (CON).

overall_design: 16S rDNA microbiota profiling was conducted using fecal samples collected from non-pregnant, age-matched females, GD19 pregnant mothers, and male and female PN21 pups just prior to weaning.

first: Amit

last: Ganguly

first: Tien

last: Dong

first: Venu

last: Lagishetty

first: Jonathan

last: Jacobs

first: Sherin

middle: U

last: Devaskar


title: p53 regulates pluripotency of embryonic stem cells via microenvironmental fibronectin-integrin interaction

city: 沈阳市

first: Zonghua

state: 辽宁省

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

institute: Northeastern University

summary: Feeders make necessary contributions to maintaining pluripotency and have been widely used for culturing embryonic stem cells (ESCs).  Here, we showed p53 in feeders is required for ESC self-renewal. Following ablation of p53 in feeders, ESCs attenuated their pluripotent characteristics, with hyperactivation of ERK.  We established that p53 in feeders transcriptionally actives MMP-2 or -9, thereby promoting degradation of fibronectin, preventing its interaction with integrins in ESCs and subsequent activation of integrin/FAK/ERK pathway.  Based on these, we developed a new 2i or 1i system for ESC culture.  Moreover, treatment of human pluripotent stem cells, or tissue stem cells with a fibronectin-integrin inhibitor strongly increased Sox2 and Oct4 levels.  Our findings demonstrate a cross-cell function for p53 in regulating pluripotency, reveal a novel feeder-action mechanism beneficial for developing new stem cell culture conditions.

overall_design: For samples of ES cells cultured on control and p53-defective feeders, as well as Control and p53-defective feeders samples, ES cells cultured on control feeders but removal of feeders and replaced feeders with integrin α5β1 inhibitor ATN161 in culturing ESCs


title: Nucleus Accumbens MEF2C Mediates the Maintenance of Peripheral Nerve Injury-induced Physiological and Behavioral Maladaptations

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Pre-clinical and clinical work has demonstrated altered plasticity and activity in the nucleus accumbens (NAc) under chronic pain states, highlighting critical therapeutic avenues for the management of chronic pain conditions. In this study, we demonstrate that myocyte enhancer factor 2C (MEF2C), a master regulator of neuronal activity and plasticity, is repressed in NAc neurons after prolonged spared nerve injury (SNI). Viral-mediated overexpression of Mef2c in NAc neurons partially ameliorated sensory hypersensitivity and emotional behaviors in mice with SNI, while also altering transcriptional pathways associated with synaptic signaling. Mef2c overexpression also reversed SNI-induced neuronal hyperexcitability and sensitized dopamine release after phasic stimulation. Transcriptional changes induced by Mef2c overexpression were different than those observed after desipramine treatment, suggesting a mechanism of action different from antidepressants. Overall, we show that interventions in MEF2C-regulated mechanisms in the NAc are sufficient to disrupt the maintenance of chronic pain states, providing potential new treatment avenues for neuropathic pain.

overall_design: C57BL/6J or DBA/2J mice (8-9 weeks old) were obtained from Jackson Laboratories and maintained on a 12-hour light/dark cycle with ad libitum access to food and water. Tibial SNI was performed on the left sciatic nerve under inhaled isoflurane. In Sham-operated mice, the same procedure was followed, but the nerves were left untouched. Stereotaxic coordinates for bilateral viral vector injections into the NAc were as follows with respect to bregma: AP, +1.60mm; ML: ±1.50mm; DV, -4.40mm at an angle of 10° from the midline. AAV8-hSyn-Mef2c-Egfp and AAV8-hSyn-Egfp were supplied by the Akbarian Lab at the Icahn School of Medicine at Mount Sinai. Approximately 7x10^9 viral particles were administered into the NAc of each hemisphere.

first: Randal

middle: A

last: Serafini

first: Zahra

last: Farzinpour

first: Vishwendra

last: Patel

first: Abigail

last: Kelley

first: Kerri

last: Pryce

first: Farhana

last: Sakloth

first: Collin

last: Teague

first: Angelica

last: Torres-Berrio

first: Eric

last: Nestler

first: Li

last: Shen

first: Schahram

last: Akbarian

first: Anushree

middle: N

last: Karkhanis

first: Robert

last: Blitzer

first: Venetia

last: Zachariou


title: Global gene expression analysis of HDFs, cdMSCs and MSCs.

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

summary: Regenerative medicine using mesenchymal stem cells (MSCs) have gained great outcomes.Thus, in this study, we aimed to induce MSC-like characters in fibroblasts by chemical direct conversion.

overall_design: We induced msenchaymals stem cells' character in human dermal fibroblasts by cultureing with specific compounds.

first: Osam

last: Mazda


title: RNA-seq analysis of melanoma cell lines with enhancer deletions.

city: St. Louis

first: Charles

last: Kaufman

state: Missouri

address: 4565 McDonnell Science Building

institute: Washington University School of Medicine

summary: This study investigates the impact of Sox10 enhancer deletion on transcriptional plasticity and drug resistance in melanoma cell lines.

overall_design: RNA-seq profiling of A375 and WM115 cells with a Sox10 enhancer region deleted

first: Sophia

last: DeGeorgia


title: Foregut endoderm differentiation from Human H1 ESCs examining Retinoic Acid dependent patterning during day5-6 developmental window

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: To define Retinoic Acid regulated genes in Human ESC differentiated foregut endoderm, endoderm was treated with or without 2uM Retinoic Acid for 24 hours (day5-6) of differentiation protocol, and bulk RNA-seq was performed on day6 or day9.   Treatment with 2uM CHIR99021 and 50ng/mL BMP4  for 72 hours (days6-9) done to mimic respiratory fate inducing signals.

first: Scott

last: Rankin

first: Jacek

last: Biesiada


title: Prevention of acute thrombosis with vascular endothelium antioxidative nanoscavenger

city: Nanjing

first: Yixin

last: Zhong

state: Jiangsu

address: Zhongda Hospital, Southeast University, Nanjing, China.

department: Center of Interventional Radiology and Vascular Surgery

institute: Zhongda Hospital, Southeast University

summary: Antiplatelet drugs have represented a milestone in treating patients at high risk of thrombosis. However, their clinical use remains limited by bleeding-associated risk and limited efficacy. Excessive reactive oxygen species (ROS) produced by damaged vascular endothelial cells, have been shown to stimulate thrombosis. Here, we propose that a ROS-chemotactic nanoscavenger (MDCP), formed by crosslinking melanin and catalase, prevents acute thrombosis by protecting vascular endothelial cells from oxidative stress. We demonstrate that treatment with MDCP inhibits ROS-induced apoptosis of endothelial cells, thereby maintaining endothelial integrity and preventing collagen exposure, which consequently prevents platelet activation and thrombosis. By avoiding direct interference with platelet function, this modulation of vascular redox homeostasis via MDCP provides a promising alternative antithrombotic strategy that addresses the bleeding risk of current clinical antithrombotic drugs.

overall_design: Transcriptomic profiles of rat abdominal aortas comparing FeCl3-induced thrombosis to saline control. The dataset includes 4 biologically independent replicates per condition.

first: Qiankun

last: Ni

first: Liandi

last: Huang

first: Guangchao

last: Qing

first: Gao-Jun

last: Teng

first: Xing-Jie

last: Liang

first: Haidong

last: Zhu


title: Epigenetic modification, as a distinctive therapeutic molecule for Parkinson’s disease gene therapy.

first: Yujung

last: Chang

address: 98 Hannamdaero, Yongsan-gu

institute: Stand Up Therapeutics Inc.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by the loss of dopaminergic neurons (DN) in the substantia nigra and disruption of cellular maintenance. Here, we demonstrate that NDST3-mediated epigenetic reprogramming halts neuronal degeneration and restores motor function in an animal model of PD.

overall_design: RNA-seq, CUT&RUN, ATAC-seq and scRNA-seq experiment conducted on 6-OHDA-induced PD model with NDST3 treatment.

first: Junsang

last: Yoo


title: SAMHD1 facilitates SARS-CoV-2 infection through HNF1-mediated ACE2 expression in lung epithelial Calu-3 cells

city: Iowa City

first: Pak Hin Hinson

last: Cheung

state: Iowa

address: 51 Newton Raod

department: Department of Microbiology and Immunology

institute: University of Iowa

summary: SAMHD1 protein is a restriction factor against board spectrum of viruses through dNTPase- and dNTPase-independent mechanisms. Moreover, it limits spontaneous- and virus-induced innate immune responses by suppressing proinflammatory cytokine and IFN-I production. Some viruses that escape the restriction functions of SAMHD1 may utilize SAMHD1-mediated innate immune suppression to establish effective infection by better IFN antagonism. Previously, we found that, instead of being a restriction factor, SAMHD1 was a proviral factor facilitating SARS-CoV-2 replication in human macrophages and immortalized human kidney cells HEK293T by suppressing IFN response. However, it is unclear about the function of SAMHD1 to the primary target and producer cells of SARS-CoV-2. In the current study, we found that SAMHD1 was a proviral factor to facilitate SARS-CoV-2 replication in Calu-3 cells, which were lung epithelial cells endogenously expressing viral entry factors such as ACE2 and TMPRSS2. Unlike human macrophages and HEK293T cells, inhibition of IFN antiviral response by baricitinib, a JAK1/2 inhibitor, did not revert the suppression of SARS-CoV-2 in SAMHD1 knockout Calu-3 cells. Through the experiments with pseudotyped viruses, we found that spike-protein mediated viral entry was suppressed in SAMHD1 knockout Calu-3 cells. Through mRNA-seq, we found that SAMHD1 knockout repressed ACE2 expression of Calu-3 cells at mRNA and protein levels. Knockdown experiments revealed that HNF1α and HNF1β were crucial for the endogenous expression of ACE2 in Calu-3 cells. Additionally, SAMHD1 knockout led to a reduction in the expression levels and ACE2-promoting function of HNF1α and HNF1β. This suggested that SAMHD1 facilitates HNF1-mediated ACE2 expression and SARS-CoV-2 replication in ACE2-expressing cells via a mechanism independent of its IFN- suppressive function

