title: FGF8 induces bone and joint regeneration at middle phalanx amputation wounds in neonate mice

city: Bryan

first: Andreea

last: Trache

state: TX

address: 402 John Sharp Pkwy

department: Medical Physiology

institute: Texas A&M University

summary: Mice and humans have limited regenerative capacity following limb amputation, with regenerative responses restricted to amputations transecting the distal digit tip, (P3). Unlike P3, amputations of the adjacent skeletal segment, the middle phalanx, P2, are non-regenerative. Here, we report that FGF8 drives synovial joint regeneration at P2 amputation wounds in neonate mice. This response is characterized by the regeneration of a synovial cavity, a skeletal nodule lined with articular-like cartilage, tendon and ligament regeneration, and partial P2 stump regeneration. FGF8-induced joint regeneration is associated with the upregulation of several, but not all, genes that characterize joint development, and is morphologically distinct from digit joint development. Lineage tracing studies demonstrate that cells at the amputation wound contribute to the regenerated joint structures. These studies provide evidence that the otherwise non-regenerative P2 amputation wound possesses tremendous regenerative capacity that is not activated under normal circumstances.

overall_design: scRNA-seq analysis of middle phalanx amputations in neonate mice (8 days postnatal, PN8).

first: Ling

last: Yu

first: Mingquan

last: Yan

first: Sarah

last: Wolff

first: Joseph

middle: D

last: Knue

first: Hannah

last: Smith

last: Dolan

first: Ken

last: Muneoka

first: Selim

last: Romero

first: James

last: Cai

first: Carissa

last: Yun

first: Devon

last: Boland

first: Regina

last: Brunauer

first: Lindsay

last: Dawson


title: The iPSC-derived pulmonary epithelial cells in micro-patterned culture plate

status: Public on Feb 18 2026

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We established a system of generating alveolar or airway organoids in a micro-patterned culture plate. In this system, various lung cell types were identified, depending on the culture condition.

overall_design: Human iPSC-derived lung progenitor cells were seeded onto micro-patterned plates and cultured in "DCIK+3i" (CHIR99021, SB431542 and Y27632) medium for 7 days to induce alveolar organoids involving alveolar type 2 cells in the DCIK+3i medium. Thereafter, the alveolar organoids were cultured in the following three conditions for 7 days: "DCIK+3i" to maintain alveolar type 2 cells, "DCI+LATS(LATS-IN-1)" to induce alveolar type 1 cells, or "PAL" to induce alveolar transitional state cells (iATCs), respectively. The organoids in each condition were dissociated using Accutase and subjected to CUT&TAG analysis.

first: Yusuke

last: Tsutsui

first: Taro

last: Tsujimura

first: Takuya

last: Yamamoto


title: Faecalibacterium prausnitzii as a probiotic strategy against metabolic dysfunction-associated steatohepatitis

city: Nanjing

first: Han

last: Chen

state: Jiangsu

address: #300 Guzhou Road, Gulou District

country: China

institute: Nanjing Medical University

type: Expression profiling by high throughput sequencing

summary: A high-fat diet (HFD) was administered to C56BL/6 mice for 16 weeks. The intragastric injections of F. prausnitzii strains was administrated and changes in serum and liver metabolic indicators were then assessed. RNA-sequence (RNA-seq) was performed to identify differently expressed genes related to F. prausnitzii treatment.

overall_design: RNA-seq profiling of the liver tissue after intragastric injections of F. prausnitzii strains.


title: Low expression of ALOX15B modulates immunosuppressive tumor microenvironment in diffuse large-B cell lymphoma via the TAP1/MHC-I axis

city: ChengDu

first: yucui

last: shang

address: No. 12 Linyin Street, Wuhou District

department: State Key Laboratory of Biotherapy and Cancer Center

institute: SiChuan University

summary: The arachidonic acid (AA) metabolism is closely related to tumor immune evasion and chemo-resistance. ALOX15B (arachidonate 15-lipoxygenase type B), located on chromosome 17p, encodes a key enzyme in AA pathway. Interestingly, the expression of ALOX15B is independent of 17p status but is epigenetically regulated. Low ALOX15B expression predicts poor prognosis, with PGE2 activation and TAP1 suppression, reducing MHC-I expression and creating an immunosuppressive microenvironment. Tucidinostat, a histone deacetylase (HDAC) inhibitor, restores ALOX15B and enhances the TAP1/MHC-I axis, thus promoting lymphoma cell apoptosis, which correlates with the effect of tucidinostat plus immunochemotherapy in a phase II trial of patients with newly diagnosed DLBCL (NCT02753647). Our study provides insight into a novel therapeutic strategy to improve patient prognosis by epigenetically modulating lymphoma metabolism and optimizing the tumor microenvironment.

overall_design: Bone marrow-derived B220+ B progenitor cells were transduced with retroviruses and then administered via tail-vein injection into C57BL/6 mice that had been sublethally irradiated (4.5 Gy, Cs137). All mice were randomly grouped before transplantation and were monitored twice a week until the start of treatment. Drug treatment was initiated 7 days after transplantation to ensure tumor engraftment in the shALOX15B group. The mice were randomly assigned to two groups: one group was treated with vehicle solution consisting of 0.2% carboxymethylcellulose saline and 0.1% Tween 80, while another group received tucidinostat at a dose of 12.5 mg/kg/day administered once daily via oral gavage. Pharmacological treatment was administered until tumors were observed in all subjects in the vehicle group. Single-cell RNA sequencing (scRNA-seq) was performed to analyze the transcriptional profiles of the tumor microenvironment or specific cell subpopulations.

first: Lanxin

last: Zhang

first: Yucui

last: Shang


title: Hh and EGFR-Ras signaling promote distinct steps of tumor progression in the Drosophila follicle epithelium

city: Marburg

first: Katja

last: Rust

address: Emil-Mannkopff-Str. 2

country: Germany

institute: Phillips-University Marburg

summary: Controlled signaling activity is vital for normal tissue homeostasis and oncogenic signaling activation facilitates tumorigenesis. Here we combine single-cell transcriptomics with in-depth genetic and imaging analysis to investigate the role of the EGFR-Ras and Hedgehog signaling pathways in homeostasis of the Drosophila follicle stem cell lineage. We find that Hedgehog signaling simultaneously promotes an undifferentiated state and induces differentiation via activation of the epithelial-mesenchymal-transition associated transcription factor Zfh1. Overactivation of Hedgehog signaling generates a mixed transcriptional state comparable to partial epithelial-mesenchymal-transition. EGFR-Ras overactivation induces cell cycle defects by activating the transcription factors Pointed and E2f1 and impedes differentiation. Overactivation of both pathways blocks differentiation and induces tumor-like growth where follicle cells exhibit a loss of tissue architecture, sustained proliferation and a reduced lifespan of the host. These findings provide new insight into how signaling pathways converge at the transcriptional level to prevent malignant cell behavior.

overall_design: Females of the appropriate genotype were raised at 18°C and shifted to 29°C for 5 days and fed wet yeast daily in the presence of males. Ovaries were dissected and late stages were removed. A single cell suspension was prepared and subjected to single-cell RNA-seqencig using 10x Chromium Next GEM Single-Cell 3´LT Kit v3.1. The resulting libraries were sequenced using NovaSeq 6000 (Illumina).

first: Sari

last: Anschütz

last: Müller

first: Andrea

last: Schubert

first: Jobelle

middle: M

last: Peralta

first: Todd

middle: G

last: Nystul


title: The iPSC-derived pulmonary epithilial cells in micro-patterned culture plate [scATAC-seq]

overall_design: Human iPSC-derived lung progenitor cells were seeded onto micro-patterned plates and cultured in "DCIK+3i" (CHIR99021, SB431542 and Y27632) medium for 7 days to induce alveolar organoids involving alveolar type 2 cells in the DCIK+3i medium. Then, the culture medium was switched to DCI+LATS(LATS-IN-1) medium to induce AT1 cells or "PAL" medium to induce alveolar transitional state cells (iATCs), respectively. The organoids in each condition were dissociated using Accutase and subjected to single-cell RNA sequencing analysis.


title: The iPSC-derived pulmonary epithilial cells in micro-patterned culture plate [CUT&Tag]


title: Modeling of spontaneous pulmonary fibrosis via cellular senescence in type 2 alveolar epithelial cells derived from human iPSCs [HFLF]

summary: Telomere dysfunction in type II alveolar epithelial (AT2) cells causes pulmonary fibrosis in a subset of patients. TRF2 is a key component of the shelterin complex (SC) which prevents abnormally shortened and uncapped telomeres and genetic variants of SC were reported in some familial cases of IPF. We conceived that in vitro senescence model of AT2 cells derived from human induced pluripotent stem cells (iPSCs) would be beneficial for elucidating the mechanism of IPF progression. Then we generated an iPSC line using a doxycycline (dox) -inducible lentiviral vector encoding the dominant negative variant of TRF2 (TRF2DN). We next differentiated this iPSC line into AT2 (iAT2) cells and expressed TRF2DN protein in a dox-inducible manner. Alveolar organoids consisting of TRF2DN-expressing iAT2 cells and human fetal lung fibroblasts showed contraction of the organoid matrices

overall_design: Alveolar organoids composed of tet-on TRF2DN iPSC line (T67)-derived alveolar epithelial cells and human fetal lung fibroblasts (HFLFs) were treated with or without doxycycline (DOX) for 8 days. For gene expression profile analysis, HFLFs were isolated from the organoids through magnetic activated cell sorting using anti-EpCAM antibody.


title: Targeting CPT1A triggers cGAS/STING activation to engage neutrophils for tumor elimination

city: Chongqing

first: Chenglong

last: LI

address: No. 30 Gaotanyan Zhengjie, Shapingba District

institute: Army Medical University

summary: Lipid metabolism plays an important role in tumor progression and immune evasion. Targeting fatty acid oxidation (FAO) has been shown to be a promising approach to treat cancers. However, the impact of FAO inhibition on tumor immune microenvironment is still less understood. In this study, we found that inhibiting FAO by targeting CPT1A dramatically triggers cGAS/STING activation through inducing cytoplasmic leakage of mitochondrial DNA. This leads to the infiltration of neutrophils into tumors and drive anti-tumor effects of a subset of neutrophils, which plays a crucial role in inhibiting tumor growth. Our current findings suggest that CPT1A could be a promising target for TNBC therapy and, moreover, we uncover an essential anti-tumor role of neutrophils upon cGAS/STING activation.

overall_design: Using CD8 antibody had a limited effect on impeding the tumor regression induced by Cpt1a depletion, suggesting that other unknown immune cells may also contribute to tumor clearance in the context of Cpt1a deficiency.Thus, we conducted single-cell RNA sequencing (scRNA-seq) on the 4T1 tumor samples to dissect the alterations in cellular composition upon Cpt1a depletion.

