title: Upregulated FoxO1 promotes arrhythmogenesis in mice with heart failure and preserved ejection fraction [control vs HF]

first: Thassio

last: Mesquita

overall_design: RNA sequencing from left ventricular tissue was performed to identify transcriptomic changes in C56Bl6 fed with a standard diet (control), High-Fat + L-NAME diet treated with AAV-scramble-sh (HFpEF-scr), and High-Fat + L-NAME diet treated with AAV-FoxO1-sh (HFpEF-FoxO1-sh).

first: Eugenio

last: Cingolani


title: foxA RNAi RNA-seq in adult males and females of Schistosoma mansoni

status: Public on Nov 15 2024

city: Houston

first: Jayhun

last: Lee

state: TX

address: 6431 Fannin St. MSE R222

department: Microbiology and Molecular Genetics

country: USA

institute: The University of Texas Health Science Center at Houston

type: Expression profiling by high throughput sequencing

summary: Schistosome foxA is enriched in the parasites' stem/progenitor cells and the esophageal gland, an anterior digestive organ required for their survival. However, the molecular makeup of the esophageal gland remains unclear. Here, we took a comparative transcriptomics approach using foxA knockdown adult parasites. Differential expression analysis reveals 37 genes commonly downregulated in foxA knockdown males and females, most of which show high enrichment in the esophageal gland.

overall_design: Adult (between 5 and 7 weeks post-infection) S. mansoni parasites were cultured in vitro for 2 weeks, during which they were treated with dsRNA against foxA (Smp_331700) 6 times at D1, D2, D3, D6, D9, and D12. Male and female worms were separated collected in different tubes. Each batch had ~20 worms. Three batches per knockdown per sex were collected.

first: Pallavi

last: Yadav

first: Sabona

middle: B

last: Simbassa

first: Ryan

last: Sloan

first: Phillip

middle: A

last: Newmark


title: Single-Cell RNA Sequencing Reveals Age-Related Changes in Epidermal Cell Populations and Interactions

city: Kyoto

first: Satoshi

last: NAKAMIZO

state: Kyoto

address: 54 Shogoin-Kawahara, Sakyo

country: Japan

institute: Kyoto University

summary: Utilizing single-cell RNA sequencing, we analyzed epidermal cells from young (20-30 years old) and elderly (60+ years old) subjects. Our findings reveal that aged epidermis exhibits increased expression of inflammation-related genes and pathways associated with nonsense-mediated decay, oxidative phosphorylation, and apoptotic signaling, predominantly in keratinocytes. Furthermore, we observed a reduction in cell-to-cell interactions from the proliferative basal and granular layers to other epidermal cells. This study underscores how epidermal aging primarily impacts keratinocytes and diminishes intercellular interactions, unveiling a novel mechanism of skin aging.

overall_design:
Excess upper eyelid skin was obtained from three young (age range: 20-30 years) and three older (age range: 60-80 years) patients undergoing double eyelid surgery or elective blepharoplasty for ptosis at Kyoto University Hospital and an affiliated plastic surgery clinic. Patients receiving systemic immunotherapy or anticancer agents and those with skin diseases were excluded. For the skin samples, the epidermis was separated using dispase, and epidermal suspension was prepared using 0.25% trypsin/EDTA. The cells were used to prepare a library using the 10X Chromium Next GEM Single Cell 3' Kit, and scRNA-seq was performed.

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

last: Nakamizo

first: Kenji

last: Kabashima


title: Systems level analysis of lipid metabolism in oxygen-induced retinopathy [liver RNA-Seq]

city: Boston

first: Charandeep

last: Singh

address: 150 Harrison Avenue

institute: Tufts Medical Center

summary: Activation of anaplerosis takes away glutamine from the biosynthetic pathway to the energy-producing TCA cycle. Especially, induction of hyperoxia driven anaplerosis in neurovascular tissues such as the retina during early stages of development could deplete biosynthetic precursors from newly proliferating endothelial cells impeding physiological angiogenesis and leading to vasoobliteration. Using an oxygen-induced retinopathy (OIR) mouse model, we investigated the metabolic differences between OIR-resistant BALB/cByJ and OIR susceptible C57BL/6J strains at system levels to understand the molecular underpinnings that potentially contribute to hyperoxia-induced vascular abnormalities in the neural retina. Our systems level in vivo RNA-seq, proteomic, and lipidomic profiling and ex-vivo explant studies show that the medium-chain fatty acids serves as an alternative source to feed the TCA cycle. Our findings strongly implicate that medium-chain fatty acids could suppress glutamine-fueled anaplerosis and ameliorate hyperoxia-induced vascular abnormalities in conditions such as retinopathy of prematurity.

overall_design: 12 days old OIR hyperoxia and normoxic mouse livers from OIR resistant and susecptible strains were compared to find out metabolic changes responsible to protect against OIR


title: Single nucleus RNA sequencing of mosiac Pax2 and Pax8 mutant proximal tubules

city: Ann Arbor

first: Jeffrey

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

summary: Pax2 and Pax8 are homologous transcription factors required for kidney development and medullary urine concentration. However, their function in  proximal tubule homeostasis and response to acute kidney injury is unknown. Mice with proximal tubules consisting of a mosaic of wild-type and Pax2/8 mutant proximal tubules cells were generated. Gene expression of mutant and wild-type proximal tubule cells was compared under homeostatic conditions using single-nucleus RNA sequencing.

overall_design: Female mice heterozygous for the X-linked phosphoenolpyruvate carboxykinase Cre driver and conditional Pax2, Pax8, and tdTomato/green fluorescent protein reporter alleles were generated. The proximal tubules of these mice were composed of wild-type and Pax2/8 mutant cells due to random X-inactivation. 12-week-old uninjured mice were euthanized, and their kidneys were flash-frozen for single-nucleus RNA sequencing.


title: Androgen receptor inhibition increases MHC Class I expression and improves immune response in prostate cancer

city: San Francisco

first: Xiaolin

last: Zhu

state: CA

institute: UCSF

summary: Tumors escape immune detection and elimination through a variety of mechanisms. Here, we used prostate cancer as a model to examine how androgen-dependent tumors undergo immune evasion through downregulation of the major histocompatibility complex class I (MHCI). We report that response to immunotherapy in late-stage prostate cancer is associated with elevated MHC expression. To uncover the mechanism, we performed a whole genome CRISPRi screen and identified AR as a repressor of the MHCI pathway. Syngeneic mouse models of aggressive prostate cancer deficient in AR also demonstrated increased tumor immunogenicity and promoted T cell mediated tumor-control. Notably, the increase in MHCI expression upon androgen receptor blockade is transient and correlates with resistance to AR inhibition. Mechanistic studies identified androgen response elements upstream of MHCI transcription start sites which increased MHCI expression when deleted. Together, this body of work highlights another mechanism by which hormones can promote immune escape.

overall_design: C42B cells were treated with enzalutamide or DMSO and observed for 3 months. RNA was extracted for RNA-seq at time 0 (day 0) and days 7, 28, 49, and 91 for both treatment conditions, each with one replicate (except day 0).

first: Lisa

middle: N

last: Chesner

first: Felix

middle: Y

last: Feng

first: Amy

middle: E

last: Moran


title: The single-cell transcriptome data of pig embryonic stem cells cultured without feeder cells

status: Public on Nov 17 2024

city: Seoul

first: Chang-Kyu

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary: Here, we examined the effect of LDN-193189, an inhibitor of the BMP signaling pathway, on pig embryonic stem cells (ESCs) in the absence of feeder cells to develop a feeder-free culture system. Feeder cells play an important role in supporting the pluripotency of pig ESCs by blocking trophoblast and mesodermal differentiation through inhibition of the BMP pathway. Transcriptome analysis revealed that LDN-193189 treatment instead of coculturing with feeder cells could help maintain the pluripotency and homogenous cell population of pig ESCs by stimulating the secretion of chemokines and suppressing differentiation. We confirmed that LDN-193189-treated pig ESCs cultured without feeder cells maintained pluripotency for an extended period and were capable of differentiating in vivo and in vitro. The pig ESCs represented distinct characteristics of pig epiblasts as an in vivo counterpart at a transcriptomic level. In summary, we developed feeder-free culture systems for pig ESCs, and our findings will improve the understanding of pluripotency gene networks and comparative embryogenesis.

overall_design: The single-cell transcriptomic profiling of pig embryonic stem cells cultured with feeder cells, LDN-193189 treated pig embryonic stem cells cultured without feeder cells, and fetal fibroblasts.

first: Kwang-Hwan

last: Choi

first: Dong-Kyung


title: Inducible CCR2+ nonclassical monocytes mediate the regression of cancer metastasis

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

summary: Classical monocytes (CMs) can be converted into conventional dominant Nr4a1-dependent nonclassical monocytes (N-NCMs). Upon activation of Nod2 signaling, CM also can be converted into noncanonical Nod2-dependent inducible NCMs (I-NCMs). The transcriptional profiles and typical markers specific for those two NCM subsets yet to be determined. To transcriptionally characterize N-NCM and I-NCM, we performed transcriptional profiling analysis using RNAseq data obtained from the flow-sorted NCM subsets. Through the comprehensive RNAseq analysis, we identified typical transcriptional markers specific to N-NCM and I-NCM. By virtue of those specific markers, we identified the potential I-NCM populations in multiple cellular settings.

overall_design: To purely collect N-NCM and I-NCM, we sorted the blood NCMs from MDP-treated Nod2KO mice and Nr4a1KO mice, respectively.  The flow-sorted NCMs were used for bulk RNA sequencing.

first: Xianpeng

last: Liu

first: Ankit

last: Bharat


title: HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos (response) [RNA-seq]

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

country: China

institute: Yunnan University

summary: Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a critical factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through co-phase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF–HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.

overall_design: To investigate the effect of dPCIF1/H3.3/HIRA/GAF on the zygotic gene activation of Drosophila embryo, we established a variety of mutants. We then performed gene expression profiling analysis using data from RNA-seq of mutant embryos and wild-type embryos at 1-4 time points.