overall_design: To gain mechanistic insight, mRNA-seq was performed to profile the transcriptome of SAMHD1 knockout Calu3 cells (KO) and compared with that of the control Calu-3 cells (Ctrl). Two clones of KO cells were generated through CRISPR/Cas9 with one single guide RNA having different target sequences. Ctrl cells were mock control treated similarly as the KO cells but were transduced with empty vector. 8 x 105 Calu-3 Ctrl, KO1 and KO2 cells were seeded in 6 well plates in biological triplicate. Cells were cultured in 2mL DMEM/F12 with 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. At 20 hours after seeding, cells were washed once with DPBS and lysed with RLT plus lysis buffer. Cellular RNA was purified with RNeasy Plus kit following manufacturer’s instructions. All RNA samples got RNA integrity Number (RIN) scores equal to or more than 9.9 as determined by Agilent BioAnalyzer by Genomics Division of Iowa Institute of Human Genetics (University of Iowa). RNA samples were processed through Illumina Stranded mRNA Prep (illumina) and sequenced by Element Aviti24 using Cloudbreak FS-High output flow cell at 150 cycle (2x75) by the Genomics Division.

first: Hua

last: Yang

first: Fernando William

last: Moreira Santana

first: Shravya

last: Honne

first: Baek

last: Kim

first: Li

last: Wu


title: Raw RNA-seq data of wild type and overexpression lines for the rice gene OsDOF3.

city: Shanghai

first: Han

last: Lu

address: No.220 Handan Road Shanghai

institute: Fudan university

summary: Crop production is persistently threatened by a multitude of destructive diseases. In rice, the Ca2+ sensor RESISTANCE OF RICE TO DISEASES1 (ROD1) is a key regulator of defense against major pathogens, including those causing blast, sheath blight, and bacterial blight. However, the molecular mechanisms underlying ROD1-mediated immune suppression remain largely elusive. Here, we characterize an immune signalling cascade comprising the B3-domain transcription factor OsVAL2, the DOF transcription factor OsDOF3, as well as their downstream target OsCSE encoding a caffeoyl shikimate esterase. We demonstrate that the OsVAL2-OsDOF3-OsCSE module promotes lignin deposition and cell wall fortification to confer broad-spectrum disease resistance. ROD1 interacts with and sequesters OsVAL2 in the cytoplasm, thereby preventing its nuclear translocation and subsequent initiation of this immune program. Our findings reveal a spatiotemporal regulatory mechanism that maintains immune homeostasis, highlighting the crucial role of cell wall remodelling in crop disease resistance.

overall_design: RNA-seq analysis was conducted on leaves collected from field-grown rice plants at the pre-heading stage, including OsDOF3 overexpression (Ubi_OsDOF3_FLAG) and wild type (TP309) materials.Besides this, there were no additional treatments.

first: Yangxuan

last: Liu

first: Mingjun

last: Gao


title: The effect of expressing dephosphorylated GYS on MSCs

first: Xu

last: Yongyue

address: Tsinghua University

institute: Tsinghua University

summary: Mesenchymal stem cells (MSCs) are widely used in regenerative medicine, including the treatment of pulmonary fibrosis. However, implanted MSCs disappear within days, constraining therapeutic efficacy, which is largely attributed to nutrient deprivation. In this study, we established glycogen metabolism engineering strategies in mammalian cells. By expressing a functionally optimized glycogen synthase (GYSmut), MSCs could accumulate large amounts of glycogen rapidly as a reserve substance. We performed RNA-seq on engineered MSCs to understand its effects.

overall_design: MSCs were transduced with lentivirus expressing mutated dephosphorylated GYS1 (GYSmut group), while MSCs of the control group expressed GFP.

first: Yongyue

last: Xu

first: Mamatali

last: Rahman

first: Zhaoyan

last: Wang

first: Qiong


city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

summary: N6-methylenadenosine (m6A) modification, the most abundant epitranscriptomic modification in eukaryotic mRNAs, has been shown to play crucial roles in regulating various aspects of mRNA metabolism and functions. In this study, we applied the Cre-Loxp conditional knockout system to investigate the role of core component of the m6A methyltransferase complex, METTL14 and METTL3, in retinal development. Our results showed that double absence of Mettl14 and Mettl3 caused structural disturbance in the retina and prolonged proliferation activity of retinal progenitor cells. Interestingly, this did not affect the generation of various retinal cells, but this severely disrupted their distribution. In addition, double deletion of Mettl14 together with Mettl3 caused a stronger phenotype than the Mettl14 single deletion. In conclusion, our study demonstrated that Mettl14 and Mettl3 work cooperatively to regulate retinal development, and that this basis of regulation is mainly dependent on m6A modification.

overall_design: retinas of postnatal day 7 pups of different genotype were collected and processed for RNA-Seq sequencing and analyses.

first: Shuyi

last: Chen


title: miR-548aj-3p and miR-3127-3p suppress RANKL-facilitated inflammatory cytokines and catabolic factor in osteoarthritis and rheumatoid arthritis

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Osteoarthritis (OA) and rheumatoid arthritis (RA) are high prevalent joint diseases in global. The common pathological features include synovial inflammation, swelling, joint destruction, and bone remodelling. Arthritis development is associated with joint inflammation, particularly in inflamed synovial cells. Synovial inflammation, driven by cytokines such as interleukin-1 beta (IL-1β) and interleukin-6 (IL-6), is a crucial factor in arthritis as it contributes to joint destruction. RANKL is a vital factor that is linked to the activity of osteoclasts and the erosion of bone. Increased levels of RANKL related with the proinflammatory cytokines and cartilage degradation enzymes expression, playing a role in the course of arthritis. Medicines for arthritis have been limited by side effects and individual variability in therapeutic response. More effective treatment and drug options are needed to improve disease progression. miRNAs directly modulate gene transcription as potential option for arthritis therapeutic. Our study revealed that RANKL stimulation in OA and RA synovial fibroblasts upregulated the expression of IL-1β, IL-6 (pro-inflammatory cytokines) and MMP-13 (catabolic factor) by suppressing miR-548aj-3p and miR-3127-3p. Administration of miR-548aj-3p and miR-3127-3p mimics substantially inhibited the expression of IL-1β, IL-6 and MMP-13. We propose a potentially efficacious miRNA therapeutic approach for the treatment of arthritis, with a specific focus on OA and RA.

overall_design: To explore the therapeutic potential of miRNAs affected by RANKL in osteoarthritis (OA) and rheumatoid arthritis (RA), we isolated synovial fibroblasts from the knees of OA and RA patients and stimulated the cells with RANKL.We then conducted miRNA expression profiling analysis using data obtained from miRNA-seq of 4 different cell samples. We performed a comparative miRNA expression profiling analysis of miRNA-seq data for synovial fibroblasts with or without RANKL stimulation.

first: Yu-Han


title: Single-nucleus chromatin and gene expression profiling across hundreds of skeletal muscle samples reveals context-specific regulation

city: Ann Arbor

first: Arushi

last: Varshney

state: MI

address: 100 Washtenaw Ave

institute: University of Michigan

summary: Skeletal muscle is relevant to several polygenic metabolic traits and diseases including type 2 diabetes (T2D). Identifying genetic mechanisms underlying these traits requires pinpointing the relevant cell-types, regulatory elements, target genes, and causal variants. Here, we used genetic multiplexing to generate population-scale single nucleus (sn) chromatin accessibility (snATAC-seq) and transcriptome (snRNA-seq) maps across 287 frozen human skeletal muscle biopsies representing 456,880 nuclei. We identified 13 cell-types that collectively represented 983,155 ATAC summits. We integrated genetic information to identify 6,866 expression quantitative trait loci (eQTL) and 100,928 chromatin accessibility QTL (caQTL) (5% FDR) across the five most abundant cell-types, and show atlas-level snATAC maps often miss peaks. We identified 12,046 e-caQTL colocalizations and inferred causality between chromatin accessibility and gene expression through mediation analyses. 3,378 genome-wide association study (GWAS) signals across 43 relevant traits colocalized with sn e/caQTL, 52% in a cell-type-specific manner. 77% (3,616) GWAS signals colocalized with caQTLs and not eQTL, highlighting the importance of sn-caQTL maps for GWAS functional studies. GWAS-e/caQTL colocalization showed distinct cell-type-specific regulatory paradigms. For example, a C2CD4A/B T2D GWAS signal colocalized with caQTLs in muscle fibers and imputed chromatin contacts nominated VPS13C - a glucose uptake gene. The caQTL peak overlapping caSNP rs7163757 showed allelic regulatory activity differences in a human myocyte cell line massively parallel reporter assay. These results illuminate the genetic regulatory architecture of human skeletal muscle at high-resolution epigenomic, transcriptomic, and cell state scales and serve as a template for population-scale multi-omic mapping in complex tissues and traits.