last: Li

first: Tingfang

last: Gao

first: Qiuling

last: Zhao

first: Zhidong

last: Wang

first: Mengsi

first: Zhi

first: Xuehang

last: Meng


title: Inhibition of the non-lysosomal glucosylceramidase GBA2 accounts for the efficacy of sinbaglustat in a murine model of Sandhoff disease

city: Allschwil

first: Pijus

last: Brazauskas

address: Hegenheimermattweg 91

country: Switzerland

institute: Idorsia Pharmaceuticals

summary: Sinbaglustat is a small molecule under investigation as a treatment for lysosomal storage disorders. It inhibits two enzymes involved in glycosphingolipid (GSL) metabolism, the non-lysosomal glucosylceramidase (GBA2) and, with a lower affinity, glucosylceramide synthase (GCS). High  doses of structurally related dual GBA2/GCS inhibitors such as miglustat, and pure GCS inhibitors have shown efficacy in a transgenic mouse model (Hexb-/-) of Sandhoff disease, aGM2 gangliosidosis. Whether the inhibition of GBA2 alone confers protection is unknown. We first assessed the functional profile of sinbaglustat relating to GBA2 and GCS inhibition in cellular models and wild-type (WT) mice. Then we investigated sinbaglustat’s potential efficacy in preventing disease manifestation in Hexb-/- mice upon chronic treatment with two dose levels (30 and 300 mg/kg/day), aimed at predominant inhibition of GBA2 or GBA2 and GCS. Non-treated WT mice served as controls. Sinbaglustat inhibited GBA2 more potently than GCS in GM2 gangliosidosis patient-derived fibroblasts and primary mouse neurons. The dual inhibition profile was also reflected in a dose-dependent, bell-shaped modulation of glucosylceramide, the substrate of GBA2 and product of GCS  , in wild-type mouse brain. At the two sinbaglustat dose levels that we tested in Hexb-/- mice, glucosylceramide levels in cerebral cortex were elevated, indicating GBA2 target engagement. Only the high 300 mg/kg/day dose reduced in addition the levels of various other GSLs compared to Hexb-/- untreated mice, demonstrating GCS target engagement in the central nervous system. In the liver and plasma, sinbaglustat dose-dependently decreased many GSLs including hexosaminidase A substrates. Sinbaglustat partially reversed the increase in mRNA expression of several neuroinflammation-related genes in the hippocampus of Hexb-/- mice. Sinbaglustat treatment at both dose levels delayed the age at which Hexb-/- mice started to develop motor impairments by about 2-4 weeks. The 30 mg/kg/day dose increased median survival of Hexb-/- mice by approximately 13.5%, the 300 mg/kg/day dose by approximately 18%.  The study indicates that sinbaglustat could represent a viable treatment option for GM2 gangliosidosis if data from the mouse model translate to human. Importantly, our data also reveal that GBA2 inhibition in the central nervous system is largely responsible for sinbaglustat’s therapeutic effect in Hexb/- mice.

overall_design: RNAseq of the hippocampus of Hexb/- mice (hexβtm1R1p) and WT littermates treated with singablustat from week 4 to week 15 at either 30 mg/kg/day, for primary inhibition of GBA2, or 300 mg/kg/day, for inhibition of both GBA2 and GCS. Untreated Hexb /- and untreated WT mice served as comparator and control.

first: Michel

middle: A

last: Steiner

first: Kostantin

last: Dobrenis

first: Catherine

last: Vaillant

first: Jesper

last: Ryge

first: Bérengère

last: Renault

first: Richard

last: Welford


title: Modeling of spontaneous pulmonary fibrosis via cellular senescence in type 2 alveolar epithelial cells derived from human iPSCs [epithelial]

first: Shimpei

last: Gotoh

overall_design: Alveolar organoids composed of tet-on TRF2DN iPSC line (T67)-derived alveolar epithelial cells and human fetal lung fibroblasts (HFLFs) were treated with doxycycline (DOX) for 8 days, supplemented with compounds during the final 3 days of the treatment. For gene expression profile analysis, epithelial cells were isolated from the organoids through magnetic activated cell sorting using anti-EpCAM antibody.

first: Yusuke

last: Tsutsui

first: Takuya

last: Yamamoto


title: Human PSC-based Modeling of Pulmonary Fibrosis Identifies p300/CBP Inhibition as a Suppressor of Alveolar Transitional Cell State [BLM]

summary: In this study, we conducted a drug screening using an in vitro pulmonary fibrosis model and identified p300/CBP inhibitors as candidate therapeutic agents. We investigated the mechanisms underlying the emergence of the alveolar transitional cell state (ATCS) with human PSC-derived alveolar organoids.

overall_design: Alveolar organoids composed of SPC-GFP reporter iPSC line (B2-3)-derived alveolar epithelial type 2 (AT2) cells and human fetal lung fibroblasts (HFLFs) were treated with DMSO or BLM for 3 days , followed by an additional 3-day incubation with or without compounds. For gene expression profile analysis, HFLFs were isolated from the organoids through magnetic activated cell sorting using anti-EpCAM antibody.


title: The iPSC-derived pulmonary epithilial cells in micro-patterned culture plate [scRNA-seq]

first: Satoko

last: Sakurai


title: KDM5B promote tumorigenesis in MCF-7 cells

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: RNA-seq analysis was performed to identify key genes and signaling pathways responding to KDM5B knockdown in MCF-7 cells.

overall_design: six independent sample groups with knock down of KDM5B (shKDM5B) and controls (shSCR) in MCF-7 cell lines and were analyzed through RNA-seq.

first: Yunkai

last: Yang

first: Baowen

last: Yuan

first: Yan


title: Single-cell RNA-seq of Xenopus laevis spinal cord during metamorphosis

city: Klosterneuburg

first: Yuri

last: Ignatyev

address: Am Campus

country: Austria

institute: ISTA Austria

summary: We performed single-cell RNA sequencing of the Xenopus laevis spinal cord during metamorphosis, from swimming stages (NF37–38, NF47–48) to limb stages (NF54–55, NF57–58), using the 10x Genomics platform. This dataset captures the evolutionary swim-to-limb transition in a single organism and enables analysis of how spinal circuit composition changes to support aquatic versus terrestrial motor patterns.

overall_design: Spinal cord tissue was dissected from 295 NF47-48, 10 NF54-55, and 5-10 NF57-58  animals and pooled into 4 (NF47-48 and NF54-55) or 6 (NF57-58) technical replicates. At NF37-38, due to the small body size, the dorsal trunk was dissected from 230 animals, removing the belly and head at hindbrain boundary, and pooled into 4 total replicates. For all stages, acquired tissue was dissociated with liberase to obtain single-cell suspension according to previously published methods, and FACS-sorted for the presence of GFP using a BD FACS Aria III Cell Sorter. All animals, except for one replicate from NF57-58 batch, were transgenic Xla.Tg(tubb2b:maptGFP)Amaya (EXRC), expressing GFP under neuron-specific tubb2b transcriptional control, enabling us to enrich neuronal cells. Cells were further sequenced and analyzed using scRNA-seq.

first: Mariano

middle: I

last: Gabito

first: Lora

middle: B

last: Sweeney


title: Splicing Factor 3a Subunit 1 Promotes Colorectal Cancer Growth via Anti-programmed cell death of Syntaxin12.

city: Asahikawa

first: Hiroaki

last: Konishi

address: 2-1-1-1, Midorigaoka-higashi

institute: Asahikawa Medical University

summary: SF3A1 is a subunit of the SF3a complex, an integral component of U2 snRNP, playing a crucial role in intron recognition and pre-RNA splicing during the splicing process. Notably, we observed that SF3A1 exerts its growth-promoting effects specifically in cancer cells, despite no discernible alteration in expression levels between tumor and normal cells. Genetic mutations in SF3A1 may play a role in pancreatic cancer development, and a reported correlation exists between SF3A1 gene polymorphisms and colorectal cancer (CRC) risk. However, the specific mRNAs with which SF3A1 interacts in CRC and whether this interaction is directly implicated in tumor growth remain unclear. In this study, our purpose was to elucidate the mechanisms of SF3A1-mediated tumor progression in colorectal cancer cells.

overall_design: RNA sequencing profile of HCT116 transfected scrambled RNA or siRNA of SF3A1. RNA sequencing of RNA immunoprecipitation using IgG antibody or anti SF3A1 antibody.


title: CUL4B and KDM5B ChIP-sequencing in MCF-7 cells

summary: Estrogen receptor-positive (ER+) breast cancer is the predominant subtype of breast cancer. Here, we investigate the functional interplay between lysine demethylase 5B (KDM5B) and the Cullin-RING ligase 4B (CRL4B) complex in modulating cholesterol metabolism to promote ER+ breast cancer progression. We found that disrupting the KDM5B–CRL4B axis impairs cholesterol homeostasis and inhibits tumor growth.

overall_design: Examination of KDM5B and CUL4B target genes in MCF-7 cell line.

last: Wang


title: The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguard metabolic and cellular homeostasis

city: La Jolla

first: William

last: Dion

state: CA

address: 10550 N Torrey Pines Rd

country: USA

institute: Scripps Research

summary: Proteostasis is vital for cellular health, with disruptions leading to aging, neurodegeneration and metabolic disorders. Traditionally, proteotoxic stress responses were studied as acute reactions to various noxious factors; however, recent evidence reveals that many proteostasis genes exhibit ~12h ultradian rhythms under physiological conditions in mammals, driven by an XBP1s-dependent 12h oscillator. By examining the chromatin landscape of this oscillator, we identified RBBP5 as an essential epigenetic regulator of global proteostasis dynamics. Mechanistically, as the core subunit of the SET1/COMPASS complex, RBBP5 co-activates XBP1s to facilitate dynamic proteostasis gene expression by marking promoter-proximal H3K4me3, which further recruits the Integrator Complex and SWI/SNF chromatin remodelers. Functionally, RBBP5 is indispensable for regulating both the 12h oscillator and acute transcriptional response to various proteotoxic stresses, including ER stress and nutrient deprivation. RBBP5 ablation causes increased susceptibility to proteotoxic stress, chronic inflammation, and hepatic steatosis in mice, along with impaired autophagy and reduced cell survival in vitro. In humans, lower RBBP5 expression is associated with reduced adaptive stress-response gene expression and hepatic steatosis. Our findings not only highlight a previously unrecognized epigenetic timing mechanism distinct from circadian regulation but also establish RBBP5 as a central regulator of proteostasis, essential for cellular resilience and organismal health.

overall_design: Rbbp5 (flox/flox); Rosa26 CRE (+/+) MEFs were cultured in full DMEM supplemented with 10% FBS, treated with (RBBP5 KO) or without tamoxifen for seven days before subject to full medium or EBSS treatment for 16 hours.

first: Bokai

last: Zhu

first: Syeda

last: Kubra

first: Hannah

last: Luong

first: Jian-Hua

last: Luo

first: Jia-Jun

last: Liu

first: Silvia


title: Dissecting the binding behavior of the multi-RRM endosomal mRNA transporter Rrm4 [RNA-seq]