first: Guoqiang

last: Zhang


title: High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations [LARRY lineage barcode of single cells]

status: Public on Nov 16 2024

city: Hangzhou

first: Shou-Wen

address: No. 18 Shilongshan Road, Xihu District

institute: Westlake University

summary: In vivo lineage tracing holds great potential to reveal fundamental principles of tissue development and homeostasis. However, lineage tracing in humans relies on DNA mutations that are extremely rare. In mice, the improved genetic labeling approach has low resolution over cell division histories. Here, we demonstrated for the first time that frequent epimutations on DNA methylation can be exploited to infer lineage histories in normal cells, enabled by our newly developed computational method MethyTree. Using both in-house and public sparse single-cell DNA methylation datasets with known lineage labels, MethyTree reconstructed lineage histories at high resolution and accuracy across different cell types, stages, and species. Applying MethyTree, we identified the first fate decision in human embryo development and pinpointed in total ~230 clones of hematopoietic stem cells in mice. Our study opens the door for high-resolution, noninvasive lineage tracing in mice, humans and beyond.

overall_design:
In this study, we carried out an in vitro lineage tracing experiment using blood progenitors extracted from a single adult mouse and generated single-cell multi-omic readouts. Specifically, we extracted Lin−cKit+Sca1- blood progenitors from a single mouse, introduced LARRY lineage barcodes in these cells by lentiviral infection, cultured them in vitro for 6 days in a media that supports cell expansion and pan-myeloid differentiation, and finally profiled these cells with a modified Camellia-seq protocol that we developed recently to obtain LARRY lineage barcode, transcriptome, and DNA methylome simultaneously in single cells. This table only contains data on the LARRY lineage barcode of single cells.
Please note that this is a lineage tracing experiment without standard processed format and thus only raw data fastq files are included in the records.

first: Mengyang

last: Chen

first: Ruijiang

last: Fu

first: Li

last: Li


title: RNA-seq analysis of human CD8 CAR-EGFR T cells in expansion and repeated hypoxic coculture

city: Singapore

first: Shijun

last: Ma

address: 60 Biopolis St, Singapore 138672

country: Singapore

institute: Genome Institute of Singapore, A*STAR

summary: Human CD8 EGFR CART cells during expansion and repeated hypoxic coculture were collected at different time points and subject to RNA-seq to identify key players in T cell differentiation and hypoxia-induced exhaustion. The RNA-seq data together with other functional analysis identified P4HA1 as an important enzyme that regulates T cell early differentiation and terminal exhaustion. To investigate the mechanism, P4HA1 inhibitor DPCA was used to treat the human CD8 cells during early expansion and repeated coculture and the cells were harvested for RNA-seq analysis.

overall_design: Part 1) Naïve CD8 cells were isolated from PBMC of healthy donors and stimulated with CD3/CD28 and infected with CAR-virus. The CD3/CD28 antibodies and CAR virus were washed away on Day 5 and expanded in medium with IL7/15 for another 7 days before being subjected to repeated coculture under normoxia/hypoxia. CD8 CAR T cells were collected at indicated time points for RNA-seq. Part 2) Human CD8 CART cells were expanded or cocultured as described above. Cells were treated with either P4HA1 inhibitor DPCA or DMSO as vehicle control and collected at different time points for RNA-seq analysis.

first: Li-Teng

last: Ong

first: Zemin

last: Jiang

first: Qiang

last: Yu


title: BPDCN MYB Fusions Regulate Cell Cycle Genes, Impair Differentiation and Induce Myeloid-Dendritic Cell Leukemia [HoxCutRun]

first: Christopher

last: Booth

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: MYB fusions are recurrently found in select cancers, including blastic plasmacytoid dendritic cell neoplasm (BPDCN), an acute leukemia with poor prognosis. They are markedly enriched in BPDCN compared to other blood cancers, and in some patients are the only obvious somatic mutation detected. This suggests they may alone be sufficient to drive dendritic cell transformation. MYB fusions are hypothesized to alter the normal transcription factor activity of MYB, but mechanistically how they promote leukemogenesis is poorly understood. Using CUT&RUN chromatin profiling, we found that in BPDCN leukemogenesis, MYB switches from being a regulator of dendritic cell lineage genes to aberrantly regulating G2/M cell cycle control genes. MYB fusions found in BPDCN patients increased the magnitude of DNA binding at these locations, and this was linked to BPDCN-associated gene expression changes. Furthermore, expression of MYB fusions in vivo impaired dendritic cell differentiation and induced transformation to generate a mouse model of myeloid-dendritic acute leukemia. Therapeutically, we present evidence that all-trans retinoic acid (ATRA) may cause loss of MYB protein and cell death in BPDCN.

overall_design: Mouse hematopoietic Hoxb8-FL cells were generated as described (Redecke et al Nat Methods 2013). Wild-type MYB (MYBWT), truncated MYB (MYBTR) or MYB-PLEKHO1 (MYBPLE) were then exogenously expressed in Cdkn2a-WT (CWT) or Cdkn2a-KO (CKO) Hoxb8-FL cells. These cells were co-cultured with MS5 stroma (HoxMS5) or transplanted into recipient mice to generate leukemia (HoxLeu).

first: Juliette

middle: M

last: Bouyssou

first: Andrew

last: Lane


title: BPDCN MYB Fusions Regulate Cell Cycle Genes, Impair Differentiation and Induce Myeloid-Dendritic Cell Leukemia [HoxRNASeq]

overall_design: Mouse hematopoietic Hoxb8-FL cells (Redecke et al Nat Methods 2013) were maintained in vitro in an undifferentiated state (HoxInVitro_Undiff) or differentiated to pDCs (HoxInVitro_pDC). Wild-type MYB (MYBWT), truncated MYB (MYBTR) or MYB-PLEKHO1 (MYBPLE) were then exogenously expressed in Cdkn2a-WT (CWT) or Cdkn2a-KO (CKO) Hoxb8-FL cells. These cells were co-cultured with MS5 stroma (HoxMS5) or transplanted into recipient mice to generate leukemia (HoxLeu).


title: BPDCN MYB Fusions Regulate Cell Cycle Genes, Impair Differentiation and Induce Myeloid-Dendritic Cell Leukemia [K562CutRun]

overall_design: MYB-V5 knock-in K562 cells were generated expressing V5-tagged MYB from the endogenous MYB locus. Four genotypes were generated: wild-type MYB (MYB-WT), truncated MYB (MYB-TR), MYB-PLEKHO1 fusion and non-targeted controls (NTC). Cut&Run was performed using five antibodies: MYB, H3K27ac, V5 (2 antibodies) and control IgG.


title: BPDCN MYB Fusions Regulate Cell Cycle Genes, Impair Differentiation and Induce Myeloid-Dendritic Cell Leukemia [BPDCNCutRun]

overall_design: Cut&Run was performed for MYB, H3K27ac and control IgG on normal plasmacytoid dendritic cells (pDCs), primary blastic plasmacytoid dendritic cell neoplasm (BPDCN) cells, BPDCN patient-derived xenograft (PDX) cells, and the BPDCN cell line CAL1

first: Katsuhiro

last: Togami


title: High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations

type: Methylation 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: Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition

city: Suita

first: Yuki

last: Akieda

state: Osaka

address: 3-1, Yamadaoka

department: Research Institute for Microbial Diseases

institute: Osaka University

summary: Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength-dependent manner to pattern developing tissues. However, developing tissues also undergo dynamic morphogenesis, which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition-related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/β-catenin signalling gradient, which acts as a morphogen to establish embryonic anterior-posterior patterning, revealed that unfit cells with abnormal Wnt/β-catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/β-catenin gradient formation and consequent anterior-posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues, this system may support tissue robustness and disease prevention.

overall_design: β-catCA (constitutive active form of β-catenin)-expressing (GFP+) cells, or βcatCA-unexpressing (GFP-) cells from β-catCA-mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA-seq.

first: Yasuyuki

last: Ohkawa

first: Tohru

last: Ishitani


title: Systems level analysis of lipid metabolism in oxygen-induced retinopathy [retina_RNAseq]

first: Charandeep

last: Singh

overall_design: 12 days old OIR hyperoxia and normoxic mouse retina from OIR resistant and susceptible strains were compared to find out metabolic changes responsible for protecting against OIR


title: Interspecies comparison receals Hmga1 as driver of cardiac regeneration [Mnase-seq]

city: Utrecht

first: Mara

last: Bouwman

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The prospect of repairing the heart after a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish, amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species, the molecular mechanisms driving cardiomyocyte cell cycle re-entry remain insufficiently understood. In this study, we employed spatial transcriptomics and identified high-mobility group AT-hook 1a (Hmga1a) as being upregulated in cardiomyocytes of the injury border zone in zebrafish, but not in mice. Through knock-out and cardiomyocyte-specific overexpression of hmga1a, we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition, a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically, Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally-regulated genes and induced a border zone-like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac repair after injury.

overall_design: TOMOseq was performed on mouse and zebrafish hearts at 3, 7 and 14 days post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.

first: Dennis

last: de Bakker

first: Phong

last: Nguyen

first: Hessel

last: Honkoop

first: Jeroen

last: Bakkers


title: Single-cell dissection of multifocal bladder cancer reveals malignant and immune cells variation between primary and recurrence tumor lesions

city: Shanghai

first: Ya

last: Han

address: Siping road

institute: Tongji University

summary: Bladder carcinoma (BLCA) is characterized by a high rate of post-surgery relapse and multifocality, with multifocal tumors carrying a 40% higher risk of recurrence compared to single tumors. Recurrence is a major contributor to bladder cancer-specific mortality. However, understanding interregional or intraregional malignant heterogeneity and cellular communication within the primary and recurrence tumor microenvironment (TME) remains a significant challenge. Here, we employed single-cell RNA sequencing (scRNA-seq) to analyze separate tumor lesions from five multifocal bladder cancer patients (comprising three primary tumors and two recurrence tumors).

overall_design:
We employed scRNA-seq to examine cellular heterogeneity and intercellular crosstalk within the primary and recurrence tumor microenvironments.
***Submitters state that, due to policy restrictions, the original data were stored in GSA (HRA005670).