overall_design: Massively Parallel Reporter Assay experimenatal design: Cloning: We ordered oligos as 230 bp sequences where 197 bp comprise the variant of interest flanked on both by 98 bp of genomic context, and the additional 33 bp are cloning adapters. Within this panel, we included a set of ∼50 negative control sequences defined by a previous publication107 We added 20 bp barcodes via a 2-step PCR amplification process then incorporated the barcoded oligos into a modified pMPRA1 vector (a gift from Tarjei Mikkelsen108, Addgene #49349) upstream of the GFP reporter gene using Golden Gate assembly. After transforming and expanding in NEB 10-beta electrocompetent bacteria, we sequenced this version of the MPRA library to establish a barcode-oligo pairing dictionary. We performed a second Golden Gate assembly step to insert an ENCODE-annotated promoter for the human MYBPC2 gene in between the oligo and barcode. Finally, we used restriction cloning to port the assembled MPRA block (oligo, barcode, promoter, GFP) to a lentiviral transfer vector, which was used by the University of Michigan viral vector core to produce infectious lentiviral particles. Primer sequences used for cloning and sequencing library preparation along with the MYBPC2 promoter sequence are included in a separate table. MPRA Experiment For each replicate, we infected 4x106 LHCN-M2 human skeletal myoblasts with our MPRA library at an MOI of ∼10. After infection, we passaged the cells for one week to remove any unincorporated virus or contaminating transfer plasmid, then differentiated the cells for one week. We isolated RNA and gDNA from each replicate using the Qiagen AllPrep DNA/RNA mini kit. We reverse transcribed RNA into cDNA with a GFP-specific primer, then constructed indexed sequencing libraries for both the cDNA and gDNA libraries using Illumina-compatible primers.859 Data Analysis After quality checks and filtering, we calculated the sum of barcode counts for each oligo within a replicate. We used DESeq2 v1.34.094 to perform normalization and differential expression analysis. We  used a nested model to identify oligos with significant activity (relative to plasmid input) and significant allelic bias (between reference and alternate alleles). All results were subject to a Benjamini-Hochberg FDR of 5%

first: Adelaide

last: Tovar

first: Jacob

middle: O

last: Kitzman

first: Stephen

middle: C

last: Parker


title: Raw RNA-seq data of overexpression and knockout mutant lines for the rice gene OsVAL2.

overall_design: RNA-seq analysis was conducted on leaves collected from field-grown rice plants at the pre-heading stage, including OsVAL2 overexpression (Ubi_OsVAL2_FLAG) and gene knockout (CR_osval2) materials.Besides this, there were no additional treatments.


title: Genetically engineered hybridized OMVs for treatment of implant-associated infections and relapse prevention through host immunomodulation

city: Zhengzhou

first: Yingying

address: Jianshedong Road

institute: Zhengzhou University

summary: Implant-associated infections (IAIs) are refractory to elimination and local immunosuppressive microenvironment exacerbates the therapeutic difficulty, further causing the persistence and relapse. Therefore, exploring immune-strengthening therapeutics holds great promise to reverse suppressive host immunity and thoroughly eradicate chronic or repetitive infections. Bacterial outer membrane vesicles (OMVs) emerge as a potential immunostimulatory candidate, which is however, still suffer from lacking active targeting capability and non-specific systemic inflammatory storms. Herein, we genetically engineered bone marrow-derived mesenchymal stem cells (BMSCs) to express CXCR4 and isolated the cell membranes (mBMSCCXCR4) to hybridize them with OMVs derived from Escherichia coli (E. coli) to finally produce nanovesicles (mBMSCCXCR4@OMV). Due to the hybridized membrane structure of mBMSCCXCR4, the resulting nanovesicles generated excellent targeting capability towards bone marrow and were obviously uptaken by bone marrow-derived macrophages, triggering the efficient transition to pro-inflammatory M1 status through TLR/NF-κB pathway. This alteration promoted its innate bactericidal capacity and antigen presentation. Subsequent activation of T cells and B cells derived from bone marrow and inhibition of myeloid-derived suppressor cells (MDSCs) facilitated the in vivo clearance of infections through adaptive immunity via mouse models. In addition, mBMSCCXCR4@OMV also boosted  memory B cells and bacteria-specific antibody responses. Together, this study warrants our mBMSCCXCR4@OMV to eradicate complicated IAIs and provides a whole-stage protection to prevent the postsurgical relapse, marking a significant immunotherapeutic advancement in the post-antibiotic era.

overall_design: RAW264.7 cells were treated with PBS or mBMSCCXCR4@OMV (50 μg mL-1).


title: Melatonin Enhances Vitrified Mouse Blastocyst Development by Mitigating Oxidative Stress and Preserving Mitochondrial Function

city: shanghai

first: dan

last: zhou

address: shanghai

department: Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine

institute: Tongji University

summary: This study aimed to investigate the benefits of melatonin supplementation during blastocyst vitrification and thawing process and explore underlying mechanisms to prevent apoptotic event.

overall_design: We evaluated blastocysts in three groups: fresh blastocysts (Control), non-melatonin treated vitrification (VT), and melatonin treated vitrification (MVT). We compared their developmental potential and oxidative stress levels to analyze effects of optimized melatonin supplementation. Additionally, transcriptome analysis in blastocysts by Smart-seq2 was performed to investigate the underlying transcriptional mechanism. The antioxidant enzyme and mitochondrial function protein expression were investigated by immunofluorescence staining.

first: Dan

last: Zhou

first: Qiaoyu

first: Miaoxin

first: Wenqiang


title: Global transcriptome analysis reveals Salmonella Typhimurium employs nitrate metabolism to combat bile stress

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Salmonella Typhimurium is an enteric pathogen that is highly tolerant to bile. Next-generation mRNA sequencing was performed to analyse the stress and adaptive responses of S. Typhimurium to bile. We identified the cellular pathways affected during bile stress in wild type (WT) and a mutant lacking cspE (ΔcspE), which plays an essential role in protection from bile stress. We observed transcriptional upregulation of several genes involved in nitrate metabolism, in response to bile stress. These genes were also differentially expressed between the bile-resilient WT and the bile-sensitive ΔcspE strain. To understand the role of nitrate metabolism in bile stress response, we generated a strain lacking fnr (Δfnr), which is the global regulator of nitrate metabolism in S. Typhimurium. fnr was highly induced in the bile treated WT strain but not in the ΔcspE strain. Notably, the Δfnr strain was susceptible to bile-mediated killing. Our studies revealed a new role for fnr in mediating the bile stress response. Importantly, overexpression of fnr lowered reactive oxygen species and significantly enhanced the survival of the bile-sensitive ΔcspE strain. We also observed that S. Typhimurium pre-treated with nitrate displayed better growth in the presence of bile. Together, these results demonstrate that nitrate-dependent anaerobic metabolism promotes adaptation of S. Typhimurium to bile.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA-sequencing was performed to understand the differences between S. Typhimurium 14028s wild type (WT) strain, which is bile resilient and bile sensitive ΔcspE strain (cspE gene knockout). The gene expression profile was obtained for control and bile treated WT and ΔcspE strains (in three biological replicates) at 90 minutes post bile treatment.

first: Madhulika

last: Singh

first: Deepti

last: Chandra

first: Sirisha

last: Jagdish

first: Dipankar

last: Nandi


title: Roquin-deficient T cells drive pancreatitis and tumorigenesis through IL-17 and Th17-inappropriate Cytokine production

city: Planegg-Martinsried

first: Vigo

last: Heissmeyer

state: Bavaria

address: Großhadernerstr. 9

department: Institute for Immunology, Biomedical Center Munich

country: Germany

institute: LMU Munich

summary: Pancreatitis can trigger pancreatic ductal adenocarcinoma (PDAC), however, the underlying origins can be diverse and cellular and molecular mechanisms remain elusive. We show that combined genetic inactivation of the RNA-binding proteins Roquin-1 and Roquin-2 in T cells induced pancreatitis, pancreatic neoplasia and accelerated PDAC formation, if KrasG12D was expressed in acinar cells. In the pancreas, Roquin-deficient T cells were highly activated, recruited proinflammatory neutrophils via IL-17A secretion, and inappropriately produced G-CSF that, in a feed-forward loop, further induced and mobilized neutrophils. Consistently, neutralization of IL-17 or G-CSF ameliorated pancreas pathology. Roquin repressed G-CSF in two ways. It directly inhibited CSF3 mRNA expression through its 3'-UTR, and indirectly, because Roquin loss-of-function imposed transcriptional reprogramming by NF-kB and established an active enhancer at the Csf3 locus in Th17 cells. Together, we identified critical cellular and humoral components and epigenetic, transcriptional and post-transcriptional mechanisms within a regulatory circuit that prevents pancreatic cancer formation.

overall_design: RNAseq in primary pancreas cancer cell lines and primary cancer tissue taken from KrasG12D, p48cre mice reconstituted with either WT or DKOT bone marrow.