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

summary: RNA-binding proteins (RBPs) are central players in determining the life cycle of RNA molecules. These proteins are often modular in arrangement, featuring multiple RNA-binding domains, to enhance RNA recognition and functionality. How these multiple RNA-binding domains within individual RBPs work in concert to recognize mRNA targets is still poorly studied. In the model fungus Ustilago maydis, the multi-RRM domain protein Rrm4 plays a key role in mediating the long-distance mRNA transport on the cytoplasmic surface of early endosomes, thereby precisely regulating spatiotemporal gene expression. Rrm4 contains three RNA-recognition motifs (RRMs), organized in an ELAV-like pattern: a tandem RRM domain (RRM1,2) and a separate third RRM domain (RRM3). Utilizing Rrm4 variants with mutations in the RRM domains, we conducted a differential iCLIP analysis to dissect the RNA recognition code of individual RRM domains. Our study reveals that Rrm4 exhibits two binding mode: (i) a one-to-one interaction where the third RRM domain alone binds RNAs by recognizing the shot UAUG motif. (ii) an intricate composite binding mode where all three RRM domains cooperatively bind RNA. Improtantly, our finding demonstrates that it is not the simple one-to-one interaction but rather the complex cooperative binding mode, involving all three RRM domains, is critical for Rrm4 function in maintaining the unipolar growth of the fungal hyphae.

overall_design: Differential gene expression analysis comparing hyphal cells either lacking rrm4 gene or carrying mutations in one or all RRM domains of Rrm4 with wildtype hyphal cells expression functional Rrm4 protein.

first: Nina

middle: K

last: Stoffel

first: Srimeenakshi

last: Sankaranarayanan

first: Anke

last: Busch

first: Julian

last: König

first: Michael

last: Feldbrügge


title: Loss of Larp1 disrupts the synaptic localization of TOP mRNAs and impairs spatial memory.

city: New Haven

first: Carson

middle: C

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

summary: Post-transcriptional regulation of mRNAs allows for rapid and local control of gene expression. In vertebrates, the mTOR Complex 1 pathway post-transcriptionally controls the translation and stability of terminal oligopyrimidine motif mRNAs (TOP mRNAs), which encode ribosomal proteins and other essential factors. These mRNAs also preferentially localize to neuronal synapses, axons and dendrites, suggesting a role in growth and/or plasticity. To determine brain functions of TOP regulation, we generated mice where La-related protein 1 (Larp1), the TOP regulator downstream of mTORC1, is inactivated in neurons. These mice are viable but brain size is significantly reduced. The translation of TOP mRNAs is derepressed, but mRNA levels are depleted more than 50%. Depletion was exacerbated at synapses, reversing the enrichment observed in wild-type neurons, and accompanied by impaired spatial memory. These observations highlight the importance of post-transcriptional regulation of TOP mRNAs for brain growth and neuronal functions underlying learning and memory.

overall_design: RNA was isolated from 3 Nestin-Cre male mice and 3 Nestin-Cre;Larp1-flox/flox mice and used to prepare RNA-seq libraries using the NEB Ultra II Directional RNA-seq library preparation kit.

first: Mark

middle: S

last: Williams

first: Maegan

middle: J

last: Watson


title: A pipeline to unravel complexity of the human peripheral blood B cell compartment through multiomic cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) analyses

city: Milwaukee

first: Bonnie

last: Dittel

address: 8727 Watertown Plank Rd

institute: Versiti

summary: Classifying heterogeneous human B cells into discrete subsets based on surface phenotype alone remains a major challenge. We discovered a mouse splenic IgM+IgDlow/- B cell subset (BDL) that induces proliferation of CD4+Foxp3+ T regulatory cells, making them a therapeutic target for autoimmunity. Because they are rare and lack sufficient cell surface markers, a multiomic strategy is required to identify and track them. The lack of correlation between mRNA expression levels and cell surface expression is a drawback to a transcriptome-only scRNA-seq approach because ‘novel’ cell populations identified by surface protein transcripts may prove impossible to validate. Thus, a pipeline was developed using human peripheral blood (PB) IgM+IgDlow/- B cells. First, a standardized flow cytometry gating scheme (CD27 versus IgD and CD24 versus CD38) that captures all major human PB B cell subsets was utilized. Second, CD19+IgM+IgDlow/- PB B cells were tagged with the four markers using cellular indexing of transcriptomes and epitopes by sequencing. Biaxial plots similar to flow cytometry were used to identify naïve, transitional, and memory B cells, and then confirmed with scRNA-seq. These studies using a multiomic workflow allowed the identification of IgM+IgDlow/- B cells by cell surface expression that could subsequently be analyzed for unique transcriptional profiles.

overall_design: We performed scRNA sequencing to characterize BDL, a rare B cell subset in the heterogeneous CD19+IgM+IgDlow/- B cell compartment within human peripheral blood. We combined this technology to CITE-sequencing to obtain measurement at the protein and transcriptome level and to multiplex samples in order to measure these data simultaneously across three deidentified human donor samples: (3) CD19+IgM+IgDlow/- B cells and (1) CD19+IgM+IgDhigh B cells (negative control). All samples were stained with a panel of ADT (CD27, CD21, CD24, CD38) which were used to recreate flow cytometric analyses at the single cell level.

first: Nathan

last: Meinhardt

first: Anthony

last: Veltri

first: Cody

last: Gurski

first: Sophia

last: Valenti

middle: N


title: Effects of propofol on human brain organoids at different maturational stages

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: Human brain organoids were derived from the H1 human embryonic stem cell line and exposed at different developmental stages to propofol (50 µM) for 3 days in vitro (div). Human brain organoids were investigated in four experimental groups at two developmental stages, 60 div and 90 div, including mock-treated groups as control and propofol-treated groups (from 47-50 div or 77-80 div, n=5 each). Our results suggest that propofol affects synapse-associated gene expression and neuronal activity differently at specific developmental stages.

overall_design: Four experimental groups at two developmental stages, 60 div and 90 div, including mock-treated groups as control and propofol-treated groups (from 47-50 div or 77-80 div, n=5 each).

last: Schaefer

first: Sudena

last: Wang


title: Multifunctional exosomes inhibiting autophagy ameliorate immune tolerance in non-small cell lung cancer

city: Changchun

first: Simiao

state: other

address: Jilin university

institute: Simiao Wang

summary: The modulation of tumor autophagy to enhance antitumor immunity has garnered significant attention, underscoring its critical role in cancer immunotherapy. However, advanced strategies for precise autophagy-regulating drug delivery remain a pressing need. Here, we introduce a targeted exosome-based drug delivery system capable of simultaneously loading antibodies and nucleic acid drugs while ensuring their accurate release in the tumor microenvironment (TME). We developed a dual-stimulation electroporation system integrating nanosecond electric pulses and ultrasound to enhance exosome production, yielding IL-7 mRNA-enriched exosomes overexpressing CD64 receptors for efficient anti-PD-L1 antibody capture. These multifunctional autophagy-inhibiting and immunomodulatory exosomes (AI-Exos) are designed to inhibit autophagy and modulate immune responses in lung cancer. Upon delivery to the tumor site, AI-Exos mediate the enzymatic cleavage of peptide bonds to release IL-7 mRNA. This process induces autophagy suppression and restores MHC-I expression, which synergizes with anti-PD-L1 immune checkpoint inhibition to overcome acquired drug resistance and enhance antitumor efficacy. In conclusion, this study proposes an innovative methodology utilizing engineering exosomes for the co-delivery of protein antibodies and genetic materials. This approach establishes a promising strategy to advance cancer immunotherapy through targeted autophagy modulation.

overall_design: Single-cell sequencing analysis of immune cells in mouse non-small cell lung cancer after drug treatment.


title: Decoding hypoxia-induced DNA Methylation patterns in Meningioma tumorigenesis

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

type: Methylation profiling by genome tiling array

summary: Tumor development relies on numerous factors, including the capacity to adapt to hypoxic conditions. Hypoxic microenvironment is a critical driver of the malignant phenotype, which is often correlated with meningioma grade, aggressive behavior, therapeutic resistance, and higher recurrence rates, leading to poor prognosis. Epigenetic alterations are key regulators of gene expression. Changes in DNA methylation patterns are the most extensively characterized epigenetic modifications associated with tumorigenesis. Metastasis, severity, and recurrence of meningioma have all been associated with hypo- and hypermethylation of various genes. We aim to identify the hypoxia-induced genome-wide DNA methylation profile of meningioma.

overall_design: Genomic DNA was extracted from hypoxia-treated and non-treated (Normoxic) IOMM-Lee cells (2 replicates for each) using QIAamp DNA Mini Kit (QIAGEN). The DNA concentration and quality were measured using a NanoDrop 2000 (ThermoFisher Scientific) spectrophotometer. With the use of the EZ DNA Methylation kit (Zymo Research), the extracted DNA was sodium bisulfite converted. Bisulfite-treated samples were subsequently processed using the Illumina Infinium MethylationEPIC v2.0 array (Illumina), as per the manufacturer's instructions.

first: Ritu

first: Aniruddha

last: Chatterjee


title: Unraveling Hypoxia-Driven Gene and Methylation Signatures in Meningioma: Identifying Novel Biomarkers and Therapeutic Targets

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

overall_design: Refer to individual Series


title: Circadian reprogramming of protein homeostasis and glycolipid metabolism in diabetic nephropathy

city: Zhengzhou

first: Xiao-Qian

last: Li

state: Henan

address: No. 1, East of Jianshe Street, Erqi District

department: Nephrology Hospital

institute: the First Affiliated Hospital of Zhengzhou University

summary: Background Dysfunction of the circadian clock has been implicated in the pathogenesis of a variety of diseases, including metabolic disorders, inflammatory conditions, and cancer. While the significance of circadian rhythm in diabetic nephropathy is gaining attention, the specific alterations in circadian profiles in diabetic nephropathy remain unexplored. Methods In the present study, we performed RNA sequencing on renal cortex samples collected every 4-hour across the day from both control and diabetic mice. The rhythmicity of genes was identified using the JTK_CYCLE algorithm for each group. Genes that lost, acquired, or sustained rhythmicity in diabetic mice were denoted the circadian dysregulation gene-set. Subsequent bioinformatic analyses focused on this gene set to investigate the circadian reprogramming in diabetic nephropathy. Results We observed significant circadian disruption in the kidney of diabetic mice, marked by both the gain and loss of rhythmicity, along with alterations in the phase and amplitude of genes that retained rhythmic expressions. Circadian disturbances such like phase shifts and alterations in relative amplitude or mesor, were noted in core clock genes. Furthermore, genes that lost rhythmicity in diabetic nephropathy were predominantly associated with protein homeostasis and glycolipid metabolism, whereas those that gained rhythmicity were mainly linked to gene regulation, fatty acid metabolism, and protein transport. The genes in the circadian dysregulation gene-set that exhibit differential expression at least at one Zeitgeber time, were most prominently enriched in lipid metabolic process. WGCNA and correlation analysis revealed co-expression networks involving core clock genes and PPAR signaling pathway with renal triglyceride levels. Conclusions Our study reveals substantial circadian disruption in diabetic nephropathy, with significant impacts on protein homeostasis and glycolipid metabolism. Furthermore, our findings highlight the potential influence of circadian system dysregulation on the disorder of fatty acid metabolism in diabetic nephropathy.