Please note that processed data files have been updated on Feb 24, 2025.

first: S

last: Liu

first: Y


title: Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA-seq]

middle: D


title: Crypt density and recruited enhancers underlie intestinal tumour initiation

first: Ramesh

middle: A.

last: Shivdasani

address: 450 Brookline Ave. SM1060

department: Medical Oncology

summary: Oncogenic mutations that drive colorectal cancer can be present in healthy intestines for long periods without overt consequence. Mutation of Adenomatous polyposis coli (Apc), the most common initiating event in conventional adenomas, activates Wnt signaling, hence conferring fitness on mutant intestinal stem cells (ISCs). Apc mutations may occur in ISCs that arose by routine self-renewal or by dedifferentiation of their progeny. Although ISCs of these different origins are fundamentally similar, it is unclear if both generate tumours equally well in uninjured intestines. Also unknown is whether cis-regulatory elements are substantively modulated upon Wnt hyperactivation or as a feature of subsequent tumours. Here, we show in two mouse models that adenomas are not an obligatory outcome of Apc deletion in either ISC source but require proximity of mutant intestinal crypts. Reduced crypt density abrogates, and aggregation of mutant colonic crypts augments, adenoma formation. Moreover, adenoma-resident ISCs open chromatin at thousands of enhancers that are inaccessible in Apc-null ISCs not associated with adenomas. These cis-elements explain adenoma-selective gene activity and persist, with little further expansion of the repertoire, as other oncogenic mutations accumulate. Thus, cooperativity between neighbouring mutant crypts and new accessibility at specific enhancers are key steps early in intestinal tumourigenesis.

overall_design: To examine the effects of Apc loss (constitutive Wnt activation) on different cell types and in different contexts, we performed RNA-seq on primary mouse intestinal stem cells (ISCs) and intestinal organoids with and without Apc loss. Primary ISCs were isolated from the proximal (Duodenum) or distal (Ileum) one-third of the intestinal length and Apc loss was driven by either Lgr5-Cre (ISC-restricted) or Atoh1-Cre (intestinal secretory lineage) mouse strains. Whole organoids were examined 10 days after isolated crypts were plated.

first: Liam

last: Gaynor

first: Harshabad

first: Guodong

last: Tie

first: Shariq

last: Madha

first: Unmesh

last: Jadhav

last: Mancini

first: Mikio

last: Hoshino

first: Frederic

last: de Sauvage

first: Kazutaka

last: Murata

first: Krithika

last: Badarinath

first: Swarnabh

last: Bhattacharya


title: Crypt density and recruited enhancers underlie intestinal tumour initiation [ATAC-seq]

overall_design: To assess the effects of Apc loss (constitutive Wnt activation) in intestinal stem cells (ISCs) of different origins, in combination with other oncogenic mutations, and in mutant intestinal organoids, we performed ATAC-seq to determine the effects of these mutations on chromatin accessibility.

last: Singh

first: Andrew


title: Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk sortChIC Hmga1a OE]

first: Mara

last: Bouwman

first: Dennis

last: de Bakker

first: Hessel

first: Phong

last: Nguyen


title: Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]

last: Honkoop

first: Jeroen

last: Bakkers


title: Transcriptional regulation of adipocyte lipolysis by IRF2BP2 [CUT&RUN]

status: Public on Nov 14 2024

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Adipocyte lipolysis controls systemic energy levels and metabolic homeostasis. Lipolysis is regulated by post-translational modifications of key lipolytic enzymes. However, less is known about the transcriptional mechanisms that regulate lipolysis. Here, we identify the transcriptional factor interferon regulatory factor-2 binding protein 2 (IRF2BP2) as a repressor of adipocyte lipolysis. Deletion of IRF2BP2 in primary human adipocytes increases lipolysis without affecting glucose uptake, whereas IRF2BP2 overexpression decreases lipolysis. RNA-seq and ChIP-seq analyses reveal that IRF2BP2 directly represses several lipolysis-related genes, including LIPE (HSL, hormone sensitive lipase), which encodes the rate-limiting enzyme in lipolysis. Adipocyte-selective deletion of Irf2bp2 in mice increases Lipe expression and free fatty acid levels, resulting in elevated adipose tissue inflammation and glucose intolerance. Altogether, these findings demonstrate that IRF2BP2 restrains adipocyte lipolysis and opens new avenues to target lipolysis for the treatment of metabolic disease.

overall_design: Adipocyte precursor cells were stimulated with differentiation cocktail for 1 day, and cells were subjected to H3K27ac CUT&RUN assay.

first: Yang

last: Chen

first: Lin

last: Liu

first: Lan

last: Cheng

first: David

last: Merrick

first: David J.

last: Steger

first: Patrick

last: Seale


title: Transcriptional regulation of adipocyte lipolysis by IRF2BP2 [RNA-seq]

overall_design: To investigate the role of IRF2BP2 controlling adipocyte lipolysis and lipolysis genes transcription. Human adipocytes (control, knockout or GFP, overexpression) were collected for RNA-seq.


title: Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus


title: Antigen experience history directs distinct functional states of CD8+ CAR T cells during the anti-leukemia response [ATAC-Seq]

city: Denver

first: James

last: Scott-Browne

state: Colorado

address: 1400 Jackson St, K806

institute: National Jewish Health

summary: Adoptive transfer of immune cells expressing chimeric antigen receptors (CARs) is an effective therapy for B-lineage malignancies. However, most patients will relapse and this therapeutic has yet to show strong efficacy in other hematologic or solid tumors. One opportunity for improvement lies in the ability to select or generate T cells that have the highest potential for potent anti-tumor responses and T cell persistence. Here, we dissect the biology of CD8+ CAR T cells by controlling whether the T cell has encountered cognate TCR antigen prior to CAR generation. We find that prior antigen experience influences multiple aspects of in vitro and in vivo CAR T cell functionality, boosting effector function and leukemia clearance in the setting of limiting target antigen density. However, this comes at the expense of proliferative capacity, resistance to dysfunction, and clearance of wildtype leukemia in the setting of limiting CAR+ cell dose. Epigenetic and transcriptomic comparisons of these cell populations uncover that modulation of the Runx2 transcription factor differentially impacts CAR T cell functionality depending on prior cell state. Collectively, our data demonstrate that prior antigen experience status determines functional attributes of a CAR T cell, as well as amenability to functional enhancement by transcription factor modulation.

overall_design: To investigate the role of prior T cell antigen experience in responses of CD8+ chimeric antigen receptor (CAR) T cells to leukemia, we adoptively transferred C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells into C57BL/6-background CD45.1+ hosts, followed by vaccination with ovalbumin, anti-mouse CD40, and PolyI:C to generate memory CD8+ T cells ("memory-derived"), or used naïve C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells from naïve hosts ("naïve-derived"). We then transduced both populations with an anti-mouse CD19 CAR containing CD28 costimulatory domain and CD3zeta domain, and either pMSCV-mRUNX2-IRES-eGFP or empty pMSCV-IRES-eGFP. Memory or naive-derived T cells with or without RUNX2 were compared by RNAseq at Post-CAR Transduction ("PostCAR", Day 0, in vitro, Note: this timepoint is actually 5 days post activation but keeping with 'Day 0' nomenclature to match previous data).

first: Kole R.

last: DeGolier

first: Terry J.

last: Fry

first: Etienne

last: Danis

first: James P.


title: The miR-22-5p/Clec4e axis has diagnostic potential in fructose-induced nonalcoholic fatty liver disease

first: Zheng

last: Hui

address: 170 Xinsong Road, Minhang District

institute: Minhang Hospital, Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease.MicroRNAs play roles in the onset and progression of the disease. This study aimed to screen microRNA profiles and potential RNA networks for the diagnosis and treatment of NAFLD. Mice were high-fructose diet (HFrD) fed to induce NAFLD. MicroRNA expression profiles of the livers in HFrD mice and chow-diet fed mice were analyzed by RNA-seq. We successfully constructed high fructose induced NAFLD. There are 13 differentially expressed (DE) miRNAs in the livers of NAFLD mice. In summary, this study furthered our understanding of the genome mechanisms and the development of potential biomarkers for the treatment of fructose-induced NAFLD.

overall_design: Male C57BL/6J mice aged 10-11 weeks were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). HFrD containing 10% kcal from fat, 70% kcal from carbohydrate, and 20% kcal from protein were purchased from Research Diets (D08040107, Research Diets, USA). After a 2-week intervention period in which mice were fed either a normal diet (ND) or HFrD, mice were anesthetized with 10% chloral hydrate.

first: Hui

last: Zheng

first: Yifan

last: Zhu

first: Suying

last: Pu


title: New mechanisms for oral epithelial basal stem cell plasticity during re-epithelialization after injury

city: Iowa City

first: Brad

last: Amendt

state: IA

address: 1-675 Bowen Science Building (BSB) - 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

summary: The oral mucosa undergoes daily insults and stem cells in the epithelial basal cell layer are required to regenerate gingiva tissue to maintain oral health. The Iroquois Homeobox 1 (IRX1/Irx1) protein is expressed in the stem cell niches in human/mouse oral epithelium and mesenchyme under homeostasis. We found that Irx1+/- heterozygous (Het) mice have delayed wound closure, delayed morphological changes of regenerated epithelium, as well as defective keratinocyte proliferation and differentiation during wound healing. RNA-seq analyses between wildtype and Irx1+/- mice at 3 days post injury (dpi), found impaired epithelial migration and decreased keratinocyte-related genes upon injury. Irx1 expressing cells are found in the gingival epithelial basal cell layer, a stem cell niche for gingival maintenance. Irx1 expressing cells are also found in cell niches in the underlying stroma. Irx1 activates Sox9 in the transient amplifying layer to increase cell proliferation and EGF signaling is activated to induce cell migration. Krt14CreERT lineage tracing experiments reveal defects in the stratification of the Irx1+/- heterozygous mouse oral epithelium. Irx1 is primed at the base of the gingiva in the basal cell layer of the oral epithelium, facilitating rapid and scarless wound healing through activating Sox9 and the EGF signaling pathway.

overall_design: To investigate the role of transcription factor Irx1 during mouse gingival regeneration, we injured the mouse gingival in front of the right lower molar row of both wildtype and Irx1+/- mice. We collected 3 day-post-injury (3dpi) gingival tissue from both left (uninjured control) and right (3dpi) side and isolated total RNA to assess the transcriptomic change in wildtype and Irx1+/- mice.

first: Dan

last: Su

first: Tadkamol

last: Krongbaramee

first: Samuel

last: Swearson

first: Yan

last: Sweat

first: Mason

first: Fan

last: Shao

first: Steven

last: Eliason


title: Engineering spatially-confined conduits to tune nerve self-organization and allodynic responses via YAP-mediated mechanotransduction

city: Beijing

first: Xiaobin

last: Luo

address: Tsinghua Garden, Haidian District

institute: Tsinghua University

summary: Chronic allodynia stemming from peripheral stump neuromas can persist for extended periods, significantly compromising patients’ quality of life. Conventional managements for nerve stumps have demonstrated limited effectiveness in ensuring their orderly termination. In this study, we present a spatially confined conduit strategy, designed to enhance the self-organization of regenerating nerves after truncation. This innovative approach elegantly enables the autonomous slowing of axonal outgrowth in response to the gradually constricting space, concurrently suppressing neuroinflammation through YAP-mediated mechanotransduction activation. Meanwhile, the decelerating axons exhibit excellent alignment and remyelination, thereby helping to prevent failure modes in nerve self-organization, such as axonal twisting in congested regions and overgrowth beyond the conduit's capacity.