first: Timsse

last: Raj

first: Desheng

last: Hu

first: Gualdrini

last: Francesco

first: Polletti

last: Sara

first: Jessica

last: Zöller

first: Elaine

middle: H

last: Wong

first: Sebastian

last: Müller

first: Gaja

last: Bianco

first: Katja

last: Steiger

first: Maike

last: Becker

first: Sophie

last: Isays

first: Jürgen

last: Ruland

first: Danijela

last: Heide

first: Carolin

last: Daniel

first: Jana

last: Schor

first: Roland

last: Rad

first: Gioacchino

last: Natoli

first: Mathias

last: Heikenwälder


title: Advantages of Magnetic Compression in Rat Colonic Anastomosis: A Comparative Study with a Transcriptomic Perspective

city: Xi'an

first: Shuqin

last: Xu

address: Zhuque street

institute: xianjiaotong univeisity

summary: Background: Colorectal anastomosis is a common procedure in colorectal cancer surgery, but traditional suturing is technically demanding and prone to complications. Magnetic compression anastomosis (MCA) offers a simpler, minimally invasive alternative with favorable outcomes. This study compares the healing effects of MCA and conventional suturing in rat colonic anastomosis and investigates the molecular mechanisms involved.  Methods: Twenty male Sprague-Dawley rats (200-230 g) were randomly divided into an MCA group and a suture (control) group. The survival rates, and histological and transcriptomic profiles of the anastomotic sites were compared. Results: The survival rate of the MCA group (100%) was significantly higher than that of the control group (70%). Histological examination showed improved tissue alignment and more continuous mucosal surfaces in the MCA group. Transcriptomic analysis revealed that differentially expressed genes between the MCA and control groups were highly enriched in immune-inflammatory pathways. PPI network analysis identified IL-1β as a key molecule, with significantly elevated expression in the MCA group. Results: The survival rate of the MCA group (100%) was significantly higher than that of the control group (70%). Histological examination showed improved tissue alignment and more continuous mucosal surfaces in the MCA group. Transcriptomic analysis revealed that differentially expressed genes between the MCA and control groups were highly enriched in immune-inflammatory pathways. PPI network analysis identified IL-1β as a key molecule, with significantly elevated expression in the MCA group. Conclusion: MCA is a simple, low-complication method for colonic anastomosis in rats. Transcriptomic analysis suggests that IL-1β may play a pivotal role in enhancing the efficacy of MCA in promoting anastomotic healing.

overall_design: Six colonic anastomotic tissue samples were collected from rats, including three from the magnetic compression anastomosis (MCA) group and three from the suture (control) group. After two weeks of healing, tissues at the anastomotic sites were excised, immediately frozen in liquid nitrogen, and stored at −80 °C. Total RNA was extracted using TRIzol reagent, and sequencing libraries were prepared with the NEBNext Ultra RNA Library Prep Kit. High-throughput RNA sequencing was performed on the DNBSEQ-T7 platform. The aim was to compare gene expression profiles between the MCA and suture groups to explore molecular mechanisms associated with enhanced anastomotic healing.


title: CRISPR-Cas9 base editor screening identifies the spectrum of MEN1 mutations impacting menin inhibitors in clinical trials [CRISPRseq]

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: Menin inhibitors have entered clinical trials for KMT2A-rearranged and NPM1 mutant acute leukemias and are demonstrating promising activity. CRISPR-Cas9 base editor screening previously predicted several MEN1 mutations that have arisen in patients receiving SNDX-5613 and confer menin inhibitor resistance. The extent to which MEN1 mutations will impact each menin inhibitor is currently unknown. We leveraged advances in CRISPR-Cas9 base editing technology to predict the MEN1 mutation profile that will impact five different menin inhibitors in clinical trials. We found key similarities (M327) and differences (C334, E368, V372) in the profile of MEN1 mutations that affect each compound. The co-crystal structure of menin bound to each compound suggests resistance mechanisms related to how each menin inhibitor binds in the KMT2A binding pocket of menin. Our in vitro and in vivo validation suggests that the MEN1 mutations identified and validated with this approach are likely to arise and impact all menin inhibitors.

overall_design: This screen was performed in two different MV4;11 cell lines, each constitutively overexpressing a SpCas9 nickase fused to a deaminase enzyme capable of making either A>G edits or C>T edits (A>G editor: ABE8e (V106W), SpG-SpyoCas9 (D10A), pRDA_867, addgene plasmid #231109; C>T editor: TadA-CDd, SpG-SpyoCas9 (D10A), pRDB_092, addgene plasmid # #231110), hereafter called MV4;11 A>G and MV4;11 C>T. With the genomic perturbation platform at the Broad institute, we designed and cloned a guide RNA (sgRNA) library tiling the coding exons of MEN1 (target transcript: NM_000244.4). We then transduced our MEN1-targeting library into MV4;11 A>G and MV4;11 C>T cell lines. After 48 hours, the transduction efficiency was 15%, suggesting a low frequency of multiple guide infection of the same cell. Cells were selected with puromycin and expanded, and drug treatment was initiated 10 days after library transduction. We treated with roughly the 75% growth inhibitory concentration at day 5 and the 97.5% growth inhibitory concentration at day 9 and used this as the concentration during the screen: 13.8 nM DS-1594, 17.3 nM JNJ-6617, 23.4 nM KO-539, 51.6 nM SNDX-5613, 25.2 nM DSP-5336. During the screen, cells were treated in three technical replicates for each condition (DMSO and each of the 5 menin inhibitors). We maintained 2,000x coverage of each sgRNA during the duration of the 21-day screen, during which time cells were split and drug replenished every 3-to-4 days. The screen was terminated after 21 days, at which point the cells exhibited resistance based on their accelerating growth towards the end of the screen. Genomic DNA isolation, library preparation, and sequencing were then performed.

first: Wallace

last: Bourgeois

first: Jevon

last: Cutler


title: Galectin-9 regulates CD4+ T cell proliferation via intracellular HLA-DR binding in dendritic cells

city: Nijmegen

first: Guido

last: van Mierlo

address: Geert Grooteplein Zuid 28

country: Netherlands

institute: Radboudumc

summary: To initiate T cell-mediated immunity, dendritic cells (DCs) present antigen to specific T cells through the establishment of an immune synapse. Despite its critical importance, the spatiotemporal dynamics of membrane receptor organization during synapse formation in DCs have been only partly characterized. Galectins, a family of β-galactoside binding proteins, exert crucial roles in homeostasis and pathological processes but the molecular mechanisms underlying galectin function are largely unresolved. Here, we demonstrate that intracellular galectin-9 (gal9) is required for T cell activation. Murine and human DCs lacking gal9 showed impaired induction of CD4+, but not CD8+, T cell proliferation, suggesting a conserved function for gal9 in modulating DC–T cell interactions. Live-cell imaging further revealed that galectin-9-depleted DCs fail to establish stable immunological synapses with T cells, resulting in reduced T cell clustering and activation. Unbiased co-immunoprecipitation and mass spectrometry identified HLA-II as a gal9 binding partner in DCs, and we observed a marked reduction of HLA-II recruitment to the immune synapse as the underlying mechanism. Conditional gal9 knockout in DCs led to enhanced tumor growth, compared to their WT counterparts, underscoring galectin-9 role in T cell-dependent anti-tumor immunity. Collectively, this study provides the first detailed account of gal9-mediated HLA-II organization at the synaptic site of DCs, revealing a novel mechanism by which galectins orchestrate immune receptor positioning from within the cytoplasm to enhance CD4+ T cell activation.

overall_design: Wildtype and galectin-9 knockdown dendritic cells

first: Andrea

middle: R

last: Furones

first: Laia

middle: Q

last: Cano


title: Metformin Promotes Proliferation of Mouse Female Germline Stem Cells by Histone Acetylation Modification of Traf2

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We used ChIP-seq to analyze the mechanism of metformin promoting the proliferation of mouse female germline stem cells（mFGSCs） through H3K27ac

overall_design: Detection of the effect of metformin on H3K27ac binding sites in mFGSCs

first: Jiaqi

last: Chen


title: Gene expression comparison between human glioma cells: U87-MG wild-type and CHI3L1 knock-out (clone 1 and 2)

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: U87-MG human glioma cells were subjected to CRISPR/Cas9 genetic engineering to knock-out CHI3L1 gene. We then compared gene expression profiles between maternal cells (wild-type, WT) and two clones obtained throught CRISPR/Cas9 pipeline: clone 1 (KO1) and clone 2 (KO2)

overall_design: We extracted RNA from 3 subsequent cell culture passages after 48h of growth (n=3 for each condition: WT, KO1 and KO2). We assessed the quality of extracted RNA for an RIN of >9. We prepared libraries with KAPA Stranded mRNA-Seq Kit (Roche) and then performed pair-end sequencing: 2x 76 cycles, target number of reads: 25 million per sample on Illumina HiSeq 1500.

first: Salwador

last: Cyranowski

first: Bartłomiej

last: Gielniewski

first: Paulina

last: Szadkowska

first: Bozena

last: Kaminska


title: RNA-seq of SCC7 cancer cells treated with different conditioned media from cancer cell-induced TAM

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

summary: We analyzed the transcriptomes of murine  squamous cell (SCC7) treated with different conditioned media from BMDM, M1-BMDM, M2-BMDM or SCC7-induced BMDM.

overall_design: BMDM cells were treated by control media (DMEM), 20ng/ml INF-γ，20ng/ml IL-4, or 75% SCC7 conditioned media (CM) for 24 h to obtain M0-BMDM CM,  M1-BMDM CM, M2-BMDM CM and  SCC7-TAM CM respectively. Then different CM from BMDM was used to treat SCC7 cells for another 24 h. Then the RNA of SCC7 cells was extracted and underwent RNA-seq.