first: Lei

last: Cheng

first: Tian-Fen

last: Chen

first: Lu-Yao

first: Yi-Nuo

last: Ma

first: Xiao-Hui

first: Ting-Yu

last: Fu

first: Jing

last: Xiao

first: Zhan-Zheng

last: Zhao


title: The Impact of Silencing Hepatic AATF on Transcriptomic and Metabolomic Signatures in Experimental MASH

city: Mysore

first: Divya

middle: P

last: Kumar

state: Karnataka

address: SS Nagar

department: Biochemistry

institute: JSS Medical College

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects 30% of the global population and has emerged as a significant public health concern. It is a multifactorial pathological condition driven by various molecular influencers. Thus, identifying and understanding the molecular drivers of MASLD pathogenesis is essential for developing targeted therapeutic strategies. Here, we elucidate the role of apoptosis antagonizing transcription factor (AATF) as a molecular driver in the pathogenesis of MASLD. Liver-specific silencing of AATF reduced body weight, liver weight, and insulin resistance in WD mice compared to WD controls. Biochemical, histological, and molecular analyses showed reduced liver injury, and steatosis. Transcriptomics analysis showed reduced cellular stress response, inflammation and fibrosis in WDsiAATF. Furthermore, untargeted metabolomics revealed increased biosynthesis of glycerophospholipids and promoted fatty acid oxidation while reducing the triglyceride accumulation. These findings show a molecular link between AATF and hepatic lipid metabolism, implying that AATF could be a promising therapeutic target for MASLD.

overall_design:
We used adeno-associated vectors (AAV) to create a liver-specific AATF knockdown model in C57bl6 mice in order to study the molecular involvement of AATF in metabolic dysfunction-associated steatohepatitis (MASH). For 12 weeks, the mice were fed either chow diet normal water or western diet sugar water to create diet-induced MASH models. AAV carrying siAATF or null was injected into the mice via tail vein at week 12, and they were observed for an additional 12 weeks. Gene expression analysis was done using RNA sequencing in liver tissues obtained at the end of the study from four groups. Three replicates were used in the analysis.
Comparisons were made between Western Diet Control (WDC) and Chow Diet Control (CDC), Western Diet siAATF (WDsiAATF) and Western Diet control (WDC), and chow diet siAATF (CDsiAATF) and chowe diet control (CDC).

first: Kumar

last: Divya Prasanna


title: Gene expression profile of hypoxia-treated IOMM-Lee cells (malignant grade 3 meningioma cells)

summary: Tumor development relies on numerous factors, including the capacity to adapt to hypoxic conditions. Hypoxic microenvironment is a critical driver of the malignant phenotype, which is often correlated with meningioma grade, aggressive behavior, therapeutic resistance, and higher recurrence rates, leading to poor prognosis. Hence, the exploration of genes involved in tumor adaptation to hypoxia can reveal novel molecular targets for the development of hypoxia-targeted therapeutics for meningioma.

overall_design: We generated transcriptomic profiles of IOMM-Lee cells (representative of Grade 3 meningioma) exposed to chronic hypoxic conditions (~ 0.2% O2 for 48 hours) using data obtained from RNA-seq. Three biological replicates of each hypoxia-treated and hypoxia-untreated (Normoxic) sample.


title: Hif2α–Lox mediated collagen remodelling is crucial for embryo invasion

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

summary: The mouse uterine gene expressions on pregnancy day 6 were investigated by Visium spatial transcriptome. Contributions of Hif2a-Lox axis was examined by comparing uterine-specific KO mice of Hif2a or Lox with their littermate control.

overall_design: The day when the vaginal plug was detected was considered day 1 of pregnancy. Pregnant mice were euthanized by cervical dislocation on designated days of pregnancy for the evaluation of pregnancy phenotypes and sample collection. Embryo attachment sites were observed as blue bands soon after intravenous injection of 1% solution of Chicago blue dye (Sigma-Aldrich) in saline on day6. Collected tissues were snap-frozen. Frozen sections (10 μm) were mounted on gene expression slides and sent to KOTAI Biotechnologies for subsequent procedures. After reaction with Proteinase K for 30 min, the sections were hybridized with spatial tags on the slides and reverse-transcribed in situ. The synthesized cDNAs were subjected to RNA-sequencing using DNBseq (MGI), producing 300 million reads/sample.

first: Yasushi

last: Hirota


title: Dissecting the binding behavior of the multi-RRM endosomal mRNA transporter Rrm4 [iCLIP]

first: Kathi

last: Zarnack

summary: RNA-binding proteins (RBPs) are central players in determining the life cycle of RNA molecules. These proteins are often modular in arrangement, featuring multiple RNA-binding domains, to enhance RNA recognition and functionality. How these multiple RNA-binding domains within individual RBPs work in concert to recognize mRNA targets is still poorly studied.  In the model fungus Ustilago maydis, the multi-RRM domain protein Rrm4 plays a key role in mediating the long-distance mRNA transport on the cytoplasmic surface of early endosomes, thereby precisely regulating spatiotemporal gene expression. Rrm4 contains three RNA-recognition motifs (RRMs), organized in an ELAV-like pattern: a tandem RRM domain (RRM1,2) and a separate third RRM domain (RRM3). Utilizing Rrm4 variants with mutations in the RRM domains, we conducted a differential iCLIP analysis to dissect the RNA recognition code of individual RRM domains. Our study reveals that Rrm4 exhibits two binding mode: (i) a one-to-one interaction where the third RRM domain alone binds RNAs by recognizing the shot UAUG motif. (ii) an intricate composite binding mode where all three RRM domains cooperatively bind RNA. Improtantly, our finding demonstrates that it is not the simple one-to-one interaction but rather the complex cooperative binding mode, involving all three RRM domains, is critical for Rrm4 function in maintaining the unipolar growth of the fungal hyphae.

overall_design: This study employs  a comparative iCLIP approach to investigate the RNA binding properties of individual RRM domains in the RBP Rrm4. By comparing the RNA binding landscapes of Rrm4 variants, each carrying a mutation in one of the RRM domains, with the wildtype Rrm4, we aim to elucidate the contributions of each RRM domain to RNA binding.

first: Nina

last: Stoffel

first: Srimeenakshi

last: Sankaranarayanan

first: Anke

last: Busch

first: Julian

last: König

first: Michael

last: Feldbrügge


title: Transcripts identified by microarray analysis that were deregulated in E13.75+18h cultures of NMRI ureters upon treatment with NOGGIN.

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E13.75+18h ureters upon treatment with NOGGIN.

overall_design: Ureters of E13.75 NMRI embryos were dissected and cultured for 18h in medium containing 10 µg/ml NOGGIN  (treated) or in medium without NOGGIN (control). Total RNA from these ureters was analyzed by microarray analysis.

first: Andreas

last: Kispert


title: Hh and EGFR-Ras signaling promote distinct steps of tumor progression in the Drosophila follicle epithelium

city: San Francisco

first: Todd

last: Nystul

address: 513 Parnassus Ave, Box 0412

institute: UCSF

summary: Controlled signaling activity is vital for normal tissue homeostasis and oncogenic signaling activation facilitates tumorigenesis. Here we combine single-cell transcriptomics with in-depth genetic and imaging analysis to investigate the role of the EGFR-Ras and Hedgehog signaling pathways in homeostasis of the Drosophila follicle stem cell lineage. We find that Hedgehog signaling simultaneously promotes an undifferentiated state and induces differentiation via activation of the epithelial-mesenchymal-transition associated transcription factor Zfh1. Overactivation of Hedgehog signaling generates a mixed transcriptional state comparable to partial epithelial-mesenchymal-transition. EGFR-Ras overactivation induces cell cycle defects by activating the transcription factors Pointed and E2f1 and impedes differentiation. Overactivation of both pathways blocks differentiation and induces tumor-like growth where follicle cells exhibit a loss of tissue architecture, sustained proliferation and a reduced lifespan of the host. These findings provide new insight into how signaling pathways converge at the transcriptional level to prevent malignant cell behavior.

overall_design: Females of the appropriate genotype were raised at 18°C and shifted to 29°C for 14 days and fed wet yeast daily in the presence of males. Ovaries were dissected and late stages were removed. A single cell suspension was prepared and subjected to single-cell RNA-seqencig using 10x Chromium Single-Cell 3’ Reagent Version 2 Kit. The resulting libraries were sequenced using Illumina HiSeq 2500 (Illumina).

first: Sari

last: Anschütz

first: Hannah

last: Müller

first: Andrea

last: Schubert

first: Jobelle

last: Peralta

first: Katja

last: Rust


title: Human PSC-based Modeling of Pulmonary Fibrosis Identifies p300/CBP Inhibition as a Suppressor of Alveolar Transitional Cell State [epithelial]

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: In this study, we conducted a drug screening using an in vitro pulmonary fibrosis model and identified p300/CBP inhibitors as candidate therapeutic agents. We investigated the mechanisms underlying the emergence of the alveolar transitional cell state (ATCS) with human PSC-derived alveolar organoids.

overall_design: Alveolar organoids composed of SPC-GFP reporter iPSC line (B2-3)-derived alveolar epithelial cells and human fetal lung fibroblasts (HFLFs) were treated with DMSO or BLM for 3 days, followed by an additional 3-day incubation with or without compounds. For gene expression profile analysis, epithelial cells were isolated from the organoids through magnetic activated cell sorting (MACS) using anti-EpCAM antibody.

first: Yusuke

last: Tsutsui

first: Takuya

last: Yamamoto


title: Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution [scRNA-seq]

city: Barcelona

first: Yolanda

last: Andres Lopez

address: C/ Baldiri Reixac, 4-8

country: Spain

institute: Institute of Molecular Biology of Barcelona

summary: Biological processes are fundamentally dynamic, yet existing methods for capturing these temporal changes are limited. We present scDynaBar, a novel approach that integrates CRISPR-Cas9 dynamic barcoding with single-cell sequencing to enable the recording of temporal cellular events. In this system, genetic barcodes accumulate mutations over a 4-week timeframe and then are sequenced together with the transcriptome of each single cell. We propose that this gradual accumulation of genetic diversity can be exploited to create a time-ordered record of cellular events. To demonstrate this, we apply the system to track the transition from a pluripotent state to a two-cell (2C)–like state in mouse embryonic stem cells (mESCs). The results provide compelling evidence for the transient nature of the 2C-like state. Additionally, our system shows consistent mutation rates across diverse cell types in a mouse gastruloid model, underscoring its robustness and versatility across various biological contexts. This technique not only improves our ability to study cellular dynamics but also creates exciting new opportunities for future applications based on recording temporal signals at the single-cell level—in other words, using dynamic barcoding as a molecular clock.

overall_design: scDynabar data for three different experiments using mESCs: time course (collection at days 0, 4, and 10); Zscan4 (using scDynabar along with a pZscan4-CreERT2 construct, collection at day 12); and gastruloid experiment (scDynabar cells differentiated into gastruloids and collected at day 6).