overall_design:
To investigate the genetic mechanism of CC for pain relief, mRNA sequencing was performed on nerve stumps.
These include control samples (CON), different gradients of truncated cone shaped conduits CC 4:2, 4:4 (labeled as EXP 42, EXP 44).
Furthermore, to verify the effect of YAP, vertaporfin loaded groups (VP42) were also done.

first: Jia

last: Yang

first: Yonggang

last: Zhao

first: Toshitatsu

last: Nagayasu


title: Antigen experience history directs distinct functional states of CD8+ CAR T cells during the anti-leukemia response

city: Aurora

first: Terry

last: Fry

state: CO

institute: University of of Colorado Denver and Children's Hospital Col

first: Kole R

last: DeGolier

first: Terry J

first: Etienne

first: James

middle: P

last: Scott-Browne


title: Insulin mitigates acute ischemia induced atrial fibrillation and sinoatrial node dysfunction ex vivo

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: Acute atrial ischemia is a well-known cause of postoperative atrial fibrillation (POAF). However, the cellular and electrophysiological mechanisms through which ischemia contributes to the development of POAF are not well understood. Administering insulin 30 minutes before ischemia and during reperfusion with 25 minutes of ischemia greatly reduced the vulnerability to AF.

overall_design: Bulk mRNA sequence was used to compare the mRNA expression difference among conditions including non-ischemia (IS-0), ischemia for 25 mins (IS-25), and ischemia for 25 mins with insulin pretreatment.

first: Wuqiang

first: Huiliang

last: Qiu

last: Li


title: HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos [RNA-Seq]

first: Liangliang

last: Wang

overall_design: To investigate the effect of dPCIF1/H3.3/HIRA/GAF on the zygotic gene activation of drosophila embryo, we established a variety of mutants. We then performed gene expression profilinf analysis using data from RNA-seq of mutant embryos and wild-type embryos at 2-3 time points.

first: Guoqiang

last: Zhang

first: Yaqi

last: Miao

first: Yuan

last: Song

first: Yawei

first: Yuanxiang

last: Zhu

first: Wenxin

first: Qinmiao

last: Sun

first: Dahua

last: Chen


title: HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos [ATAC-seq]

overall_design: Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) for wild type, M-Z+ HIRA mutant, and M-Z+ dPCIF1 mutant drosophila embryos.


title: The effect of methylation on the let-7-BCL2L1-BCL2 axis and the potential use of hypomethylating and BH3 mimetic drugs in histiocytic neoplasms

city: Ariel

first: Mali

last: Salmon-Divon

address: Ariel university, Ariel Israel, Ramat HaGolan St 65, Ari'el

country: Israel

institute: Department of Molecular Biology, Ariel University

type: Methylation profiling by genome tiling array

summary: The histiocytoses [Erdheim-Chester Disease (ECD), Langerhans cell histiocytosis (LCH), and Rosai-Dorfman-Destombes disease (RDD)] are characterized by the infiltration of monocytes, macrophages, and dendritic cells in normal tissues, leading to significant morbidity due to disruption of critical organ systems. While their pathogenesis involves MAPK-ERK pathway mutations, their epigenetic landscape remains poorly understood.  Epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNA are crucial in gene expression regulation and cancer development. We previously identified a distinct non-coding RNA profile in histiocytosis patients compared to controls.  We analyzed the DNA methylation profile of 30 patients and found significant alterations in 23,322 methylation sites compared to controls, independent of age, gender, mutation type, or disease site. We observed a significant hypermethylation in the let-7b transcript, resulting in decreased let-7b expression. This led to the lack of regulation on the anti-apoptotic proteins BCL2L1, which was overexpressed in 21/21 (100%) patients' biopsies and BCL2 in 11/21 biopsies (52%). Treatment with the hypomethylating agent, 5-Azacytidine, restored let-7b expression, reduced BCL2L1 levels, and induced apoptosis in BRAFV600E mutant cells. Additionally, BCL2L1 and BCL2 inhibitors also induced apoptosis.     This novel epigenetic mechanism suggests that hypomethylating agents or BH3 mimetic drugs may offer new therapeutic targets for histiocytosis.

overall_design: Methylation profiles of six ECD, 14 LCH, and 10 RDD patients were analyzed from diagnostically confirmed tumor biopsies by Illumina EPIC-methylation array according to the manufacturer protocol. These were compared to controls, suture granulomas (n=4), localized inflammatory reactions characterized by non-neoplastic histiocytic infiltrates.

first: Oshrat

last: Hershkovitz-Rokah

first: Eli

middle: L

last: Diamond

first: Jamal

last: Benhamida

first: Omar

last: Abdel-Wahab


title: Alternative splicing is an FXRα loss-of-function mechanism and impacts energy metabolism in hepatocarcinoma cells.

city: Clermont-Ferrand

first: David

middle: H

last: VOLLE

address: 28 place Henri Dunant

country: France

institute: INSERM

summary: Farnesoid X receptor α (FXRα) is a bile acid-activated nuclear receptor that sets the expression of glycolytic and lipogenic target genes by interacting with the 9-cis-retinoic acid receptor α (RXRα). Jointly with recruited cofactors, the current FXRα proteins reported so far in human and rodent have been described to regulate both isoform (α1-4)- and tissue-specific gene expression profiles in order to integrate energy balance and adapt metabolism. Here, we studied the biological functions of a FXRα naturally occurring spliced exon 5 isoform (FXRαse5) lacking the second zinc-binding module of the DNA Binding Domain (DBD). We show that the FXRαse5 is expressed in all FXRα-expressing tissues and cells from human and mouse, and that it is not able to either bind to its response element or activate FXRα dependent transcription. In parallel, this spliced variant displayed differential interaction capacities with its obligate heterodimer partner RXRα that may account for silencing of this permissive dimer for signal transduction. Finally, deletion of exon 5 by gene edition in HepG2 cells leads to FXRα loss-of-function, increased expression for LRH1 metabolic sensor and CD36 fatty acid transporter in conjunction with changes in glucose and triglycerides homeostasis. All together, these findings highlighted a novel mechanism by which alternative splicing may regulate FXRα gene function to fine-tune adaptive and/or metabolic responses. Taking this into account could deepen our understanding on how splicing events might hinder FXRα activity to regulate specific transcriptional programs and contribute to modify energy metabolism in normal tissues and metabolic diseases.

overall_design: To verify whether and to what extent the FXRαse5 isoform may modulate FXRα transcriptional network through specific binding to other FXRE DNA sequence motifs, we used RNA sequencing to explore the transcriptome of HepG2 overexpressing either FXRα1 or FXRαse5. By comparing genes regulated by these two FXRα isoforms with the empty control vector, we generated the heatmap and the Venn diagram of the RNAseq datasets

first: Claude

last: Beaudoin

last: Volle


title: Airway neutrophils actively enhance the therapeutic efficacy of flagellin in treating pneumococcal pneumonia

city: Lille

first: Jean-Claude

last: Sirard

address: 1 rue du Professeur Calmette

institute: Center for Infection and Immunity of Lille - Pasteur Institute of Lille

summary: Host-directed therapy, using nasal administration of the Toll-like receptor 5 agonist flagellin in combination with antibiotics, has demonstrated effectiveness against pneumococcal pneumonia. In this study, we investigated the immune mechanisms underlying the protective effects. Transcriptomic analysis of lung tissue during infection revealed that flagellin not only enhanced pathways associated with myeloid cell infiltration into the airways and antimicrobial functions, but also promoted the early and transient mobilization of neutrophils and inflammatory monocytes. Neutrophils were identified as crucial for the protective effects of flagellin. The adjunct activity of flagellin correlated with the increased recruitment of neutrophils into airways, their localization at the periphery of bronchi, alveoli, and lung vessels, along with alterations in phagocytic activity. Lastly, single-cell analysis highlighted that the treatment stimulated the recruitment of specific neutrophil subsets capable of enhancing antibacterial effectiveness. In conclusion, this study highlights neutrophils as an appealing target for host-directed therapy in infection.

overall_design: Eight weeks-old female mice were infected with Streptococcus pneumoniae and treated 12 hours post-infection with amoxicillin alone or in combination with flagellin. Bronchoalveolar lavages were sampled 4 hours post-treatment and processed for RNA isolation and sequencing.

first: Laura

last: Matarazzo

first: Charlotte

last: Costa

first: Rémi

last: Porte

first: Jean-Michel

last: Saliou

first: Martin

last: Figeac

first: Fabien

last: Delahaye

first: Amélie

last: Bonnefond

first: Benoit

last: Kloeckner

first: Aymeric

last: Silvin

first: Florent

last: Ginhoux

first: Christelle

last: Faveeuw

first: Mara

last: Baldry

first: Christophe

last: Carnoy


title: Characteristics of a CCL21-gene modified dendritic cell vaccine utilized for a clinical trial in non-small cell lung cancer

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

summary: Samples are from a phase I clinical trial of a vaccine consisting of monocyte-derived DCs (moDCs) modified to express the chemokine CCL21 given in combination with pembrolizumab, conducted in patients with advanced non-small cell lung cancer. Single cell RNA sequencing of pre- and post-transduced vaccines was performed to characterize the cellular composition of these vaccines and assess the trascriptional impact of the transduction process. The same vaccine production procedure was also applied to blood obtained from healthy donors to investigate the effects of donor source on DC vaccine phenotype.

overall_design: Monocyte-derived dendritic cells isolated from PBMCs of patients and health donors were modified to express the chemokine CCL21. We used single-cell RNA sequencing to evaluate 1) the cellular composition and transcriptional impact of the transduction process in patient samples and 2) their deviation between patients and healthy donors upon the transduction.

first: Michael

middle: S

last: Oh

first: Camelia

last: Dumitras

first: Ramin

last: Salehi-Rad

first: Kostyantyn

last: Krysan

first: Zhe

last: Jing

first: Aaron

last: Lisberg

first: Edward

last: Garon

first: Bin

last: Liu

first: Steven

last: Dubinett


title: HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos [ChIP-Seq]

first: Liangliang

last: Wang

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

summary: Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a critical factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through co-phase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF–HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for dPCIF1, HIRA, PolII-Ser5P, GAF, and ZLD in drosophila embryos.