first: Tong

last: Ji


city: Nagoya

first: Hiroyuki

last: Tsuji

address: Furocho

department: Bioscience and Biotechnology Center

institute: Nagoya University

summary: Transcriptome analysis of inflorescence meristems of rice cultivar Koshihikari and a near isogenic line that have a chromosomal segment from rice cultivar Habataki Gn1.

overall_design: inflorescence meristems were isolated from rice, RNA was extracted and RNA-seq library was prepared according to the method of CEL-seq2. The libraries were sequenced by illumina Hiseq pratform.

first: Moeko

last: Sato


title: Intraspecific sequence variation and complete haplotype-resolved assemblies refine the identification of rapidly evolving regions in humans

status: Public on Nov 29 2025

city: Durham

first: Yanting

last: Luo

state: NC

address: 289 CARL Building, 213 Research Dr

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Humans exhibit significant phenotypic differences from other great apes, yet pinpointing the underlying genetic changes has been limited by incomplete reference genomes and a reliance on a single assembly to represent a species. We aligned 20 telomere-to-telomere (T2T) assemblies spanning great ape evolution and variation to define 1,596 consensus human ancestor quickly evolved regions (Consensus HAQERs), regions that diverged rapidly between the human-chimpanzee ancestor and an ancestral node of modern humans. Unlike prior HAQER sets based on single assemblies for a species, Consensus HAQERs incorporate population variation, reducing the likelihood of intraspecies variation appearing to be interspecies divergence. These regions contain signatures of elevated mutation rates, ancient positive selection, bivalent regulatory function, and are enriched in disease-linked loci, often emerging in previously inaccessible repetitive DNA. Through multiplex, single-cell enhancer assays, we identify HAQERs as active enhancers in the developing brain and cardiomyocytes, highlighting their potential contributions to human-specific gene regulation.

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design: For the brain experiment, an input library of STARR-seq plasmids along with an EGFP transfection reporter plasmid are delivered to the developing mouse cerebral cortex (E14.5) via in utero electroporation. Following 48 hours of incubation, mouse brains are harvested and GFP+ cells are isolated via Fluorescent Activated Cell Sorting. Single cell sequencing is then performed to recover gene expression, EGFP transfection reporter plasmid expression, and STARR-seq reporter expression. For the heart experiment, an input library of STARR-seq plasmids along with an EGFP transfection reporter plasmid are transfected into cardiomyocyte cells differentiated from human induced pluripotent stem cells of the DU11 cell line. Following 2 days of incubation, a single cell suspension is created and GFP+ cells are isolated via Fluorescent Activated Cell Sorting. Single cell sequencing is then performed to recover gene expression, EGFP transfection reporter plasmid expression, and STARR-seq reporter expression.

first: Seth

last: Weaver

first: Federica

last: Mosti

first: Michael

last: Thomas

first: Ravi

last: Karra

first: Debra

middle: L

last: Silver

first: Craig

middle: B

last: Lowe


title: HIV Nef amplifies mechanical heterogeneity to promote immune evasion

city: New York

first: Louise

last: Leyre

address: 413 E 69th St

department: Infectious Diseases

institute: Weill Cornell Medicine

summary: Intracellular pathogens must evade cytotoxic immunity to establish persistent infection. Although immune escape is typically viewed through a biochemical lens, the ability of certain pathogens to alter mechanical properties of infected cells suggests that biophysical mechanisms may also contribute. Here, we show that a subset of CD4+ T cells infected with the human immunodeficiency virus (HIV) resist elimination through a soft phenotype that impairs killing by mechanosensitive cytotoxic T lymphocytes (CTLs). This phenotype arises from the combined effects of the HIV virulence factor Nef, which remodels the actin cytoskeleton, and intrinsic heterogeneity in basal cytoskeletal properties of T cells. Although cells that are sufficiently soft to resist CTLs are relatively rare, this property can be detected in HIV-infected CD4+ T cell clones from people living with HIV, implicating a role for this mechanism in reservoir persistence. These findings define a biophysical paradigm of immune evasion with implications for HIV cure strategies.

overall_design: RNAseq data from CD4+ T cells infected with human HIV (WT) or HIV with a mutation in the Gag TW10 epitope (TW10esc) with and without the presence of TW10-specific CTLs. Data was collected from four donors: 8882165, B027, G092504, and RG138.

first: Farah

last: Mustapha

first: Alberto

last: Herrera

first: Esther

last: Lee

first: Emily

last: Huntsman

first: Paul

last: Zumbo

first: Jared

last: Weiler

first: Isabella

last: Ferriera

first: Tan

last: Huynh

first: Parul

last: Sinha

first: Ethan

last: Naing

first: Cristian

last: Ovies

first: Connor

last: Smith

first: Colin

last: Kovacs

first: Micheal

last: Galiano

first: Nada

last: Wahman

first: Doron

last: Betel

first: Kiera

last: Clayton

first: Morgan

last: Huse

first: R

last: Jones


title: Digital twins for in vivo metabolic flux estimations in patients with brain cancer II

first: Wajd

middle: N.

last: Al-Holou

address: 1500 E Medical Center Dr

department: Neurosurgery

summary: Recent advancements in metabolic flux estimations in vivo are limited to preclinical models, primarily due to challenges in tissue sampling, tumor microenvironment heterogeneity, and non-steady state conditions. To address these limitations and enable flux estimation in human patients, we developed two machine learning-based frameworks. First, the digital twin framework integrates first-principles stoichiometric and isotopic simulations with convolutional neural networks to estimate fluxes in patient bulk samples. Second, the 13C-scMFA framework combines patient scRNA-seq data with 13C-isotope tracing, allowing single-cell-level flux quantification. These studies allow quantification of metabolic activity in neoplastic glioma cells, revealing frequently elevated purine synthesis and serine uptake compared to non-malignant cells. Our models also identify metabolic heterogeneity among patients and mice with brain cancer, in turn predicting treatment responses to metabolic inhibitors. Our frameworks advance in vivo metabolic flux analysis, may lead to novel metabolic therapies, and identify biomarkers for metabolism-directed therapies in patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Intracranial syngeneic TRP GBM tumors and patient-derived GBM tumors (GBM12, GBM38, and HF2303) were harvested and dissociated using Collagenase Type II (Invitrogen, 17101015) with rotation at 37°C. The cell suspension was passed through a 40um strainer (Fisherbrand, 22363547), centrifuged, and resuspended followed by application of RBC lysis buffer (Biolegend).

first: Baharan

last: Meghdadi

first: Wajd N.

first: Andrew J.

last: Scott

first: Anjali

last: Mittal

first: Ningning

last: Liang

first: Sravya

last: Palavalasa

first: Abhinav

last: Achreja

first: Alexandra

last: O'Brien

first: Kathy

last: Do

first: Zhe

last: Wu

first: Jiane

last: Feng

first: Nathan R.

last: Qi

first: Vijay

last: Tarnal

first: Sriram

last: Venneti

first: C. Ryan

last: Miller

first: Jann N.

last: Sarkaria

first: Weihua

last: Zhou

first: Theodore S.

last: Lawrence

first: Costas A.

last: Lyssiotis

first: Daniel R.

last: Wahl

first: Deepak

last: Nagrath


title: Nrf2 activation ameliorates behavioural and brain oscillatory function alterations induced by prenatal valproic acid exposure selectively in female rats

city: Guelph

first: Olivia

middle: Olga Fraser

last: Williams

state: ON

address: 50 Stone Road West

department: Biomedical Sciences

country: Canada

institute: Unviersity of Guelph

summary: In this dataset we include the expression data obtained by dissected prefrontal cortical tissue from sprague-dawley rats exposed to saline or valproic acid on gestation day 12.5 in utero. This data was used to obtain prefrontal cortical genes in adolescence to determine sex differences in a model of autism spectrum disorder.

overall_design: 19 Total samples were analyzed

first: Williams

last: Olivia

first: Perreault

last: Melissa


title: Collagen Alignment and Spatial Transcriptomics Analysis (CASTA) reveals gene programs associated with collagen alignmet in colorectal cancer

city: Nashville

first: Maxwell

middle: Stuart

last: Hamilton

state: TN

address: 2215 Garland Ave, Medical Research Building IV

department: Cancer Biology

institute: Vanderbilt University

summary: The use of immune checkpoint blockade is limited to the minority of colorectal cancers that are highly infiltrated by CD8+ T cells. Therefore, a method to improve CD8+ T-cell infiltration has the potential to expand the use immune checkpoint blockade to more patients. Barriers of aligned collagen surrounding tumors have been proposed as one mechanisim of CD8+ T-cell exclusion. We use 5 colorectal cancer patient samples to examine the relationship between collagen alignment and gene expression.

overall_design: Five CRC patient samples were collected and Visium v2 spatial transcriptomics was performed. Collagen was imaged in serial sections and spatially-resolved quantification of collagen alignment was integrated with the spatial transcriptomics data.