first: Irene

last: Hernando-Herráez

last: Andrés-López


title: Distinct Roles for SETα and SETβ in Early Cell Fate Decisions [RNA-Seq]

city: Jerusalem

first: Eran

last: Meshorer

address: Institute of Life Sciences, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram

department: Department of Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: SET, the nuclear proto-oncogene, is primarily expressed as SETα in embryonic stem cells. Upon pluripotency exit, a transcriptional switch driven by alternative promoters causes SETβ to largely replace SETα expression. Functional distinctions between the two isoforms have been difficult to ascertain, partly due to the redundancy between SETα and SETβ in their protein structure and activity. In this study, we use embryonic stem cells (ESCs) with inducible SET isoform-specific expression to investigate the differences between both SET isoforms. Time-course RNA-seq analyses in SET-KO backgrounds as well as isoform-specific ChIP-seq experiments reveal regulatory functions for SETα and SETβ. Despite sharing many binding sites and binding partners, SETα has a stronger activation function on its target genes, while SETβ downregulates FGF4. As KLF5 specifically regulates SETα, this implicates SET isoform switching at the KLF5/FGF signalling axis during primitive endoderm specification. Together, we propose a model of how distinct roles of SETα and SETβ may regulate cell identity in the early blastocyst.

overall_design: RNA-seq of WT and SETa or SETb isoform specific KO of R1 ESCs. In addition, RNA-seq of  SET isoform specific addback/overexpression experiments and in KH2 ESCs.

first: Patrick

last: Lim


title: Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution [RNA-seq]

overall_design: We applied scDynabar in mESCs using different gRNA sequences and two versions of Cas9 (BE3 and canonical Cas9). Data was collected for bulk processing across different time points.


title: Grain amaranth genes coding for an RNA-binding and a small, unknown function protein, respectively, enhance thermotolerance when overexpressed in Arabidopsis thaliana

city: Irapuato

first: Octavio

last: Martinez de la Vega

state: Guanajuato

address: km 9.6 Libramiento Norte

department: Unidad de Genómica Avanzada (Langebio)

country: Mexico

institute: Cinvestav

summary: Two genes coding for an RNA-binding and a small, unknown function protein overexpressed in Arabidopsis thaliana were studied. RNA-Seq experiments were performed with leaves from each line at 5 different times. Additionally, samples of leaves from two lines were evaluated. The data set is comprised by 30 samples.

overall_design: Transcriptomes analysis to define the thermotolerance of A. thaliana plants overexpressing an unknown function RNA binding protein from grain amaranth.

first: G

last: Cabrales-Orona

first: A

last: Reyes-Rosales

first: N

last: Martínez-Gallardo

first: L

last: Sánchez-Segura

first: O

last: Martínez-De la Vega

first: P

last: Palmeros-Suárez

first: J

last: Délano-Frier


title: CD44v6 Is Associated with Tumor Aggressiveness and Chemoresistance in Bladder Cancer

city: Madrid

first: Carolina

last: Rubio

state: Madrid

address: Avda Complutense, 40

institute: CIEMAT

summary: Bladder cancer represents a significant clinical and public health challenge. This malignancy is characterized by a very high propensity for recurrence and progression, underscoring the critical need for novel biomarkers to enhance early detection, prognosis, and specific therapeutic strategies. In the quest for such biomarkers, the CD44 family, particularly its variant isoform CD44v6, has emerged as a molecule of interest due to its pivotal roles in tumorigenesis and cell migration. Here we present a comprehensive study that elucidates the expression patterns and functional significance of CD44 and CD44v6 in bladder cancer. Utilizing robust methodological frameworks that include gene expression analyses, immunohistochemistry for protein localization, and a series of in vitro and in vivo functional assays, we systematically investigate the roles of these glycoproteins in bladder cancer pathology. Our analysis demonstrates a strong association between either elevated CD44 or CD44v6 expression and adverse clinical outcomes. Functional investigations attribute enhanced proliferative, migratory, and invasive capacities of bladder cancer cells to CD44v6 expression, indicating its contributory role in tumor aggressiveness and, importantly, in resistance to cisplatin treatment. In summary, our study places CD44 and CD44v6 as key biomarkers and putative therapeutic targets in bladder cancer. By shedding light on their mechanistic roles in cancer progression, we pave the way for the development of targeted therapeutic strategies that could potentially improve patient management and outcomes in bladder cancer.

overall_design: Cell lines were established sellecetd for high expression levels of CD44v6 from J82 and RT112 cell lines. miRNAs expression levels was compared between the parental cell lines and the newly generated CD44v6 cell lines.

first: Iris

last: Lodewijk

first: Ignacio

last: Reina

first: Esther

last: Montesinos

first: Miguel

last: Alonso-Sánchez

first: Laura

last: García-Gómez

first: Álvaro

last: Martín de Bernardo

first: Lucía

last: Morales

first: Cristian

last: Suárez-Cabrera

first: Mercedes

last: Pérez-Escay

first: Omaira

last: Alberquilla

first: Rebeca

last: Sánchez-Domínguez

first: Félix

last: Guerrero-Ramos

first: Rosa

last: García-Martin

last: Parrilla

first: José

middle: L

last: Rodríguez-Peralto

first: Jesús

last: Paramio

first: Marta

last: Dueñas


city: Xuzhou

first: Hui

last: Wang

address: 209 Tongshan Road, Kejiao A513

department: Pathogenic Biology and Immunology

institute: XuZhou Medical University

summary: Aging accelerates central nervous system remyelination failure and neurodegeneration. Microglia promote remyelination by phagocytosing myelin debris, but this function is impaired by aging-related CD22 upregulation. However, the molecular mechanisms counteracting premature aging-related microglial dysfunction and remyelination impairment remain unclear. Here, we report that Aurka-Bhlhe41 axis prevents premature aging-like microglial dysfunction and promotes remyelination by restraining progressive CD22 upregulation. We identified that microglia-enriched Bhlhe41 was negatively autoregulated and inhibited by Aurka loss. Bhlhe41- or Aurka-deficient young mice exhibited aging-like microglial morphology, phagocytic deficits, progressive CD22 upregulation, and remyelination impairment in cuprizone-induced demyelination model. Conversely, ectopic Bhlhe41 expression induced hypertrophic microglia, and counteracted phagocytic deficits and CD22 upregulation in Aurka-deficient microglia. CD22 blockade restored phagocytic function and remyelination in Bhlhe41-deficient mice. Notably, a conserved pattern of CD22 upregulation was observed in human PCDH9high microglia subsets with BHLHE41 downregulation. These findings offer insights into potential therapeutic strategies to combat aging-related neurodegeneration and central nervous system functional decline.

overall_design: Microglia from young Bhlhe41 dtomato-Cre/+ mice (control mice, N = 3) and Bhlhe41 dTomato-Cre/dTomato-Cre  mice (Bhlhe41 deficient mice) were enriched by 40% Percoll followed by FACS sorting of CD45low CD11b+ Cx3cr1+ cells. Gene expression microarray analysis was performed using SurePrint G3 Mouse GE v2 8x60K Microarray.

first: Weixin

last: Yan

last: Li


first: Carolina

last: Rubio

overall_design: Analysis of bladder cancer cell lines, including J82 and RT-112 parental cell lines, as well as newly established J82 CD44 Low, J82 CD44 High, J82 CD44v6 and RT-112 CD44 Low, RT-112 CD44 High and RT-112 CD44v6 cell lines, by means of RNASeq analysis. CD44 Low cell lines represent low CD44 receptor expression, CD44 High cell lines show high CD44 receptor expression and CD44v6 cell lines present high CD44v6 receptor expression. Comparative analyses between the different cell lines were performed. 3 biological replicates of each cell line were included in this analysis.

first: Iris

last: Lodewijk

first: Ignacio

last: Reina

last: Montesinos

last: Alonso-Sánchez


title: Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation [Cross-linked RIP-seq]

city: Cambridge

first: Mohamed

middle: A.

last: El-Brolosy

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant mRNA decay induces sequence-dependent upregulation of so-called adapting genes. How cytoplasmically generated mRNA fragments impact nuclear transcription remains poorly understood. Using genome-wide CRISPR screens, we uncover ILF3 as an RNA-binding protein connecting cytoplasmic mRNA decay and transcription during TA, and show it is required for a range of TA substrates. ILF3 is enriched at adapting genes’ RNAs, and its artificial recruitment via dCas13 promotes gene expression. Using tiling oligonucleotide screens, we identify trigger RNA fragments that activate adapting genes when introduced into cells. Further functional dissection reveals critical role for homology between trigger and target sequences. These findings enhance our molecular understanding of TA and inform design of programmable oligonucleotides for gene expression augmentation.

overall_design: Cross-linked RIP was performed using the Magna Nuclear RIP (Cross-Linked) Nuclear RNA-Binding Protein Immunoprecipitation Kit (Millipore Sigma) according to the manufacturer’s protocol using at least 2x 107 WT or rescued Actg1-NSD MEFs per replicate. For the cross-linked RIP, fixed nuclei were subjected to sonication using Bioruptor (Diagenode) to generate fragments of 200–600 bp in size prior to IP. Enriched ‘input’ samples were generated by reserving 10% of the starting lysate; the remaining volume was subjected to IP using the with 10 µg Anti-ILF3 antibody (abcam; ab92355 and BD Biosciences; Clone 21/DRBP76) coated onto protein A/G magnetic beads as described in the Magna RIP technical manual. RNA purified from both IP and input samples was concentrated by ethanol precipitation and resuspended in equivalent volumes of RNase-free water to be used to generate RNA-seq libraries. For the cross-linked total RNA RIP-seq, sequencing libraries were generated using 10 ng of RNA from input and IP samples using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech).

first: Jonathan

last: Weissman


overall_design: Analysis of bladder cancer patient samples, including both non-muscle invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC) patients, embedded in FFPE, by means of RNASeq analysis. Differences between CD44 and CD44v6 expression were used for comparative analysis.

first: Esther

first: Miguel

first: Laura

last: García-Gómez

first: Álvaro

last: Martín de Bernardo

first: Lucía

last: Morales

last: Suárez-Cabrera

last: Alberquilla

last: Sánchez-Domínguez


title: Spatial transcriptomics of HIV-associated non-Hodgkin lymphomas by EBV status and cell of origin

city: Ann Arbor

first: Elliott

middle: Daniel

last: SoRelle

state: MI

address: 1137 Catherine St.

department: Microbiology & Immunology

institute: The University of Michigan

summary: Non-Hodgkin Lymphoma (NHL) is the main cancer-related mortality for people living with HIV (PLWH), who have elevated risk for lymphoma relative to the general population. NHL genetic and molecular classifications have been intensely studied and correlated with clinical outcomes, but critical unanswered questions relevant to malignancy persist. For example, tumors positive for Epstein-Barr virus (EBV) account for 30-50% of HIV-associated NHLs, are particularly aggressive, and have poorer clinical outcomes – yet insights on the nature of EBV in NHL pathogenesis or potential therapeutic vulnerabilities have been limited. Here, we examined HIV-associated NHLs stratified by cell of origin (COO), molecular subtype, and EBV status using genome-wide spatial transcriptomic analyses.

overall_design: FFPE sections from ten different HIV-associated non-Hodgkin lymphoma (HIV-NHL) biopsies were analyzed with the 10x Genomics Visium V2 platform in this study. Five of the biopsied tumors were positive for Epstein-Barr virus (EBV) and five were EBV-negative. Tumors from different cells of origin (e.g., germinal center B cells, plasmablasts) were incldued in both EBV-postiive and EBV-negative sample subsets.