first: Guoqiang

last: Zhang

first: Yaqi

last: Miao

first: Yuan

last: Song

first: Yawei

last: Li

first: Yuanxiang

last: Zhu

first: Wenxin

first: Qinmiao

last: Sun

first: Dahua

last: Chen


title: Interspecies comparison reveals Hmga1 as driver of cardiac regeneration

first: Mara

last: Bouwman

overall_design: Refer to individual Series


title: Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics

city: Chicago

first: Denis

last: Cipurko

address: 900 E 57th St

department: Biological Sciences Division

institute: University of Chicago

summary: Purpose: Here, we describe a method, Array-seq, to repurpose classical oligonucleotide microarrays for spatial transcriptomics profiling. We demonstrate that Array-seq yields spatial transcriptomes with high detection sensitivity and localization specificity using histological sections from mouse tissues as test systems. Moreover, we show that the large surface area of Array-seq slides enables the generation of spatial transcriptomes at high throughput by profiling multi-organ sections, in three dimensions by processing serial sections from one sample, and across whole human organs using spleen sections.  Experimental Methods: To generate Array-seq slides, we first obtain microarrays carrying custom-design probes that contain common sequences flanking unique barcodes at known coordinates. Second, we perform a simple, two-step reaction that produces mRNA capture probes across all spots on the microarray and thereby creates Array-seq slides set for spatial transcriptomics. Following in-situ mRNA capture, reverse transcription, libaray preparation, Array-seq libraries are sequenced using the Illumina sequencing-by-synthesis (SBS) platform.

overall_design: A total of 5 Array-seq experiments were run on the following tissues: (1) Mouse Main Olfactory Bulb (MOB), (2) Mouse kidney (4 replicates, adjacent sections used for Array-seq and Visium), (3) 3D Mouse kidney (100-μm spacing between 8 individual sections from a single kidney to generate a 3-dimensional dataset), (4) Multi-organ (A single Array-seq caputre area was used for 2 mouse brain sections, 3 mouse kidney sections, 3 mouse liver sections), (5) Whole mount human spleen section. 6-8 week old C57BL/6J mice were used for all mouse experiments.

first: N

last: Chevrier

first: D


title: Transcriptional regulation of adipocyte lipolysis by IRF2BP2 [ChIP-seq]

first: Ryan

last: Calhoun

overall_design:
Adipocyte precursor cells were stimulated with differentiation cocktail for 1 day, and cells were then subjected to chromatin collection for IRF2BP2 ChIP

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Yang

first: Lin

first: Lan

last: Cheng

first: David

last: Merrick

first: David J.

last: Steger

first: Patrick

last: Seale


title: Hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment

first: Zizheng

last: Suo

address: No. 17, Panjiayuan Nanli, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: This study investigates the roles of neurons, microglia, astrocytes, and oligodendrocytes in the pathogenesis of postoperative cognitive impairment, focusing on a dysregulated glia-neuron cycle. We utilized 18-month male C57BL/6 mice to model this condition, conducting single-cell RNA sequencing in the hippocampus to explore the neuroglial interactions and their implications in neuroinflammation, synaptic dysfunction, and myelin loss. This dataset includes transcriptomic profiles aimed at decoding the cellular communication in aged hippocampal cells and assessing the impact of therapeutic interventions on postoperative cognitive decline.

overall_design: In this study, we examined the effects of sevoflurane anesthesia combined with surgical stress on hippocampal function in mice. The surgery group was exposed to 2.5% sevoflurane in 50% oxygen for 30 minutes using a breathing mask, while the control group received only 50% oxygen for the same duration. Sevoflurane levels were continuously monitored using a Datex anesthetic monitor. A modified exploratory laparotomy was performed on the surgery group, followed by a recovery period in 50% oxygen. After 24 hours, hippocampal tissues were collected for single-cell RNA sequencing.

first: Ting

last: Xiao

first: Yinyin

last: Qu

first: Yuxiang

last: Zheng

first: Wenjie

last: Xu

first: Bowen

last: Zhou

first: Jing

last: Yang

first: Jie

last: Yu

first: Hui

first: Cheng

last: Ni


title: Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics - Bulk RNA-seq

first: Denis

summary: Bulk RNA-seq (PME-seq) generated for analysis in parallel with Array-seq.

overall_design: To study immune processes at the organism-level, four replicates of 6 weeks old female mice were anasthesized, and transcardially perfused with PBS supplemented with 1 mM EDTA. 15 tissues (Liver, Spleen, Colon, Thymus, Kidney, Lung, Heart, Muscle, White Adipose Tissue, Brown Adipose Tissue, Bone Marrow, Inguinal Lymph Node, Skin, Small Intestine, Brain) were collected and stored in RNAlater at 4C overnight before freezing at -80C for long-term storage.

first: N

first: D


title: Effect of knockdown of Zbtb9 on gene expression during adipogenic differentiation of 3T3-L1 preadipocytes

city: Cleveland

first: Xuan

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

summary: Adipocytes play a critical role in metabolic homeostasis. Here we report that Zbtb9 acts as a positive regulator of PPARγ transcriptional activity in 3T3-L1 mature adipocytes, and PPARγ target gene expression was decreased when Zbtb9 deficiency was induced by shRNA-mediated knockdown (KD), establishing Zbtb9 as a newly identified PPARγ cofactor. Given the central role of PPARγ in adipogenesis, we also sought to investigate the role of Zbtb9 in adipogenesis in 3T3-L1 cells. Surprisingly, lipid droplet formation was significantly increased in Zbtb9 KD cells compared with the control, as was the expression of adipogenic genes including Pparg, Adipoq, Fabp4, and Cd36. The transcriptome of Zbtb9-KD fibroblasts, prior to the initiation of differentiation showed that the E2F targets pathway was significantly upregulated compared to the control cells. In addition, E2F activity was increased in Zbtb9-KD fibroblasts using luciferase reporter assay. Accordingly, RB phosphorylation was enhanced in Zbtb9-KD cells. Collectively, these results demonstrate that Zbtb9 inhibits adipogenesis as a negative regulator of Pparg expression via altered pRB-E2F1 signaling. Together, our findings revealed complex cell-state dependent roles of Zbtb9 in adipocytes, identifying a new molecule that may be important in the pathogenesis and treatment of obesity and T2D.

overall_design: Zbtb9 was knocked down in 3T3-L1 preadipocytes by 2 independent shRNAs - shRNA#1 and shRNA#2, as well as a scramble control - #shCtrl. We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 different cells, including 2 replicates for each shRNAs and 4 replicates for the scramble control, at 4 time points during adipogenesis. Comparative gene expression profiling analysis of RNA-seq data for Zbtb9 knockdown cell and control cells at each time point.

last: Buchner


title: Single-cell RNA-sequencing of human spleens reveals an IDO-1+ Tolerogenic Dendritic Cell subset in pancreatic cancer patients that is absent in normal individuals.

city: Omaha

first: Michael

last: Hollingsworth

state: NE

address: BCC 8.12.384, 601 S Saddle Creek Road

department: Eppley Cancer Institute

institute: University of Nebraska Med Center

summary: Local and systemic immunosuppression are prominent features of pancreatic cancer, rendering anti-tumor effector cells inactive and immunotherapeutic approaches ineffective. The spleen, an understudied point of antigen-presentation and T cell priming in humans, holds particular importance in pancreatic cancer due to its proximity to the developing tumor. As main effectors of antigen presentation, dendritic cells display antigens to lymphocytes, thereby bridging the innate and adaptive immune response. While tumor-infiltrating anti-inflammatory dendritic cells have been described, splenic dendritic cells have historically just been considered to stimulate the anti-tumor immune response. Here, we describe, for the first time, the presence of an immunosuppressive, tolerogenic IDO1+ dendritic cell subset in the spleens of pancreatic cancer patients that likely contributes to systemic immunosuppression that is associated with pancreatic ductal adenocarcinoma. Network analysis of scRNA seq data reveals extensive communication networks between the identified tolerogenic DC cluster and numerous immune cell populations in the spleen. Interactions with innate and adaptive immune cells suggest a broad influence on leukocyte trafficking and immune regulation within the spleen microenvironment. The identification of signaling pathways involving AHR and IDO-1, CCL19, NECTIN2, CLEC2D, and others elucidates potential mechanisms underlying the immunosuppressive functions of this cell type.

overall_design: We performed single-cell RNA-sequencing (scRNA-seq.) of primary human spleens and compared the immune cell signatures of spleens from 4 PDAC patients with the spleens of 3 normal individuals. PDAC patient spleen samples were collected on-site during distal pancreatectomy with splenectomy and processed within 2 h. Normal sample spleen processing began approximately three to 4 h post-mortem. Spleens were diced and stomached in the Stomacher 80 Biomaster (Seward TM) according to the manufacturer’s protocol. After red blood cell lysis, dead cells were removed using Dead Cell Removal MicroBeads (Miltenyi; Catalog-No.: 130-090-101). Splenocytes were given to the UNMC Genomics Core Facility to generate the scRNA-eq libraries (10x Genomics' Chromium Single Cell Platform 3′ Version 3), following standard protocol. Transcript reads were aligned to the GRCh38 Human Genome reference using the Cell Ranger 3.0.0 pipeline (10x Genomics, Inc.) to generate the matrix files containing cell barcodes, UMIs (unique molecular identifiers), and transcript counts. UMI count matrices were generated for each sample and imported into Seurat R toolkit (Version 4.September 9, 9049). Only those genes expressed in more than three3 cells and cells that expressed more than 250 genes were kept; low-quality cells (≤250 genes/cell, ≤500 UMIs/cells, and ≥20 % mitochondrial genes) were excluded. A total of 30,864 cells in all samples were analyzed. The expression data was normalized and scaled using default settings. Principal component analysis (PCA) was performed based on 2000 highly variable genes for dimensionality reduction. Data integration of PDAC and normal spleen samples was performed using the anchor-based Canonical Correlation Analysis (CCA) integration method using Seurat v5. Cell type identification and annotation in the generated dataset were performed by reference-based mapping using the Azimuth v0.5.0 package within R. Briefly, we utilized the Tabula Sapiens normal human spleen scRNAseq dataset as reference dataset for this purpose.