first: Alan

last: Simmons

first: Harsimran

last: Kaur

first: Samuel

last: Ellis

first: Ken

last: Lau

first: Robert

last: Coffey


title: Ubiquitin Specific peptidase 32 stabilizes YAP and Facilitates Triple Negative Breast Cancer Progression

first: Zehao

last: Hong

state: Henan

address: No. 1 Jianshe East Road

department: Breast surgery

institute: The First Affiliated Hospital of Zhengzhou University

summary: Triple negative breast cancer (TNBC) is the most lethal among all breast cancer subtypes, while the effective therapeutic targets are still unavailable. Recently studies revealed that the dys-regulation of Hippo signaling played important roles in TNBC progression, but targeting Hippo/YAP axis is a plausible strategy for TNBC therapy. In our study, we carried out GSEA screening for important deubiquitinases (DUBs) for Hippo signaling and identified USP32 as a key mediator for YAP stability and Hippo signaling activity for TNBC progression. USP32 depletion significantly inhibited Hippo/YAP activity and TNBC progression. Molecular mechanism studies showed that USP32 could interact with YAP, enhance YAP stability possibly by inhibiting K63-linked poly-ubiquitination. Interestingly, YAP could also bind to the promoter region of USP32 and facilitate its transcription. In general, our study revealed the positive feedback loop between USP32 and YAP in modulating TNBC progression, while targeting USP32 could be a promising strategy to disrupt such interplay between USP32 and Hippo signaling for TNBC treatment.

overall_design: RNA-seq profiling of MDA-MB-231 cells transfected with siControl or siUSP32 for 48h


title: NAT10-mediated ac4C modification promotes neuroectoderm specification of human embryonic stem cells via acetylating NR2F1 mRNA to enhance translation efficiency [RNA-seq]

city: Shanghai

first: Ji

last: Wu

summary: The expression profile data was obtained by RNA-Seq data.

overall_design: the expression profile of human embryonic stem cells (hESCs), neuroepithelial progenitors cells(NEP) and mesendoderm cells(ME)

first: Junbang

last: Ge


title: NAT10-mediated ac4C modification promotes neuroectoderm specification of human embryonic stem cells via acetylating NR2F1 mRNA to enhance translation efficiency [Ribo-seq]

summary: We use Ribo-seq to report the most comprehensive survey to date of mRNA translation in human embryonic stem cells (hESCs), neuroepithelial progenitors cells(NEP) and mesendoderm cells(ME)

overall_design: the mRNA translation profile of human embryonic stem cells (hESCs), neuroepithelial progenitors cells(NEP) and mesendoderm cells(ME)


title: RNA-seq of B16F10 cancer cells treated with different conditioned media from cancer cell-induced TAM

first: Yu

last: Zhang

summary: We analyzed the transcriptomes of B16F10 cells treated with different conditioned media from BMDM, M1-BMDM, M2-BMDM or B16F10-induced TAM.

overall_design: BMDM cells were treated by control media (DMEM), 20ng/ml INF-γ，20ng/ml IL-4, or 75% B16F10 conditioned media (CM) for 24 h to obtain M0-BMDM CM,  M1-BMDM CM, M2-BMDM CM and  B16F10-BMDM CM respectively. Then different CM from BMDM was used to treat B16F10 cells for another 24 h. Then the RNA of B16F10 cells was extracted and underwent RNA-seq.

first: Tong

last: Ji


title: Mast cell CRFR1 contributes to pancreatic cancer pain via MAPK/SPHK1 signaling

first: zhang

last: yue

address: No. 225 Changhai Road, Yangpu District, Shanghai

institute: fudan university

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer often accompanied by persistent abdominal pain and stress, significantly compromising patients’ quality of life. Previous studies have identified mast cells as crucial contributors to pancreatic cancer related pain. This study aimed to investigate the role of the mast cell receptor CRFR1 and delineate its underlying mechanisms in mediating pancreatic pain. In the current study, we demonstrated that painful PDAC patients exhibited markedly increased mast cell infiltration in peritumoral tissues, but not in tumor tissues, along with elevated levels of CRF and mast cell-specific CRFR1 expression, compared to asymptomatic patients. Consistently, in orthotopic PDAC mice models, flow cytometry and immunofluorescence staining confirmed increased CRFR1 expression in mast cells. Both pharmacological inhibition of CRFR1 and mast cell specific CRFR1 knockout suppressed mast cell degranulation and alleviated cancer pain in male and female mice. Mechanistically, RNA sequencing, western blotting, and ELISA indicated that CRFR1 activated MAPK pathway signaling, upregulated SPHK1 expression, and increased S1P levels. A rescue experiment revealed that MAPK inhibition blocked CRFR1-induced SPHK1 upregulation in vitro. Importantly, the SPHK1 inhibitor PF543 reduced abdominal hyperalgesia in mice, while this effect was abolished in mast cell deficient mice. Moreover, SPHK1 knockdown by siRNA abolished CRFR1-induced mast cell degranulation. These findings highlight the critical role of mast cell CRFR1 in mediating abdominal hyperalgesia and identify the MAPK/SPHK1/S1P axis as an essential pathway, suggesting that targeting mast cell CRFR1 may be a promising therapeutic strategy for managing pancreatic cancer pain.

overall_design: Para-tumor tissues were randomly selected from CRFR1 CKO and WT PDAC mice for RNA sequencing to explore the downstream signaling pathways of CRFR1.

first: Yue

first: Kai

last: Wei

first: Kunming

last: Tao

first: Min

last: Ma

first: Zhijie

last: Lu


title: Cohesin Facilitates Nucleosome Invasion by Transcription Factors II

city: State College

first: Shane

middle: Douglas

last: Stoeber

state: Pennsylvania

address: 406 South Frear Building

department: BMMB

institute: Penn State

summary: Nucleosomes present a major barrier to transcription factor (TF) binding. However, a subgroup of TFs known as pioneer factors (PFs) can recognize motifs covered by nucleosomes and initiate chromatin opening. PFs also bind nucleosomal substrates with high affinity in vitro, which may facilitate their nucleosome invasion in vivo. Here, we show that LexA, a bacterial TF with poor nucleosome binding in vitro, can rapidly invade into a well-positioned nucleosome from a motif positioned at the dyad when expressed ectopically in yeast. This striking contrast between LexA binding in vitro and in vivo raises the possibility that TFs can exploit nucleosome dynamics in vivo to access occluded sites. Surprisingly, we find that LexA-mediated chromatin opening can occur in the absence of DNA replication, chromatin remodeling, histone turnover, and a few histone chaperones. Instead, nucleosome invasion by LexA and a native PF, Cbf1, is promoted by the cohesin complex, illustrating intriguing a connection between cohesin and TF binding. Together, our results demonstrate that even non-pioneer TFs like LexA can bind and displace nucleosomes in vivo, through a process facilitated by cohesin.

overall_design: MNase and ChIP seq cbf1 timecourse experiments in a auxin-induced degradation strain of endogenous Cbf1 and +/-Smc3.

first: Hengye

last: Chen

first: Ruo-Wen

first: Courtney

last: Smith

first: Lloyd

last: Yang

first: Sam

last: Becker

first: Sarah

last: Vinson

first: Michael

last: Poirier

first: Lu

last: Bai


title: Cohesin Facilitates Nucleosome Invasion by Transcription Factors


title: Functional genomic dissection of MS risk loci reveals convergence of cis and trans gene regulatory mechanisms in microglia

city: Cambridge

first: Olivia

last: Corradin

address: 455 Main Street

department: Biology

institute: Whitehead Institute /MIT

summary: Neurological diseases (NDs) are a major source of unmet medical need, and translational insights have been hampered by complex underlying pathophysiologies and limitations of experimental models.  Noncoding single nucleotide polymorphisms (SNPs) at hundreds of loci have been linked to ND risk by genome-wide association studies (GWAS), but the causal genes and pathways are largely unknown. Despite the multicellular pathology of complex traits like multiple sclerosis (MS), functional studies that aim to characterize the molecular impact of disease-associated SNPs often investigate all SNPs linked to disease in the same cellular context. Here, we combine a computational approach to predict the pathogenic cell type of individual risk loci with functional CRISPR perturbation studies in iPSC-derived microglia cells (iMGLs). ND SNP enrichment in cell type-specific enhancers is similar between primary and iPSC-derived cells, and mechanistically supported by shared enhancer-promoter interactions. We apply a novel Perturb-seq platform to interrogate MS risk SNPs in iMGL, identifying likely cis-acting causal risk genes at 5 of 9 loci, as well as downstream differentially expressed genes (DEGs). Despite being found in trans to MS risk SNPs, downstream DEGs are substantially enriched for MS heritability. Downstream DEGs from all 5 target genes show significant overlap, converging on genes related to cytokinesis, phagocytosis, and mitochondrial metabolism. We then compared downstream DEGs to gene expression patterns observed in MS patient tissue studies and observed marked similarities, demonstrating that genes dysregulated as the result of GWAS loci perturbation mirrored effects observed in microglia found in MS patient lesions. Collectively, these results demonstrate that cell type aware functional studies can be used to translate ND SNP associations into mechanistic insights and reveal novel convergent biological mechanisms underlying complex traits.

overall_design: iPSC-derived microglia (iMGLs) were transduced with Vpx-associated lentivirus containing a Perturb-seq sgRNA library after 7 days in microglia maturation media.  7 days later, transduced cells were isolated by FACS for BFP expression, with gating on the top ~50% mCherry levels, representing dCas9-KRAB ZIM3 transgene expression.  After sorting cells were immediately used to prepare libraries for scRNA-seq

middle: D

last: Gallagher

first: Xochitl

last: Luna


title: Human microglia differentially respond to ß-amyloid, tau, and combined Alzheimer's disease pathologies in vivo