first: Amy

last: Chadburn

first: Ethel

last: Cesarman

first: Micah

last: Luftig


title: Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation [PRO-seq]

overall_design: PRO-seq was performed in three different batches. The first was WT versus Actg1-NSD MEFs, the second was Actg1-NSD MEFs versus Actg1-NSD; ∆Ilf3 cells, and the third was WT versus WT;∆Ilf3 cells. PRO-seq library preparation and sequencing was performed with the nascent transcriptomics core at Harvard Medical school. For each sample, we provided 2 million cells that were permeabilized, followed by library construction as described before (Mahat et al., 2016; Mimoso and Adelman, 2023).


title: Cis-regulatory chromatin contacts form de novo in the absence of loop extrusion

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Lab

summary: NIPBL promotes chromatin loop extrusion by the cohesin complex until it stalls at convergently oriented CTCF sites, forming structural loops. In contrast, a large fraction of loops connecting cis-regulatory elements (CREs) can be maintained in the absence of cohesin. However, whether de novo establishment of CRE loops requires loop extrusion remains unclear. To address this question, we characterized the formation of structural and CRE loops during the mitosis-to-G1-phase transition in the absence of NIPBL. Structural loop formation was impaired proportionally to loop length. Computational modeling supports these observations, suggesting that NIPBL enhances cohesin extrusion beyond NIPBL’s known loading function. Importantly the majority of CRE loops, regardless of length, was established independently of loop extrusion. While globally gene activation showed little impairment, NIPBL loss delayed the formation of CRE loops involving weak enhancers. Collectively, our findings reveal that post-mitotic establishment of regulatory contacts and gene transcription can occur independently of chromatin loop extrusion.

overall_design:
Hi-C was performed in NIPBL-AID cells isolated in Late G1 stage. Cells were arrested in prometaphase with nocodazole. Cells were treated with auxin prior to release into G1 for 4 hours (untreated, released cells as a control).
Using the G1E-ER4-derived cell lines: Lmna-mAID and Lmna-mAID/Lbr-dTag to achieve targeted degradation of Lamin A/C and/or LBR, followed by fluorescence-activated cell sorting (FACS) to isolate cell samples at various time points during post-mitotic G1 phase entry. Chromatin three-dimensional structural information of these samples was then acquired through Hi-C (High-throughput Chromosome Conformation Capture) analysis.
CHIP-seq and TTseq were also performed on the treated samples to help us better understand the regulatory role of NIPBL.

first: Fuhai

last: Liu

first: Nicholas

last: Aboreden

first: Gerd

last: Blobel


title: Transcriptome of Catharanthus roseus cv "Vitae Rose Red"

city: Excellent (top 5%)

first: Qifang

last: Pan

address: No 800 Dongchuan Road, Minhang District, Shanghai

institute: Shanghai Jiaotong University

summary: To investigate the transcriptional regulation of ethylene and JA signals on terpenoid indole alkaloids biosynthesis, RNA-seq data were generated and provided insights into the key TFs involved in the regulatory network of terpenoid indole alkaloids pathways.

overall_design: 2-week-old seedlings were sprayed with 100μM ethephon (ET) or 100μM MeJA and then sampled at 0, 3 and 24 h for RNA-seq.

first: Bofu

last: Deng

first: Qing

last: Miao

first: Kexuan

last: Tang


title: Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation

first: Mohamed

last: El-Brolosy

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation [RNA-seq]

overall_design: MEFs trasnduced with either Actg1-NMD or ctrl(GFP-2A-RFP)-NMD lentivectors were treated with doxycyline for three days then total RNA was isolated

first: Jonathan

last: Weissman


title: Distinct Roles for SETα and SETβ in Early Cell Fate Decisions [ChIP-Seq]

first: Eran

last: Meshorer

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SET-HA with DSG double crosslinking with 2 replicates in SET WT and SET-KO cell lines following dox-induced expression of SETa or SETb.

first: Patrick

last: Lim


title: Genomic heterogeneity drives mechanical adaptation in human tumor cells [RRBS]

city: College Station

first: Ting-Ching

last: Wang

address: 101 Bizzell St

institute: Texas A&M University

type: Methylation profiling by high throughput sequencing

summary: The progression of many solid tumors is accompanied by temporal and spatial changes in the stiffness of the extracellular matrix  (ECM). Cancer cells adapt to soft and stiff ECM through mechanisms that are not fully understood. In particular, it is well known that there is significant genetic heterogeneity from cell to cell in tumors, but how ECM stiffness as a parameter might interact with that genetic variation is not known. Here, we used the method of experimental evolution to study response of genetically variable and clonal tumor cell populations to ECM stiffness. Cell fitness increased on soft ECM over a period of several weeks in genetically variable but not clonal populations. DNA barcode-enabled clonal tracking revealed that sustained culture on soft ECM selects for a few genetic variants. These data provide the first evidence that ECM stiffness exerts natural selection on genetically variable tumor populations. Genome-wide analysis including RNA-seq, ATAC-seq and DNA methylation profiling reveal substantial differences in gene expression between selected populations and ancestral cells which are partially explained by epigenetic modifications. Soft-selected cells are highly migratory with enriched oncogenic signatures and exhibit highly unusual behaviors like spreading and traction force generation on ECMs as soft as 1 kPa. Cell spreading is the directly selected trait but not levels of integrins or adhesion proteins like talin. Overall, these data show that ECM stiffness in solid tumors may drive malignant behaviors through evolution by natural selection.

overall_design: Because selection on soft ECM may be mediated at least in part by epigenetic modifications in cells, we determined the methylation levels at CpG sites in 4 sample groups  (ancestral cultured on stiff, ancestral cultured on soft, stiff-selected cultured on stiff, soft-selected cultured on soft). Methylation status was assessed using enhanced reduced representation bisulfite sequencing  (ERRBS), a technique that combines enzymatic digestion with bisulfite conversion to achieve quantitative, base-pair resolution of cytosine methylation at CpG sites throughout the genome.

first: Suchitaa

last: Sawhney

first: Daylin

last: Morgan

first: Richard

last: Bennett

first: Richa

last: Rashmi

first: Marcos

middle: R

last: Estecio

last: Brock

first: Irtisha

last: Singh

first: Charles

middle: F

last: Baer

last: Licht

first: Tanmay

last: Lele


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18(cre/+);Bmp4(fl/fl) (Bmp4cKO) ureters.

first: Mark-Oliver

last: Trowe

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Bmp4 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Bmp4cKO and control embryos was analyzed by microarray analysis.

first: Andreas

last: Kispert


title: Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation [Perturb-seq]

last: El-Brolosy

overall_design: CRISPR-cutting perturb-seq was performed targeting 147 genes in either WT or ILF3 KO K562 cells.


title: Transcripts identified by microarray analysis that were deregulated in E12.5+18h cultures of NMRI ureters upon treatment with NOGGIN.

summary: Evaluation of the transcriptional changes in E12.5+18h ureters upon treatment with NOGGIN.

overall_design: Ureters of E12.5 NMRI embryos were dissected and cultured for 18h in medium containing 10 µg/ml NOGGIN  (treated) or in medium without NOGGIN (control). Total RNA from these ureters was analyzed by microarray analysis.


title: Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation [native RIP-seq]

overall_design: native RIP was performed using the Magna Nuclear RIP (Native) Nuclear RNA-Binding Protein Immunoprecipitation Kit (Millipore Sigma) according to the manufacturer’s protocol using at least 2x 107 WT or rescued Actg1-NSD MEFs per replicate. Enriched ‘input’ samples were generated by reserving 10% of the starting lysate; the remaining volume was subjected to IP using the with 10 µg Anti-ILF3 antibody (abcam; ab92355 and BD Biosciences; Clone 21/DRBP76) coated onto protein A/G magnetic beads as described in the Magna RIP technical manual. RNA purified from both IP and input samples was concentrated by ethanol precipitation and resuspended in equivalent volumes of RNase-free water to be used to generate RNA-seq libraries. 10ng of RNA was used to generate small RNA-seq libraries using the SMARTer smRNA-Seq Kit (Clonetech). RNA was treated with T4 Polynucleotide Kinase for 1 hr prior to library preparation to capture various potential mRNA decay intermediates that may not have a 5’P or 3’OH.

last: Weissman


title: Genomic heterogeneity drives mechanical adaptation in human tumor cells [ATAC-seq]

summary: The progression of many solid tumors is accompanied by temporal and spatial changes in the stiffness of the extracellular matrix (ECM). Cancer cells adapt to soft and stiff ECM through mechanisms that are not fully understood. In particular, it is well known that there is significant genetic heterogeneity from cell to cell in tumors, but how ECM stiffness as a parameter might interact with that genetic variation is not known. Here, we used the method of experimental evolution to study response of genetically variable and clonal tumor cell populations to ECM stiffness. Cell fitness increased on soft ECM over a period of several weeks in genetically variable but not clonal populations. DNA barcode-enabled clonal tracking revealed that sustained culture on soft ECM selects for a few genetic variants. These data provide the first evidence that ECM stiffness exerts natural selection on genetically variable tumor populations. Genome-wide analysis including RNA-seq, ATAC-seq and DNA methylation profiling reveal substantial differences in gene expression between selected populations and ancestral cells which are partially explained by epigenetic modifications. Soft-selected cells are highly migratory with enriched oncogenic signatures and exhibit highly unusual behaviors like spreading and traction force generation on ECMs as soft as 1 kPa. Cell spreading is the directly selected trait but not levels of integrins or adhesion proteins like talin. Overall, these data show that ECM stiffness in solid tumors may drive malignant behaviors through evolution by natural selection.

overall_design: We performed the assay for transposase-accessible chromatin with sequencing (ATAC-seq) to investigate differences if any in soft-selected cells cultured on soft ECM, compared with ancestral cells cultured on soft ECM.

first: Amy

middle: D


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Pax2-cre/+;Smad4(fl/fl) (Smad4cKO (UE)) ureters.

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Smad4 in the ureteric epithelium.

overall_design: Total RNA from dissected ureters of E14.5 Smad4cKO (UE) and control embryos was analyzed by microarray analysis.


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18(cre/+);Smad4(fl/fl) (Smad4cKO (UM)) ureters.