first: Clara

last: Mundry

first: Aleata

last: Triplett

first: Paul

last: Grandgenett

first: Osama

last: Shah

first: Vijender

last: Chaitankar

first: Kyle

last: McAndrews

first: Kamiya

last: Mehla

first: Quan

last: Ly

first: Jesse

last: Cox

first: Kirsten

middle: C

last: Eberle

first: Benjamin

middle: J

last: Swanson

first: Audrey

last: Lazenby

first: Kelsey

last: Klute


title: Transcriptome and DNA Methylation Analysis of Goat Pineal Gland During Puberty [RNA-seq]

city: Hefei

first: Bochao

last: Zhang

state: Anhui Province

address: No. 130 West Changjiang Road, Shushan District

institute: Anhui Agricultural University

summary: Epigenetic regulation of gene transcription may play a critical role in the onset of puberty. Previous studies have confirmed that methylation regulates gene transcription in the hypothalamus-pituitary-gonadal axis during puberty initiation, but little is known about the regulation of DNA methylation on gene expression in the pineal gland. This study aims to screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, to clarify the initiation mechanism of goat puberty and lay the foundation for improving goat reproductive performance. Pineal gland was collected from three female Anhui white goats during prepuberty (2.5 to 3.0 mo) and three during puberty (4.0 to 4.5 mo). Genome-wide hydrogen sulfite sequencing determined the DNA methylation profile, while RNA sequencing determined the transcriptome. The relationship between gene transcription and DNA methylation was determined by joint analysis. We found that there was no significant change in the whole genome methylation level of goat pineal gland before and after puberty, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland may be involved in regulating goat puberty initiation. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes was not affected by DNA methylation differences. Genes regulated by DNA methylation were mainly involved in metabolic processes, oxidative phosphorylation (OXPHOS), and signaling pathways related to thermogenesis. The differential genes ATP5F1D, CACNB2, and PTEN were significantly regulated by methylation, and the difference multiples of LIN28B, GIP, OPN1SW, and DCC were the most significant, possibly involved in puberty initiation.

overall_design: The cunnus of pubertal goats was inflamed, with histological observation of some mature follicles in the ovaries. The goats were euthanized and their pineal gland were quickly collected. All the pineal glands sample were quickly frozen in liquid nitrogen for RNA and DNA methylation sequencing analysis.

first: Huihui

last: Xie

first: Genbao

last: Zhu

first: Jianling

last: Wu

first: Jiankun

last: Cui

first: Wei

last: Qian

first: Qing

last: Yi

first: Fuqiang

last: Pan

first: Fugui

last: Fang

first: Yinghui

last: Ling

first: Yunsheng

last: Li

first: Liu

last: Ya


title: Transcriptome and DNA Methylation Analysis of Goat Pineal Gland During Puberty [Bisulfite-seq]

overall_design:
The cunnus of pubertal goats was inflamed, with histological observation of some mature follicles in the ovaries. The goats were euthanized and their pineal gland were quickly collected. All the pineal glands sample were quickly frozen in liquid nitrogen for RNA and DNA methylation sequencing analysis.
This dataset represents DNA methylation sequencing analysis.


title: Transcriptome and DNA Methylation Analysis of Goat Pineal Gland During Puberty

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


title: Enterocyte like differentiation defines metabolic gene signatures of CMS3 colorectal cancers and provides therapeutic vulnerability

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

institute: Amsterdam UMC

summary:
Colorectal cancer (CRC) is stratified into four consensus molecular subtypes (CMS1-4). CMS3 represents the metabolic subtype, but its wiring remains largely undefined. To identify the underlying tumorigenesis of CMS3, organoids derived from 16 genetically engineered mouse models are analyzed. Upon in vitro Cre-recombinase activation, transformation is established and transcriptional profiling reveals that distinct CMSs (CMS2-4) are modeled with different organoids. CMS3-like, metabolic signature-positive, organoids are induced by KRAS mutations. Interestingly, metabolic signatures are subsequently shown to result from enterocyte-like differentiation both in organoids and human cancers. Further analysis reveals carbamoyl-phosphate synthase 1 (CPS1) and sucrase-isomaltase (SI) as signature proteins. More importantly, CPS1 is crucial for de novo pyrimidine synthesis in CMS3 and its inhibition targets proliferation and stemness, facilitating enterocyte-like differentiation, while CMS2 and CMS4 models are not affected. Our data point to an enterocyte-like differentiation of CMS3 CRCs and reveal a selective vulnerability of this subtype through CPS1 inhibition.

To investigate the effect of single and combined mutations in colon and small intestine of mouse models, we have generated a large set of organoids across 16 different genotypes zooming in on microsatellite stable CRC (CMS2-4). This set of organoids includes villinCreER Apcfl/fl (A), villinCreER Apcfl/fl Trp53fl/fl (AP), villinCreER Apcfl/fl Trp53R172H/fl (AP2), villinCreER Apcfl/fl KrasG12D/+ Trp53fl/fl (AKP), villinCreER Apcfl/fl KrasG12D/+ Trp53fl/fl Smad4fl/+ (AKPS), villinCreER KrasG12D/+ (K), villinCreER KrasG12D/+ Trp53fl/fl (KP), villinCreER KrasG12D/+ Trp53fl/fl Rosa26N1ind/+ (KPN), villinCreER BrafV600E/+ Trp53fl/fl Rosa26N1ind/+ (BPN), villinCreER BrafV600E/+ Trp53fl/fl Rosa26N1ind/+ Alk5fl/fl  (BPNA2), villinCreER Apcfl/fl KrasG12D/+ (AK), villinCreER Apcfl/fl KrasG12D/+ Trp53R172H/fl (AKP2), villinCreER Apcfl/fl KrasG12D/+ Trp53fl/fl Rosa26N1ind/+ (AKPN), villinCreER Apcfl/fl Trp53fl/fl Rosa26N1ind/+ (APN), villinCreER BrafV600E/+ Trp53fl/fl (BP), and villinCreER KrasG12D/+ Trp53fl/fl Rosa26N1ind/+ Alk5fl/fl (KPNA2).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of all these organoids.


title: Inflammation switches the chemoattractant requirements for naïve lymphocyte entry into lymph nodes

status: Public on Nov 13 2024

city: San Francisco

first: Kevin

last: Chen

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

summary: CCL21 is downregulated in stroma during inflammation of the lymph node. The factors controlling this repression are unknown. ATAC-seq was performed on naïve and inflamed lymph node fibroblasts to elucidate the signals controlling CCL21 downregulation and other lymph node stromal inflammatory programs.

overall_design: ATAC-seq for CD45- CD31- gp38+ fibroblastic reticular cells (FRCs) from brachial (non-draining) and popliteal (draining) lymph nodes 24 hrs post footpad infection with lymphocytic choriomeningitis virus.

first: Kan

last: Jiang

first: Stephen

last: Brooks

first: Jason

middle: G

last: Cyster


title: Local radiation enhances systemic CAR T-cell efficacy by augmenting antigen crosspresentation and T-cell infiltration

first: Nektarios

last: Kostopoulos

address: 3400 Civic Center Blvd.

institute: University of Pennsylvania

summary: Chimeric antigen receptor (CAR) T-cell therapy targeting CD19 (CART-19) represents a significant advance in the treatment of patients with relapsed or refractory CD19+ B-cell lymphomas. However, a significant portion of patients either relapse or fail to respond. Moreover, many patients have symptomatic disease, requiring bridging radiation therapy (RT) during the period of CAR T-cell manufacturing. To investigate the impact of 1 to 2 fractions of low-dose RT on CART-19 treatment response, we developed a mouse model using A20 lymphoma cells for CART-19 therapy. We found that low-dose fractionated RT had a positive effect on generating abscopal systemic antitumor responses beyond the irradiated site. The combination of RT with CART-19 therapy resulted in additive effects on tumor growth in irradiated masses. Notably, a significant additional increase in antitumor effect was observed in nonirradiated tumors. Mechanistically, our results validate activation of the cyclic guanosine adenosine synthetase/stimulator of interferon genes pathway, tumor-associated antigen crosspriming, and elicitation of epitope spreading. Collectively, our findings suggest that RT may serve as an optimal priming and bridging modality for CAR T-cell therapy, overcoming treatment resistance and improving clinical outcomes in patients with CD19+ hematologic malignancies.

overall_design: The submission includes RNA-seq data from tumor and lymph nodes samples collected form BALB/c mice bearing two A20 lymphoma tumors, one primary treated with radiation therapy (RT) (IR tumor) and one non-treated (Non-IR tumor). The primary objective was to assess the gene expression profiles in response to different RT regiments, a sinlge dose of 8Gy or 2 regiments of 4Gy. The samples were collected 24 hours and 7 days post RT treatment. Each experimental group includes 2 or 3 bilogical replicates, except the lymph nodes samples that are three biological replicates pooled together as one sample.

first: Andrea

last: Facciabene


title: The response to thiosulfate availability in Hyphomicrobium denitrificans

city: Bonn

first: Christiane

last: Dahl

address: Meckenheimer Allee 168

department: Institut für Mikrobiologie & Biotechnologie

country: Germany

summary: Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. RT-qPCR provided initial evidence that SoxT1A and SoxT1B from H. denitrificans may be intricate components of the oxidation pathway and/or involved in its transcriptional regulation.  Here, we extend these analyses with genome-wide mRNA-Seq data for the reference strain, comparing transcription in the absence and presence of 2 mM thiosulfate

overall_design: To investigate the response of the chemoorganotrophic bacterium Hyphomicrobium denitrificans to the availability of thiosulfate as an additional electron donor, the delta tsdA reference strain, which lacks the tetrathionate-forming enzyme thiosulfate dehydrogenase was grown under two different conditions. Cells were grown on methanol under aerobic conditions either in the absence or in the additional presence of thiosulfate.

first: Jingjing


title: Spatial Transcriptomics of Lungs Infected with Coccidioides posadasii

city: Livermore

first: Dina

last: Weilhammer

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

summary: Coccidioidomycosis, or Valley Fever, is a lung disease caused by inhaling Coccidioides fungi, prevalent in the Southwestern U.S., Mexico, and parts of Central and South America. Climate change is contributing to the spread of this disease. Many cases are asymptomatic, some are often misdiagnosed, and a small subset can progress to severe illness. To better understand lung responses during late Coccidioides infection, we used 10x Visium spatial transcriptomics. We analyzed non-infected lung (D0) and infected lung at 14 days post-infection (D14).

overall_design: Spatial transcriptomics was conducted on lung tissues from mice intranasally infected with Coccidioides posadasii. Samples were taken from a non-infected lung (D0) and an infected lung 14 days post-infection (D14).

first: Oscar

last: Davalos

middle: R


title: scRNA-seq time-course of Coccidioides posadasii infected lungs

summary: Coccidioidomycosis, or Valley Fever, is a lung disease caused by inhaling Coccidioides fungi, prevalent in the Southwestern U.S., Mexico, and parts of Central and South America. Climate change is contributing to the spread of this disease. Many cases are asymptomatic, some are often misdiagnosed, and a small subset can progress to severe illness. To better understand lung responses during Coccidioides infection, we used single-cell RNA sequencing (scRNA-seq). We analyzed non-infected lungs (D0) and infected lungs at 5, 9, and 14 days post-infection (D5, D9, D14).