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: Recent studies have identified important species-dependent differences in the response of microglia to beta-amyloid pathology. Yet, whether human microglia also interact differently with the pathognomonic combination of amyloid and tau pathologies that occurs in Alzheimer’s Disease (AD) remains unclear. We generated a xenotolerant mouse model of AD that develops both plaque and tangle pathologies, transplanted stem cell derived microglial progenitors and examined the interactions between human microglia and AD pathologies with scRNA sequencing, immunohistochemistry, and in vitro modeling. Combined amyloid and tau pathologies induced robust type-I interferon and proinflammatory cytokine responses, as well as an increased adoption of a distinct “rod” morphology in human microglia. The Rod morphology could be induced with type-I interferon treatment in vitro. We provide new insights into human microglial responses to combined AD pathologies and a novel platform to investigate and manipulate human microglia in vivo.

overall_design: Cultured human iPSC-derived microglia were treated with DPBS or Interferon alpha (50 ng/ml), interferon beta (50 ng/ml), interferon gamma (100 ng/ml) for 48 hours. Cells were then collected, washed and pelleted and RNA was extracted using a standard Trizol protocol.

first: Morgan

last: Coburn

first: Ghazaleh

last: Eskandari-Sedighi

first: Jonathan

last: Hasselmann

first: Whitney

last: England


title: A miR-200b-Filamin A axis drives epicardial contribution to cardiogenesis

city: Granada

first: Francisco

last: Hernández-Torres

state: Granada

address: Avda. de la Investigación, 11

institute: University of Granada

summary: The epicardium provides essential cellular and molecular cues required for proper cardiogenesis and cardiac repair. Epicardial-derived cells (EPDCs) play a pivotal role in establishing cardiac structure, contributing to coronary vasculature formation, connective tissue organization, and post-ischemic cardiac remodeling. During EPDC emergence, the epicardium must preserve a precise balance between cellular motility and epithelial integrity. However, the mechanisms determining why some epicardial cells undergo epithelial-to-mesenchymal transition to become EPDCs while others retain an epithelial state remain unclear. We show that miR-200b is expressed in a specific subset of epicardial cells during embryonic EPDC formation. Gain- and loss-of-function experiments reveal that miR-200b regulates the overall number of EPDCs by modulating the proportion of symmetric and asymmetric cell divisions. RNA pull-down coupled with RNA-seq, together with in vitro and ex vivo functional assays, identified filamin A (FLNA)—a key regulator of spindle positioning during asymmetric division—as a direct miR-200b target in epicardial cells. FLNA loss reduced asymmetric divisions, supporting its role in promoting this division mode. Overall, our study defines a miR-200b–FLNA axis that governs symmetric versus asymmetric division to control epicardial tissue dynamics during cardiogenesis. Additionally, altered miR-200b expression after myocardial infarction in mice and humans suggests a potential role in post-injury cardiac remodeling

overall_design: Affinity pulldown of biotinylated RNA approach.  RNA seq profilling of epicardial cells transfected with Biotinylated miR-200b mimics or Biotinylated miR-scramble harvested 48 h post-transfection

first: Cristina

last: Sánchez-Fernández

first: Carlos

last: García-Padilla

first: Estefania

last: Lozano-Velasco

last: Hernandez-Torres

first: Oscar

last: Ocaña

first: Laura

last: Alonso-Herranz

first: Mercedes

last: Ricote

first: Beatriz

last: Román-Payan

first: Rita

last: Carmona

first: Diego

last: Franco

first: Jorge Nicolas

last: Dominguez

first: Amelia

last: Aranega


title: Exon-6 truncated p53 suppresses innate immune responses to facilitate immune evasion in bladder cancer

city: Tianjin

first: Chi

last: Zhang

address: No.94 Weijin Road, Nankai District

department: School of medicine

institute: Nankai University

summary: Previous studies have reported that truncated p53 exhibits pro-tumorigenic properties; however, whether it contributes to immune evasion by influencing the immune microenvironment remains unclear.

overall_design: Here, we report that E6-trunc p53 isoforms  (E6-trunc p53) inhibit type I interferon (IFN-I) signaling, thereby supporting tumor cell survival and enabling immune evasion. Ectopic expression of E6-trunc p53 reduces T-cell infiltration into tumors and markedly promotes in vivo tumor growth in an immune-dependent manner. Mechanistically, E6-trunc p53 exhibit high-affinity binding to TBK1, thereby preventing cell-intrinsic activation of innate immune pathways and suppressing IFN-I–mediated antitumor immunity. Additionally, silencing E6-trunc p53 leads to robust upregulation of IFN-I signaling and induces tumor cell death. Deletion of TBK1 or IFN-β completely abolishes the cell death triggered by knockdown of E6-trunc p53. Notably, TP53 truncating mutations correlate inversely with the extent of T-cell infiltration and predict poor responsiveness to immunotherapy in patients with bladder cancer. Collectively, our findings reveal a novel oncogenic role of E6-trunc p53 in modulating IFN-I signaling and driving tumor malignancy and immune evasion.


title: Effect of CA3 overexpression on signalling pathways in different cell lines

city: Nathan

first: Yezhou

last: Yu

state: QLD

address: 170 Kessels Road

department: School of Environment and Science

country: Australia

institute: Griffith University

summary: Carbonic Anhydrase 3 (CA3) was an understudied member of the carbonic anhydrase family. It is highly expressed in muscle tissue and contains two surface-exposed cysteine residues, which can undergo glutathionylation. The redox modification protects cells under oxidative stress. Recent studies have shown that CA3 interacts with Bcl-2–Associated Athanogene 3 (BAG3) and squalene epoxidase (SQLE), implicating CA3 in the pathogenesis of myasthenia gravis and non-alcoholic fatty liver disease. CA3 overexpression has also been reported to reduce hypoxia-induced apoptosis in cardiomyocytes. In this study, we performed RNA-seq profiling on HEK293T, MDA-MB-231, and SVCT cell lines following CA3 overexpression. HEK293T cells were analyzed only under normoxic conditions, whereas MDA-MB-231 and SVCT cells were cultured under both normoxia and hypoxia.

first: Giovanna

last: Trapani

first: Kathryn

last: Tonissen


title: mRNA transcriptome sequencing of siglecf low macrophages from tumor lungs of chimeric mice that were intranasally injected with Ad-Cre

city: Wuhan

first: Zhidong

address: Donghu Road, No. 115, Wuchang District

institute: Wuhan University

summary: The transcriptional profiling of siglecf low macrophages from tumor lungs of  Tmem173fl/fl→KrasLSL-G12D/+Lkb1fl/fl (WTKL) and Tmem173fl/fl;Lyz2-Cre→KrasLSL-G12D/+Lkb1fl/fl (LYZKL) chimeric mice.

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data in immune cells sorted from tumor-burdened lungs of WTKL  and LYZKL mice {transferring the bone marrow cells from Tmem173fl/fl,  Tmem173fl/fl;Lyz2-Cre mice into the lethally irradiated KrasLSL-G12D/+Lkb1fl/fl (KL)  mice}.

first: Dandan

last: Lin

first: Bo

last: Zhong


title: Development of Human Vaginal Epithelial Organoids as a Model for Epithelial Homeostasis and Host

status: Public on Nov 28 2025

first: Jianchen

last: Peng

address: 2005 Songhu Road

institute: Fudan University

summary: While the vaginal epithelium is essential for female reproductive health, a mechanistic understanding of its homeostasis and diseases has remained elusive, in part because of the lack of model systems that recapitulate the stem cell niche of the native tissue. Here, we establish human vaginal epithelial organoids (hVEOs) and infect hVEOs with Candida demonstrated the model's capacity to recapitulate specific inflammatory responses, confirming its utility for host-pathogen research. In summary, this study provides a robust, physiologically relevant model for dissecting the molecular pathways of human vaginal homeostasis and disease, enabling the definition of pathogenic mechanisms and the screening of novel therapeutic strategies.

overall_design: Gene expression profiling analysis of Bulk RNA-seq data from human vaginal epithelial organoids (hVEOs) infected with different type of Candida for 12 hours, including Candida albicans (SC5314, 39A), Candida parapsilosis (83P), Candida glabrata (27G) and Candida tropicalis (48T). An additional control group (C) was also included.

first: Ran

last: Chen

first: Xiaofeng

last: Gong

first: Songnian

last: Yue

first: Tianshu

last: Sun

first: Roujie

last: Huang

first: Dong

last: Wang

first: Hao

last: Hu

first: Lei

last: Li

first: Bing

last: Zhao

first: Lan

last: Zhu


title: Vascular endothelial IRE1α promotes thrombospondin-1 mRNA decay and supports the functional adaptation of pancreatic islets upon metabolic stress

first: Xiaoge

last: Zhang

state: Hubei

address: BAYI road

institute: wuhan university

summary: It remains unknown whether ER stress response signaling has a metabolic regulatory role in ECs. Here, in mice with high-fat diet-induced obesity, we found that EC-specific ablation of IRE1α selectively impaired the compensatory adaptation of pancreatic islet function in response to metabolic stress. Loss of IRE1α in ECs resulted in significantly lower intra-islet angiogenesis, accompanied by defects in the compensatory growth of pancreatic islets and their capacity of glucose-stimulated insulin secretion, consequently leading to hyperglycemia. Mechanistically, IRE1α could downregulate the intra-islet EC expression of the mRNA encoding thrombospondin-1 (THBS1/TSP1), an endogenous anti-angiogenic factor implicated in islet function regulation and prediabetes, through its RIDD activity. Importantly, EC-specific depletion of THBS1 completely corrected these islet dysfunctions arising from IRE1α deficiency in ECs. Together, our findings demonstrate a critical role of the endothelial IRE1α suppression of THBS1 in governing the vascular support that enables the homeostatic adaptation of pancreatic islets to cope with overnutrition-associated metabolic stress.