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Smad4 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Smad4cKO (UM) and control embryos was analyzed by microarray analysis.


title: Harnessing Small Molecules for Revealing Vulnerabilities in Circulating Tumor Cells.

city: Basel

first: Yongzhan

last: Zhang

address: Otto-Stern-Weg 7 HPL H17.2

institute: ETH Zurich

summary: Breast cancer is among the most commonly diagnosed cancers, accounting for 685,000 fatalities in 2020 worldwide. High mortality rate is associated with the development of metastases, a complex process involving the spread of cancer cells from the primary tumor site to secondary organs. At present, treating patients with metastatic disease is challenging, and this still represent an unmet medical need. As clinically-relevant models, circulating tumor cell (CTC)-derived models can serve as a drug screen platforms that enable drug susceptibility testing and discovery of novel compounds with anti-cancer progression activity. Here, by employing a combination of CTC-based drug screening platform, in vivo models of metastatic breast cancer, RNA sequencing, and in vitro cell assays, we identified new agents for the reduction of tumor growth and lung colonization in breast cancer. Furthermore, our transcriptomic data delineate the metastasis-relevant signaling pathways affected by these treatments.

overall_design: Cells were treated with either a control vehicle (0.25% DMSO) or 5 µM of above mentioned component for 2h and 6h, respectively. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions for sequencing.

first: Karin

last: Strittmatter


title: Effects of mitochondrial stress on intestinal tumor development depends on Apc status

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: Mitochondrial stress triggers both metabolic and transcriptomic reprogramming but its effects on tumor development remains unclear. It is also unknown whether the genetic status has any influence on the capacity of mitochondrial stress to control tumor development. To explore these issues, we generated a mouse model lacking the lipid transfer protein Stard7 in intestinal epithelial cells (IECs) and assessed tumor development in both Wnt-dependent tumor initiation and in inflammation-driven tumor development. The loss of Stard7 in both models of intestinal tumors impaired mitochondrial Complex I activity, led to a severe metabolic and lipidomic reprogramming and potentiated mTORC1 activation. As a result, levels of enzymes involved in serine biosynthesis were enhanced in Stard7-deficient IECs showing or not constitutive Wnt signaling. Strikingly, despite similar molecular signatures upon Stard7 deficiency in intestinal crypts showing or not constitutive Wnt signaling, Stard7 contributed to tumor development in AOM/DSS-treated mice but inhibits Wnt-driven cancer initiation in the intestine. Apc+/Minmice lacking Stard7 in IECs developed more tumors in the distal colon. Collectively, our results suggest that the Apc genetic status critically controls the effects of mitochondrial stress on intestinal tumor development.

overall_design: Bulk RNA-seq data, KO vs WT (6 replicates)

first: Kateryna

last: Shostak

first: Alain

last: Chariot

first: Olivier

last: Renson


title: MCF7 cells: empty vector  (Neo) vs. SPARC overexpression vector transfected before and after 5nM or 100nM docetaxel treatment

city: São Paulo

first: Ana Carolina

last: Pavanelli

state: São Paulo

address: Av Dr Arnaldo, 251

department: CTO

country: Brazil

institute: ICESP

summary:
The aim of this study was evaluate the transcriptome changes in the comparison between MCF7 cells with increased expression of SPARC and the control cells before and after docetaxel treatment .
The results generated could be of particular interest for the understanding the action of SPARC in chemosensitivity, especially to increase the specificity and effectiveness of drug treatment and overcoming resistance to chemotherapy.

overall_design: Three-condition experiment, MCF7 Neo vs. MCF7 over SPARC cells before (control) and after 5nM or 100nM docetaxel treatment.  1 control  (Neo and over SPARC before treatment) and 2 docetaxel treated  (1 Neo and  over SPARC 5nM and 1 Neo and  over SPARC 100nM).

first: Ana

first: Maria

last: Nagai


title: Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes [Micro-C, CUT&TAG, RNA-Seq, topoisomerase inhibition (DMSO, ETO, TPT), GM12878]

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Inside human nuclei, genes are transcribed within a highly packed genome, whose organization is facilitated by cohesin-mediated loop extrusion. However, how cohesin folds transcribed genes and affects transcription remain unclear. Here we report that highly expressed long genes form a “stripe-like” structure termed transcription elongation loop (TEL), which aligns between the transcription start site (TSS) and the transcription termination site (TTS). We proved that TELs formation results from the joint interactions between cohesin-mediated loop extrusion, RNA polymerase II (RNAPII) and topoisomerases. By improving the spatial resolution of single-cell 3D genome mapping to 5 kb with micrococcal nuclease (MNase) in our new single-cell Micro-C (scMicro-C) method, we directly observed the loop expansion of TELs. Furthermore, we demonstrated that TEL-associated genes have higher transcriptional burst frequency and cohesin modulates transcriptional bursting by facilitating the release of RNAPII pausing. Thus, our results demonstrated the fundamental role of cohesin in transcription regulation.

overall_design:
topoisomerase inhibition (Micro-C)
Please note that each processed data file was generated from both rep1 and rep2 samples, and is linked to the corresponding *rep1 sample records.

CUT&TAG was performed on GM12878 cells treated with DMSO, ETO (etoposide), and TPT (topotecan), respectively (two replicates per condition).

Bulk RNA-seq was performed on GM12878 cells treated with DMSO, ETO and TPT, repectively (two replicates per condition).

first: Honggui

last: Wu

first: Jiankun

first: Longzhi

last: Tan

first: Sunney


title: Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma [bWES]

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

summary: Intratumoral heterogeneity (ITH) arises from distinct subclonal expansion following genetic or epigenetic alterations, and profoundly influences how tumors response to their immune microenvironment. Tumor progression trees based on single-cell mutational profiles have made it possible to trace subclonal evolution; however, conventional tree-building methods can incorporate only a limited number of cells and mutations, restricting their application to larger single-cell data. To investigate the effect of ITH on the therapeutic response of melanoma, we have developed Trisicell (https://trisicell.rtfd.io), a computational toolkit for scalable inference of mutational ITH through assessment of single-cell genomic variant data. By applying Trisicell to genetically matched mouse melanoma datasets, we found that expressed mutations are sufficient to effectively drive subclonal evolution. On single-cell, full-length RNA sequencing data of mouse melanoma from preclinical immune checkpoint blockade (ICB) studies, the analysis showed that the subtree-seeding mutations in the trees identified distinct subclones associated with a specific developmental state and neural crest lineage markers. Using the tree to trace cell lineages, we found that neoantigens depleted by ICB were predominantly expressed in minor subclones, suggesting that post-treatment recurrence is driven by immunoediting. Moreover, these neoantigens were enriched with those derived from frameshift mutations and mutated nuclear genes. Importantly, recurrently mutated genes in ICB-responding human melanoma exhibited the same features. We next used Trisicell to analyze single-cell, full-length RNA data of brain metastases (BM) from melanoma patients treated with ICB, and discovered that relapsing BM from ICB-responding patients exhibited subclones that also expressed a higher fraction of frameshift mutations and were associated with elevated levels of infiltrated T cells. Notably, they also exhibited more mutated HLA genes and expressed high level of the novel immune checkpoint HLA-G, a putative local immunosuppressive mechanism. In summary, applying Trisicell to single-cell transcriptomic analyses allowed us to identify novel features of ICB-responding melanoma neoantigens and distinct mechanisms for adapting to immunotherapy at different sites. These results have important implications for both melanoma evolution and target identification for immunotherapies, including ICB and cancer vaccines. This is the first study to trace subclonal evolution of neoantigens at single-cell resolution, demonstrating that Trisicell and our datasets represent important resources for the field.

overall_design: 24 clonal sublines were generated from single cells of parental mouse melanoma line B2905. For each subline in culture, DNA were prepared for whole exome sequencing.

first: Farid

last: Mehrabadi

first: Eva

last: Pérez-Guijarro

first: Kerrie

last: Marie

first: Salem

last: Malikic

first: Erfan

last: Azer

first: Howard

middle: H

last: Yang

first: Charli

last: Gruen

first: Chih

first: Welles

last: Robinson

first: Huaitian

last: Liu

first: Can

last: Kizilkale

first: Michael

last: Kelly

first: Christina

last: Marcelus

first: Cari

last: Smith

first: Sung

last: Chin

first: Jessica

last: Ebersole

first: Sandra

last: Burkett

first: Aydin

last: Buluc

first: Naema

last: Nayyar

first: Philipp

last: Hähnel

first: Magali

last: de Sauvage

first: Albert

middle: E

last: Kim

first: Samuel

last: Markson

first: Ryan

last: Sullivan

first: Priscilla

last: Brastianos

first: Funda

last: Ergun

first: Glenn

last: Merlino

first: Chi-Ping

last: Day

first: S

last: Sahinalp


title: Deiodinase Gene Expression Profiles Underlie Breed-Specific Thyroid Metabolism and Heat Stress Resilience in Cattle

status: Public on Feb 17 2026

city: Zuru

first: Akeem

middle: Babatunde

last: Sikiru

state: Kebbi

address: Department of Animal Science, College of Agriculture, FUAZ, Zuru, Nigeria.

department: Animal Science

country: Nigeria

institute: Federal University of Agriculture Zuru

summary: Heat stress represents a major constraint to cattle productivity in tropical environments, with breed-specific differences in thyroid hormone metabolism potentially underlying variation in thermal resilience. This study investigated expression of selected candidate genes related to thyroid metabolism, mitochondrial function, lipid metabolism, growth signaling, and stress response across three cattle genotypes to explore the underlying roles of thyroid hormone metabolism in heat adaptation. Whole blood RNA-seq was performed on samples from heat-tolerant Kedah-Kelantan (KK), intermediate Brangus (BR), and heat-vulnerable Holstein Friesian (HF) cattle during peak heat load (Temperature-Humidity Index: 44.68). Of 20 genes analyzed, 17 showed significant differential regulation across the breeds. These findings demonstrate that breed-specific heat resilience is associated with coordinated regulation of deiodinase pathways and integrated lipid-mitochondrial-stress networks

sample_organism:
Bos taurus
Bos indicus
Bos indicus x Bos taurus

overall_design: RNA-seq profiling of three cattle genotypes representing different levels of heat tolerance: Kedah-Kelantan (n=4, heat-tolerant Bos indicus breed), Brangus (n=4, intermediate composite breed), and Holstein Friesian (n=4, heat-vulnerable Bos taurus breed). Whole blood samples were collected during peak heat stress conditions (Temperature-Humidity Index: 44.68) from clinically healthy, non-pregnant, non-lactating adult female cows.

first: Stephen

last: Egena

first: Veerasamy

last: Sejia

first: Nurulfiza

last: Isa


title: Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes [Smart-seq2, GM12878]

first: Xiaoliang

last: Xie

first: Honggui

last: Wu

first: Jiankun

last: Zhang

first: Longzhi

last: Tan

first: Sunney


title: Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma [bWTS]

first: Maxwell

last: Lee

overall_design: 24 clonal sublines were generated from parental mouse melanoma line B2905. For each subline (C1-C24), one million cells were subcutaneously implanted into each of the five C57BL6 mice. When tumor reached 1000 mm^3, they were harvested and subjected to RNA extracton and sequencing.

first: Farid

last: Mehrabadi

first: Eva

last: Pérez-Guijarro

first: Kerrie

last: Marie

first: Salem

last: Malikic

first: Erfan

last: Azer

first: Howard

last: Yang

first: Charli

last: Gruen

first: Chih

first: Welles

last: Robinson

first: Huaitian

last: Liu

first: Can

last: Kizilkale

first: Michael

last: Kelly

first: Christina

last: Marcelus

first: Cari

last: Smith

first: Sung

last: Chin

first: Jessica

last: Ebersole

first: Sandra

last: Burkett

first: Aydin

last: Buluc

first: Naema

last: Nayyar

first: Philipp

last: Hähnel

first: Magali

last: de Sauvage

first: Albert


title: Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes [RNA-seq and Smart-seq3, topoisomerase inhibition and cohesin depletion, mESC]

first: Xiaoliang

last: Xie

overall_design: Smart-seq3 was performed on single mouse embryonic stem cells with cohesin depleted for 0h, 3h, and 6h. Bulk RNA-seq was performed on mouse embryonic stem cells treated with DMSO, ETO and TPT, repectively (two replicates per condition).