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on lung cells isolated from non-infected control mice (D0) and from mice infected intranasally with Coccidioides posadasii at 5, 9, and 14 days post-infection (D5, D9, D14).

middle: A


summary: Colorectal cancer (CRC) is stratified into four consensus molecular subtypes (CMS1-4). CMS3 represents the metabolic subtype, but its wiring remains largely undefined. To identify the underlying tumorigenesis of CMS3, organoids derived from 16 genetically engineered mouse models are analyzed. Upon in vitro Cre-recombinase activation, transformation is established and transcriptional profiling reveals that distinct CMSs (CMS2-4) are modeled with different organoids. CMS3-like, metabolic signature-positive, organoids are induced by KRAS mutations. Interestingly, metabolic signatures are subsequently shown to result from enterocyte-like differentiation both in organoids and human cancers. Further analysis reveals carbamoyl-phosphate synthase 1 (CPS1) and sucrase-isomaltase (SI) as signature proteins. More importantly, CPS1 is crucial for de novo pyrimidine synthesis in CMS3 and its inhibition targets proliferation and stemness, facilitating enterocyte-like differentiation, while CMS2 and CMS4 models are not affected. Our data point to an enterocyte-like differentiation of CMS3 CRCs and reveal a selective vulnerability of this subtype through CPS1 inhibition.

overall_design: Samples were generated by intraperitoneal injection of 2 mg 4-hydroxytamoxifen (Sigma-Aldrich) in GEMMs with a C57BL/6 background. 72 hours after induction crypts were extracted from SIP and CO sections. Organoid cultures were maintained and expanded in ENR or ENR-C media as indicated above.

first: Jan

last: Medema

first: Aleksandar

last: Kirov

first: Owen

last: Sansom


title: Transcriptomic neuron types vary topographically in function and morphology

city: Martinsried

first: Inbal

last: Shainer

address: Am Klopferspitz 18

institute: Max Planck Institute for Biological Intelligence

summary: We transcriptionally profiled the neuronal types of the zebrafish larvae optic tectum and matched them with their functional and morphological properties.

overall_design:
Wild type larvae were raised until 6 or 7 dpf. The optic tectum and torus longitudinalis of 6 and 7 dpf larvae were then carefully dissected under a stereoscope followed by cell dissociation and sequencing.
Please note that batches 5, 6, and 8 the raw data with technical replica (i.e. replica 1, replica 2) were processed together, and the resulting processed data is linked to the corresponding replica 1 sample records.

first: Herwig

last: Baier


title: microRNA profile of endometrial cancer from Indian patients-Identification of potential biomarkers for prognosis

city: Bengaluru

first: Prathibha

last: Ranganathan

state: Karnataka

address: Electronic City Phase I

country: India

institute: Centre for Human Genetics

summary: Endometrial cancer is one of the major cancers in women throughout the world. If diagnosed early, these cancers are treatable and the prognosis is usually good.  However, one major problem in treating endometrial cancer is accurate diagnosis and staging. Till date, the choice method for diagnosis and staging is histopathology. Although there are few molecular markers identified, they are not always sufficient in making accurate diagnosis and deciding on therapeutic strategy. As a result, very often patients are under treated or over treated. In this study, our group has profiled microRNAs from Indian patients using NGS-based approach. We have identified differentially expressed microRNAs in endometrial cancer. These microRNAs have also been compared to data from TCGA, which represent other populations and also correlated to relevance in overall survival. Using in-silico approaches, mRNA targets of the miRNAs have been predicted. After comparing with TCGA, we have identified 16 miRNA-mRNA pairs which could be potential prognostic biomarkers for endometrial cancer. This is the first miRNA profiling report from Indian cohort and one of the very few studies which have identified potential biomarkers of prognosis in endometrial cancer.

overall_design: In order to identify miRNA markers in endometrial cancer, which may be implicated in prognosis,  biopsy samples from a. Control (Non-malignant) and  b. Endometrial cancer (endometroid) were  collected. Total RNA was isolated, then subjected to small RNA-seq. Illumina platform. miRNAs differentially expressd between the  2 groups were identified.  Using in-silico tools, mRNA targets of these miRNAs were also identified.

first: Shraddha

last: Hegde

first: Kalpesh

last: Wagh

first: Sum

last: Narayana

first: Apoorva

last: Abikar

first: Sughosha

last: Nambiar

first: Shriraksha

last: Ananthamurthy

first: Navyashree

first: Pallavi

middle: V

last: Reddihalli

first: Savitha

last: Chandraiah


title: Small-Molecule-Induced ERBB4 Activation to Treat Heart Failure

city: Leuven

first: Llewelyn

last: Roderick

address: Herestraat 49

department: Department of Cardiovascular Sciences

country: Belgium

institute: KU Leuven

summary: To determine the transcriptomic changes of small-molecule-induced activation of ERBB4 in heart failure, we tested the effects of the two small molecules (NRG1 and EF-1) of ERBB4 agonists on the HCF (human cardiac fibroblasts)  model.  The transcriptional profiles of mRNA in these samples will be measured with high throughput technology. Changes in transcriptional profiles between the activation of EF-1 and NRG1 will be compared.

overall_design: 9 HCF samples were analyzed. 3 from control, 3 from NRG1, and 3 from EF-1.

first: Julie

last: Cools

first: Eline

last: Feyen

first: Siel

last: Van Den Bogaert

first: Bo

last: Goovaerts

first: Yile

last: Fu

first: Celine

last: Civati

first: Jens

last: Van fraeyenhove

first: Michiel

last: Tubeeckx

first: Jasper

last: Van Haver

first: B

last: van Berlo

first: Eike

last: Wülfers

first: Antoine

last: de Vries

first: Nele

last: Vandersickel

first: Daniel

last: Pijnappels

first: Dominique

last: Audenaert

first: H

first: Hans

last: De Winter

first: Gilles

middle: W

last: De Keulenaer

first: Vincent

middle: F

last: Segers


title: Interplay Between Dox-Induced ICD and STING Pathway: Insights from Gene Expression in dendritic cells

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: In this RNA sequencing study, the primary objectives were to explore the intricate interplay between the STING pathway and ICD-associated DAMPs in the context of treatment with cGAMP nanoparticle and Dox. The research delved deep into the transcriptomic alterations in BMDCs when exposed to cGAMPnps and conditioned medium from Dox-treated 4T1 breast cancer cells. By analyzing these shifts in gene expression and conducting a gene ontology analysis, the study sought to understand the inflammatory pathways and other gene clusters influenced by these treatments. Ultimately, this insight aims to inform the development of STING-mediated immunotherapies by identifying potential DAMP targets.

overall_design: 4T1 breast cancer cells were initially treated with Dox at a concentration of 2 μM. Following this treatment, the medium was replaced and, after a 24-hour interval, the conditioned medium from these cells was harvested. Parallelly, BMDCs were subjected to treatments either with cGAMPnps (1 µM) alone or combined with the aforementioned conditioned medium. Subsequent to these treatments, total RNA was meticulously extracted from the BMDCs employing the TRIzol reagent. This extracted RNA was then used to craft a sequencing library using the SureSelect XT HS2 mRNA Library Preparation Kit from Agilent. The final sequencing was conducted on the Illumina NovaSeq 6000 platform, aiming to produce 150 bp paired-end reads.

first: Ting-Wen

first: Yunching


title: Sex differences and immune correlates of Long COVID development, persistence, and resolution

city: Palo Alto

first: Rebecca

last: Hamlin

address: 1291 Welch Road

department: Medicine

institute: Stanford University

summary: Sex differences have been observed in acute coronavirus disease 2019 (COVID-19) and Long Covid (LC) outcomes, with greater disease severity and mortality during acute infection in males and greater proportions of females developing LC. We hypothesized that sex-specific immune dysregulation contributes to LC pathogenesis. To investigate the immunologic underpinnings of LC development and symptom persistence, we performed multi-omic analyses on blood samples obtained during acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and 3 and 12 months post infection in a cohort of 45 patients who either developed LC or recovered. Several sex-specific immune pathways were associated with LC. Males who would later develop LC exhibited increases in transforming growth factor (TGF)-β signaling during acute infection, whereas females who would go on to develop LC had reduced TGFB1 expression. Females who developed LC demonstrated increased expression of XIST, an RNA gene implicated in autoimmunity, during acute infection compared with females who recovered. Many immune features of LC were also conserved across sexes, such as alterations in monocyte phenotype and activation state. Nuclear factor (NF)-κB transcription factors were up-regulated in many cell types at acute and convalescent time points. Those with ongoing LC demonstrated reduced ETS1 expression across lymphocyte subsets and elevated intracellular IL-4 in T cell subsets, suggesting that ETS1 alterations may drive aberrantly elevated Th2-like responses in LC. Altogether, this study describes multiple innate and adaptive immune correlates of LC, some of which differ by sex, and offers insights toward the pursuit of tailored therapeutics.

overall_design: Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from: 45 participants at approximately 3 months post SARS-CoV-2 infection, of whom 36 had developed symptoms consistent with Long COVID and 9 had fully recovered; 23 participants at approximately 12 months post SARS-CoV-2 infection, of whom 12 had persistent Long COVID (at 3- and 12-months post infection) and 11 had fully recovered by 12 months post infection despite having symptoms of Long COVID at 3 months post infection; and 21 participants during acute SARS-CoV-2 infection, of whom 15 would go on to develop Long COVID at 3 months post infection and 6 would go on to fully recover at 3 months post infection. Additionally, PBMCs from 7 other donors (AR#) were included in sublibrary prep but were part of a different experiment.

middle: E

first: Shaun

middle: M

last: Pienkos

first: Catherine

last: Blish


title: Protogenin Facilitates Trunk-to-Tail HOX Code Transition via Modulating GDF11/SMAD2 Signaling in Mammalian Embryos

city: Taipei

first: Yu-Hui

last: Wong

address: No. 155, Sec. 2, Linong St. Beitou Dist.