overall_design: To investigate the physiological functions of IRE1α in endothelial cells under the challenge of excess nutrition, we generated endothelial cell IRE1α deletion strain and established a high fat diet (HFD)-induced obesity model. We intercrossed floxed IRE1α (Ern1fl/fl) mice with the VE-cadherin-CreERT2 line to create vascular endothelial cell-specific IRE1α-knockout (Ern1EC-KO) mice by a tamoxifen (Tam)-inducible system.To explore how IRE1α promotes intra-islets angiogenesis, we performed bulk RNA-seq transcriptome analysis of islets from Ern1fl/fl and Ern1EC-KO mice after 16-weeks HFD feeding.

first: Shijia

first: Yong

last: Liu


title: The Cartilage Oligomeric Matrix Protein (COMP) Gene Is Associated with High-Grade Bladder Cancer and Promotes Bladder Cancer Cell Proliferation

city: Beijing

first: Xin

last: Hong

address: No.1 Life Garden Road, Zhongguancun Life Science Park

department: Urology

institute: Peking University International Hospital

summary: Bladder cancer (BLCA) is a globally prevalent malignancy that poses a severe threat to patient health. Accurate high/low-grade classification of BLCA is critical for tailoring effective treatment strategies. This study integrated eight single-cell RNA sequencing (scRNA-seq) datasets and bulk RNA sequencing test from bladder tissues in our hospital, performing cell subpopulation annotation, differential gene expression analysis, and pathway enrichment analysis. Focusing on Cartilage Oligomeric Matrix Protein (COMP), we evaluated drug sensitivities and validated its functional role in BLCA using 5637 cell lines. Single-cell clustering identified distinct gene expression profiles between high/low-grade bladder epithelial cells, with the unfolded protein response pathway being most significantly enriched. Integrative analysis revealed COMP as a prognostic marker, positively correlated with 16 potential therapeutic drugs. In vitro experiments confirmed that COMP promotes BLCA cell proliferation. Our findings highlight COMP as an oncogenic driver in BLCA and provide drug targets for clinical translation.

overall_design: This experimental design focuses on investigating bladder cancer, encompassing multiple interconnected research components. Firstly, tissue samples were collected from 8 bladder cancer patients (6 low-grade and 2 high-grade cases) for RNA sequencing (RNA-seq) to profile genome-wide gene expression, while 8 public single-cell RNA sequencing (scRNA-seq) datasets (2 low-grade and 6 high-grade) were re-analyzed to dissect cellular heterogeneity and cell-type-specific expression signatures. Secondly, hematoxylin and eosin (H&E) staining was used to assess histological features and pathological grading of the tissues, and immunohistochemical (IHC) staining with antibodies against GFAP, CK, SOX-10, P53, P16, Ki-67, and CD34 was conducted to evaluate phenotypic characteristics, proliferation status, tumor suppressor gene expression, vascularization, and lineage-specific markers of the tumors. Thirdly, public RNA-seq datasets were re-analyzed to perform survival analysis (including overall survival [OS] and progression-free survival [PFS]) and explore the association between COMP (Cartilage Oligomeric Matrix Protein) expression and clinical outcomes, so as to determine COMP’s prognostic value. Additionally, gain-of-function (via COMP-overexpressing plasmid transfection) and loss-of-function (via RNA interference [RNAi] with COMP-targeting siRNAs) experiments were carried out to investigate COMP’s biological role, with empty vectors and non-targeting siRNAs as negative controls respectively. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to quantify COMP expression in bladder cancer tissues, cell lines, and transfected cells, using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal reference gene for normalization. Finally, functional assays including colony formation assay (to evaluate clonogenic potential), Cell Counting Kit-8 (CCK-8) assay (to assess proliferative capacity by generating growth curves), and drug sensitivity analysis (to calculate half-maximal inhibitory concentration [IC₅₀] values and evaluate changes in drug sensitivity) were performed to further explore the effects of COMP modulation on bladder cancer cells.

first: Hui

first: Tian

first: Xiaobing

last: Yang

first: Changzhen

last: Hao


title: Transcriptome profiling of oral keratinocytes cocultured with Th17 cells during Escherichia coli infection

city: Seoul

first: Min Gyu

last: Kang

address: Daehak-ro

institute: Seoul national university

summary: Oral lichen planus (OLP) lesions show chronic T cell–mediated inflammation and increased colonization by Escherichia coli, yet the mechanisms that enhance intracellular bacterial survival in oral keratinocytes remain poorly understood. In this study, we performed bulk RNA sequencing of the mouse oral keratinocyte line IMOK to examine how Th17 cells influence epithelial transcriptional responses during E. coli infection. IMOK cells were infected with an OLP-isolated E. coli strain and either cocultured with Th17 cells using a Transwell system (preventing direct cell–cell contact) or maintained without T cells, and total RNA was collected for transcriptome profiling. Gene expression patterns were compared between E. coli–infected IMOK cells with and without Th17 coculture to identify pathways affected by Th17-mediated modulation. Differential expression and functional analyses revealed Th17-associated signatures linked to changes in apoptosis, antimicrobial responses, and host defense pathways in oral keratinocytes. These data provide transcriptional insights into how Th17 cells influence epithelial responses to E. coli infection and may contribute to understanding immune–epithelial interactions relevant to OLP-associated inflammation.

overall_design: IMOK oral keratinocytes were either maintained uninfected or infected with an OLP-isolated Escherichia coli strain. To investigate the influence of Th17-derived soluble factors on epithelial responses, infected IMOK cells were cocultured with Th17 cells using a Transwell system that prevented direct cell–cell contact. Total RNA was collected from E. coli–infected IMOK cells with Th17 coculture and from infected IMOK cells without T cells. Bulk RNA sequencing was performed to identify transcriptomic changes associated with Th17-mediated modulation of apoptosis, antimicrobial responses, and host defense pathways in oral keratinocytes.

first: Mingyu

first: Youngnim

last: Choi


title: Tbr2-dependent transcriptomic analysis

city: Houston

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

summary: Tbr2 is expressed in all ipRGC cells from development to adulthood, and the Tbr2-Opn4 transcriptional cascade is the main pathway regulating ipRGC formation. In this study, we used bulk RNA-seq to compare transcriptome profiles of E15.5 WT and Six3-Cre:Tbr2-f/f retinas, aiming to identify new regulators in ipRGC subtype development.

overall_design: Twelve retinas from E15.5 wildtype and Tbr2f/f;Six3-Cre embryos from multiple litters were pooled and RNA were extracted using RNAeasy mini kit (QIAGEN). Bulk RNA sequencing were performed in Novogene. Sequencing library were prepared using standard Illumina protocol. RNA sequencing were performed using Illumina HiSeq 6000. Illumina Casava was used for basecalling. The RNA-seq reads were mapped to the mouse genome (mm10) via STAR (v2.5). HTSeq (v0.6.1) was used to count the read numbers mapped to each gene. Differential expression analysis of two groups was performed using the DESeq2 R package (v2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value<0.05 were considered as differentially expressed.

first: Takae

last: Kiyama


title: AP-1 Mediates Cellular Adaptation and Memory Formation [scRNA-seq]

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building, 415 Curie Boulevard

institute: University of Pennsylvania

summary: Cellular responses to environmental stimuli are typically thought to be governed by genetically encoded programs. We demonstrate that cancer cells can form and maintain cellular memories when becoming drug resistant, exhibiting characteristics of cellular learning that are dependent on the transcription factor AP-1. We show that cells exposed to a low dose of therapy adapt to become resistant to a high dose, demonstrating that cells can adapt during this time of stress. The application of therapy itself results in the encoding of transient gene expression into cellular memory and that this encoding occurs for both transiently induced and probabilistically arising expression. Chromatin accessibility showed concomitant persistence. A two-color AP-1 reporter system showed that these memories are encoded in cis, constituting an example of activating cis epigenetics. Our findings establish the formation and maintenance of cellular memories as a critical aspect of gene regulation during the development of therapy resistance.

overall_design: scRNA-seq, bulk RNA-seq, and ATAC-seq profiling of WM989 A6-G3 melanoma cells under various treatment conditions


title: AP-1 Mediates Cellular Adaptation and Memory Formation [ATAC-seq]


title: AP-1 Mediates Cellular Adaptation and Memory Formation [Bulk RNA-seq]


title: Study on the Pathogenic Role and Mechanism of ADAMTS4 in Ulcerative Colitis

city: Chengdu

first: Ming

last: Chen

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

institute: West China Hospital of Sichuan University

summary: ADAMTS4 is an enzyme with proteolytic activity, primarily involved in the degradation of the extracellular matrix (ECM). In recent years, the role of ADAMTS4 in various inflammatory diseases has garnered increasing attention. Ulcerative colitis (UC) is a chronic and relapsing inflammatory bowel disease, the etiology and pathogenesis of which remain incompletely understood. This study aims to investigate the pathogenic role and mechanism of ADAMTS4 in UC and evaluate the effects of ADAMTS4 knockout on colitis. Investigating the pathogenic role of ADAMTS4 in UC holds potential significance for providing new therapeutic targets and developing novel therapeutic strategies for UC.

overall_design: RNA-Seq was performed on ADAMTS4 knockout mice and WT mice after 7 days of DSS treatment.

first: Chengwei

last: Tang

first: Zhiyin