first: Honggui

last: Wu

first: Jiankun

last: Zhang

first: Longzhi

last: Tan


title: Bulk RNA-sequencing of soft tissue sarcomas from patients undergoing neoadjuvant BO-112 and hypofractionated radiation therapy with or without nivolumab in soft tissue sarcoma

city: Stanford

first: Anusha

last: Kalbasi

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

summary: Patients undergoing neoadjuvant BO-112 and hypofractionated radiation therapy with or without nivolumab in soft tissue sarcoma were sequenced to identify changes in gene expression and pathway differences across different timepoints and treatments

overall_design: Bulk RNA-sequencing was done on 41 sarcoma samples from 14 patients at up to four timepoints for each patient.

first: Kalbasi

last: Anusha

first: Subramanian

last: Ajay

first: Pal

last: Aastha

first: Moding

last: Everett


title: Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes [Micro-C and CUT&TAG, Rpb1 depletion, mESC]

overall_design: Micro-C and CUT&TAG was performed on mouse embryonic stem cells without cohesin depletion (untreat) and with 4h cohesin depletion (IAA-4h). Include biological replicates.


title: Integrative multiomics analysis and CRISPR screening identify functional noncanonical translation loci in the mouse immune system [RNA-Seq]

city: Santa Cruz

first: Susan

last: Carpenter

address: Biomedical Sciences Building First Floor, Red Hill Road

department: MCD

institute: UC Santa Cruz

summary: Ribosome profiling has revealed thousands of noncanonical translation events across mammalian genomes, yet functional characterization has overwhelmingly focused on proliferative fitness in cancer cell lines. Here, we present a comprehensive survey of noncanonical translation in the mouse immune system and its functional consequences in macrophages. By performing a unified Ribo-seq meta-analysis across 20 public mouse leukocyte datasets - spanning macrophages, dendritic cells, neutrophils, B cells, and T cells - we define a compendium of 22,276 noncanonical coding sequences (CDSs), including upstream ORFs (uORFs), downstream ORFs, and ORFs on noncoding RNAs and pseudogenes (ncORFs). Proteogenomic integration with reanalyzed mass spectrometry data prioritizes a high-confidence subset with detectable protein products, including pseudogene-encoded and lncRNA-encoded zinc finger proteins. To move beyond cataloging, we carried out two orthogonal CRISPR screens in immortalized bone marrow-derived macrophages: a fitness screen identifying noncanonical CDSs required for macrophage viability, and a TLR1/TLR2-NFκB reporter screen uncovering CDSs that modulate innate immune signaling. These screens nominate uORFs, several conserved between mouse and human, that exert phenotypic effects on par with their cognate coding sequences. We unexpectedly discovered a family of endogenous retroviral envelope-derived proteins translated in adult myeloid cells. Among these, SYNIR is a full-length syncytin-like membrane glycoprotein that positively regulates NFκB-responsive transcription, while SEMR is a secreted protein with structural homology to the feline leukemia virus accessory protein FeLIX that drives broad transcriptional remodeling of macrophage gene programs upon knockout. Updated single-cell RNA-seq annotations and an interactive UCSC Genome Browser session integrating Ribo-seq, proteomics, and CRISPR screen data are provided as community resources. Together, these findings expand the functional landscape of noncanonical translation in immunity and establish endogenous retroviral proteins as previously unrecognized regulators of macrophage biology.

overall_design: Three gRNAs were chosen to target SYNIR and SEMR ORFs.  Three SYNIR gRNAs: 1- TGGAGTCTTGATCCCGTCTG, 2- GGGTGAACTGAACTGTAATG, 3- TATGCACAGAAGTATGACTC  SEMR gRNAs: 1- GAAACTAAGATACAGTACCA, 2- AACGTGGCAGGTGATATCAG, 3- ACCAGCCACGCAACCTAACG  And three non-targeting gRNAs were used as negative controls. Complementary oligos were ordered from IDT, reconstituted and ligated into pU6 expression vector. The vector also contained  a puromycin resistance cassette and mCherry reporter. Lentivirus was prepared as described above and iBMDM samples were e infected with a single gRNA. Infected cells were puromycin-selected for 7 days when the mCherry population reach >90%. Each gRNA-iBMDM line was treated with 200ng/ml LPS for 6 h and samples were collected for RNA processing.  RNA sequencing Total RNA was isolated from cells using TRIzol reagent (SigmaAldrich, T9424) and Direct-zol RNA Miniprep Plus kit (Zymo Research, R2072), following manufacturer’s instructions. RNA samples were sent to Novogene for 150x150 bp stranded library preparation and were sequenced on a NovaSeq X Plus sequencer.  Differential gene expression Reads were quantified with Salmon128 (--validateMappings --gcBias --seqBias) against Gencode vM31. Transcript-level abundance estimates were summarized to gene level using tximport with length-scaled TPM counts (countsFromAbundance = "lengthScaledTPM"). Differential expression was performed with DESeq2138 using default parameters and a two-factor design comparing samples with targeting- and non-targeting-gRNAs.

first: Eric

last: Malekos


title: Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma [M4_aCTLA4_scRNA]

first: Maxwell

last: Lee

overall_design: One million of the B2905 mouse melanoma cells (Nature Med 2020, 26:781) were subcutaneously implanted into each of the twenty C57BL/6 mice. They were randomized into two groups (10 mice each) to receive IgG2b control or anti-CTLA-4 treatment. Six tumors (two from IgG control and four from anti-CTLA-4 group) were harvested to prepare single-cell suspension. About 200-300 cells were sorted from each tumor for generating cDNA library by Smart-seq2 protocol (Nature Protocol 2014, 9:171), followed by RNA sequencing.

first: Farid

last: Mehrabadi

first: Eva

last: Pérez-Guijarro

first: Kerrie

last: Marie

first: Salem

last: Malikic

first: Erfan

last: Azer

first: Howard

last: Yang

first: Charli

last: Gruen

first: Chih

first: Welles

last: Robinson

first: Huaitian

last: Liu

first: Can

last: Kizilkale

first: Michael

last: Kelly

first: Christina

last: Marcelus

first: Cari

last: Smith

first: Sung

last: Chin

first: Jessica

last: Ebersole

first: Sandra

last: Kim

first: Samuel

last: Markson

first: Ryan

last: Sullivan

first: Priscilla

last: Brastianos

first: Funda

last: Ergun

first: Glenn

last: Merlino

first: Chi-Ping

last: Day

first: S

last: Sahinalp


title: Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes

first: Xiaoliang

last: Xie

overall_design: Refer to individual Series


title: Integrative multiomics analysis and CRISPR screening identify functional noncanonical translation loci in the mouse immune system [Guide-seq]

first: Susan

last: Carpenter

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: The gRNA library was synthesized as an oligonucleotide pool by Twist Bioscience and cloned into a lentiviral vector containing puromycin resistance and BFP reporter cassettes as previously described (0.1016/j.celrep.2020.108541). HEK293T cells were transfected with library plasmid and packaging vectors, and the supernatant was harvested at 72 hours. Three distinct clonal lines of NFkB-GFP+, Cas9+ immortalized bone marrow-derived macrophages were infected with lentivirus at MOI < 0.3 at day -10. After three days (day -7), lentiviral media was replaced with DMEM +10% FBS media and 10 ug/ml puromycin. After seven days of puromycin selection, each clonal line showed >90% BFP positive cells by flow cytometry, and day 0 samples were collected and stored in freezing media (90% FBS, 10% DMSO).  Essentiality screen For 14 days post-selection, cells were split every ~3 days to maintain confluency between 60-70% while ensuring >2000X gRNA library coverage. On day 14, cells from each clonal line were collected at >1000X and stored in freezing media.  Sorting CRISPR screen At day 14, cells from each clonal line were treated with 200 ng/mL Pam3CSK4. After 24 hours, cells were transferred to FACS buffer to prepare for sorting on a BD FACSAria II. GFP was excited using a 488-nm laser and detected using a 525/50-nm filter. For each clonal line, the top 20% and bottom 20% of cells were collected as GFP-high and GFP-low samples, with >100X coverage maintained in each sorted sample. Genomic DNA was collected from cell pellet and PCR amplified as previously described. Libraries were sequenced, 23-nucleotide single-end, on an Illumina NextSeq 2000 sequencer operated by the UCSC Paleogenomics Lab.  Sequenced reads were matched to gRNAs with MAGeCK count with the arguments (--trim-5 1 --sgrna-len 19). In cases where gRNAs targeted overlapping nCDS regions, arising from alternative transcripts or out-of-frame translation, gRNAs were matched to “ORF-units”, e.g. Emsy uORF1:Emsy uORF2. nCDS-loci with less than 4 gRNAs were filtered out and Mageck MLE was used to test for essentiality hits between the day 0 and day 14 samples (--control-sgrna negctrl_ids.txt --norm-method control --permutation-round 10 --remove-outliers --sgrna-efficiency gRNA_scores.tsv), where negctrl_ids.txt is the list of 1,500 negative control gRNAs and gRNA_scores.tsv is the DeepHF137 cleavage efficiency prediction for each gRNA.

first: Eric

last: Malekos


title: Kidney from two patients with collecting duct carcinoma

city: Ube

first: Hiroshi

last: Hirata

address: 1-1-1 Minami-Kogushi

department: Urology

institute: Yamaguchi University

summary: Collecting duct carcinoma (CDC) is a rare and aggressive renal malignancy with limited therapeutic options. In this study, long non-coding RNA (lncRNA) expression profiles were analyzed in two CDC cases with differential responses to immune checkpoint inhibitor (ICI) therapy. Case 1 showed a clinical response to ICI treatment, whereas Case 2 was refractory. Tumor and matched normal FFPE kidney tissues were subjected to lncRNA expression profiling using the Arraystar Human LncRNA Microarray v5.0 platform to explore potential molecular differences associated with ICI response.

overall_design: Total RNA was extracted from FFPE tumor and matched normal kidney tissues obtained from two patients with collecting duct carcinoma. One patient responded to immune checkpoint inhibitor (ICI) therapy, whereas the other did not. RNA samples were hybridized to the Arraystar Human LncRNA Microarray v5.0. Normalized expression values were generated using quantile normalization.


title: Transcriptomic Profiling on Intestine of Diabetic and Septic Mice [miRNA-seq]

city: Guangzhou

first: Fang

last: Tan

address: Dongfengdong Road 567

institute: Sun Yat-sen University Cancer Center

summary: Sepsis is a severe clinical syndrome related to an exaggerated host immune response to infection as well as systematic inflammation and serious tissue damage. Sepsis-induced intestine injury is one of the most frequent and serious complications of sepsis. This study aimed to identify new mechanisms in sepsis-induced intestine injury through transcriptome profiling (RNA-seq).

overall_design: Mice were randomly divided into 2 groups: CLP group (n=2), sham group (n=2).

first: Xinjin

last: Chi

first: Lei

last: Zheng