department: Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences

summary: Vertebral axial patterning is determined during embryogenesis via complicated regulation involving multiple signaling networks. This study revealed that protogenin (Prtg), a member of the immunoglobulin superfamily, is involved in controlling vertebral patterning. Prtg knockout (Prtg-/-) mice exhibited anterior homeotic transformations in their vertebral columns accompanied by significant alternations in the expression of numerous homeobox (Hox) genes. Transcriptomic profiling of Prtg-/- embryos revealed that genes regulated by Prtg play a pivotal role in modulating axial development, displaying prominent associations with the transforming growth factor beta (TGFβ) signaling pathway. Additionally, we observed a pronounced reduction in TGFβ signaling activity in Prtg-/- embryos, as evidenced by decreased phosphorylated Smad2 (pSmad2) levels within the developing tail region. Furthermore, we introduced human induced pluripotent stem cell-derived presomitic mesoderm-like (hiPSC-PSM) cells as an in vitro model to explore the role of PRTG in somitogenesis, specifically focusing on the collinear expression of HOX genes. Our findings indicate that PRTG knockout in hiPSC-PSM cells results in delayed posterior HOX gene expression. Intriguingly, supplementation with growth differentiation factor 11 (GDF11) successfully rescued the abnormal expression of posterior HOX genes, providing compelling evidence that PRTG’s regulation of HOX genes is mediated by the GDF11/SMAD2 signaling pathway.

overall_design: Transgenic C57BL/6 mice containing Prtg knockout allele was used in this study. Heterozygous males were mated with heterozygous females and pragnant females were sacrificed to obtain E9.5 embryos. Embryos were dissected between 12th and 13th somite and total RNA from posterior trunks were extracted by Tissue Total RNA Mini Kit (Geneaid) for RNA-seq.

first: Yu-Sheng

last: Hung


title: Transcriptome profile of S. cerevisiae treated with tauroursodeoxycholic acid (TUDCA)

city: London

first: Matthew

last: Berg

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: University of Western Ontario

summary: Cells respond to endoplasmic reticulum (ER) stress through activation of signaling pathways such as the Unfolded Protein Response (UPR) which improve the ER folding environment capacity upon changes in misfolded protein burden. Small molecules termed chemical chaperones can attenuate the UPR under stress conditions and improve folding and trafficking of specific mutant proteins. One such compound is the bile acid tauroursodeoxycholic acid (TUDCA). Despite promising results in multiple models of protein folding diseases, TUDCA’s mechanism of action remains unclear. To better define how TUDCA attenuate ER stress, we leveraged the genetically tractable budding yeast, S. cerevisiae. Consistent with properties described for TUDCA, we found it significantly improves growth of yeast subjected to ER stress caused by the N-glycosylation inhibitor tunicamycin (Tm) independently of activity of the UPR. In addition to other data, transcriptomics of strains treated with TUDCA link its ability to resuce Tm-induced stress with cell wall remodeling.

overall_design: mRNA from yeast grown in YPD treated with and without TUCDA

first: Sarah

last: Chadwick

middle: D

first: Patrick

last: Lajoie


first: Arezo

last: Torang

overall_design: SW1463 and LS513 CRC cell lines were treated with H3B120 (CPS1 inhibitor).

first: J

last: Medema


title: Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets.

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

summary: Analysis of chromatin remodelling in a neoplastic stem cell context as compared to an ontogenetically related neural stem cell context reveals multifactorial epigenetic regulation of signalling pathways known to contribute to glioblastoma development. It also identifies novel epigenetically regulated druggable target genes on a patient-specific level, including SMOX and GABBR2 which could be further developed for future translational approaches to more effectively treat this neoplasm.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4m3, H3K36me3, H3K27ac and H3K27me3 in primary human Glioblastoma Initiating Cells (GIC) and syngeneic iPSC-derived induced Neural Stem Cells (iNSC) derived from 10 glioblastoma patiens.

first: Claire

last: Vinel

first: James

last: Boot

first: Weiwei

last: Jin

first: Nicola

last: Pomella

first: Charles

last: Mein

first: Nicolae

last: Radu Zabet


title: Dual-targeting CRISPR-CasRx reduces C9orf72 ALS/FTD sense and antisense repeat RNAs in vitro and in vivo

first: Adrian

last: Isaacs

address: Cruciform Building, Gower Street

department: Neurodegenerative Diseases

institute: University College London

summary: The most common genetic cause of both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is a G4C2 repeat expansion in intron 1 of the C9orf72 gene. This repeat expansion undergoes bidirectional transcription to produce sense and antisense repeat RNA species. Both sense and antisense-derived repeat RNAs undergo repeat-associated non-AUG translation in all reading frames to generate five distinct dipeptide repeat proteins (DPRs). Importantly, toxicity has been associated with both sense and antisense repeat-derived RNA and DPRs. This suggests targeting both sense and antisense repeat RNA may provide the most effective therapeutic strategy. The RNA-targeting CRISPR-Cas13 systems offer a promising avenue for simultaneous targeting of multiple RNA transcripts, as they mature their own guide arrays, thus allowing targeting of more than one RNA species from a single construct. We show that CRISPR-Cas13d originating from Ruminococcus flavefaciens (CasRx) can successfully reduce C9orf72 sense and antisense repeat transcripts and DPRs to background levels in HEK cells overexpressing C9orf72 repeats. CRISPR-CasRx also markedly reduced the endogenous sense and antisense repeat RNAs and DPRs in three independent C9orf72 patient-derived iPSC-neuron lines, without detectable off-target effects. To determine whether CRISPR-CasRx is effective in vivo, we treated two distinct C9orf72 repeat mouse models using AAV delivery and observed a significant reduction in both sense and antisense repeat-containing transcripts. Taken together this work highlights the potential for RNA-targeting CRISPR systems as therapeutics for C9orf72 ALS/FTD.

overall_design: To determine if there were off-target transcriptional changes in patient iPSC-neurons when targeting C9orf72 with CRISPR-CasRx, we performed RNA sequencing of three independent inductions of C9 line 1 iPSC-neurons 5 days post-transduction with lentiviruses expressing CasRx and either non-targeting guide, sense transcript targeting guides 8 or 10, or antisense transcript targeting guides 11 or 17.

first: Liam

last: Kempthorne

first: Alexander

last: Cammack

first: Deniz

last: Vaizoglu


title: The EP4 antagonist vorbipiprant and an anti-PD-1 in MSS mCRC

status: Public on Nov 12 2024

city: Milan

first: Filippo

last: Pietrantonio

address: Via Venezian, 1

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: The aim of the study was to determine whether vorbipiprant, a prostaglandin EP4 receptor antagonist, can convert immune-resistant mCRC into a tumor responsive to anti-PD-1 inhibition

overall_design: Samples from human biopsies or surgical resection of primary tumor were analyzed in order to identify potential predictors of clinical response.


title: RNA sensing induced by chromosome missegregation augments anti-tumor immunity VI

city: Tokyo

first: Shunsuke

last: Kitajima

address: 3-8-31 Ariake, Koto

institute: Japanese Foundation for Cancer Research

summary: We demonstrate that dsRNA is significantly accumulated in cancer cells following pharmacologic induction of micronuclei, stimulating MAVS-mediated dsRNA sensing in conjunction with the cGAS/STING pathway. Activation of cytosolic dsRNA sensing co-operates with dsDNA sensing to up-regulate immune cell migration and antigen-presenting machinery. Tracing of dsRNA-sequence identity revealed that dsRNA-forming transcripts are predominantly generated from non-exonic regions, particularly in locations proximal to genes exhibiting high chromatin accessibility. Activation of this pathway by pulsed Monopolar Spindle 1 (MPS1) kinase inhibitor therapy, which potently induces micronuclei formation, thus induces cytoplasmic dsRNA-sensing and promotes anti-tumor immunity mediated by type I interferon signaling and cytotoxic lymphocyte activation in vivo. Taken together, these findings reveal a novel aspect of the dsRNA-sensing pathway in enhancing the anti-tumor efficacy of drugs that promote genomic instability and micronuclei formation, facilitating cancer immunogenicity.

overall_design: We invetigated the alteration of open chromatin following pulsed MPS1 treatment in H1944 cells.

first: Nobunari

last: Sasaki

first: Mizuki

last: Homme


title: DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Pluripotent stem cells are unique in their large nucleus and manifestly open chromatin structure with hypertranscriptional activities. How the nucleolus, the largest membraneless and phase-separated subnuclear organelle, maintains its structural integrity in pluripotency maintenance remains incompletely understood. By studying nucleolus-specific DEAD-box RNA helicase-18 (DDX18) in human embryonic stem cells, we discover mechanisms controlling nucleolus phase separation and chromatin organization.

overall_design: In this experiment, we characterized hESCchromatin interaction under control and DDX18 knockdown condition using  Hi-C seq.

first: Xin

last: Huang

first: Xianle

last: Shi


title: RNA sensing induced by chromosome missegregation augments anti-tumor immunity II

overall_design: We invetigated type1 IFN-dependent dsRNA-forming transcripts following pulsed MPS1 treatment in H1944 cells by utlizing J2-IP sequencing.


title: RNA sensing induced by chromosome missegregation augments anti-tumor immunity IV

overall_design: We invetigated alteration of dsRNA-forming transcripts following pulsed MPS1 treatment in H1944 cells by utlizing J2-IP sequencing.


first: Llewelyn

last: Roderick

summary: To determine the transcriptomic changes of small-molecule-induced activation of ERBB4 in heart failure, we tested the effects of the two small molecules (NRG1 and EF-1) of ERBB4 agonists on iAM (immortalized atrial cardiomyocytes)  model.  The transcriptional profiles of mRNA in these samples will be measured with high throughput technology. Changes in transcriptional profiles between the activation of EF-1 and NRG1 will be compared.

overall_design: 12 iAM samples were analyzed. 4 from control, 4 from NRG1, and 4 from EF-1.

first: Julie

last: Cools

first: Eline

last: Feyen

first: Siel

last: Van Den Bogaert

first: Bo

last: Goovaerts

first: Yile

last: Fu

first: Celine

last: Civati

first: Jens

last: Van fraeyenhove

first: Michiel

last: Tubeeckx

first: Jasper

last: Van Haver

first: B

last: van Berlo

first: Eike

last: Wülfers

first: Antoine

last: de Vries

first: Nele

last: Vandersickel

first: Daniel

last: Pijnappels

first: Dominique

last: Audenaert

first: H

first: Hans

last: De Winter

first: Gilles

last: De Keulenaer

first: Vincent

last: Segers


title: RNA sensing induced by chromosome missegregation augments anti-tumor immunity III

first: Shunsuke

last: Kitajima

overall_design: We invetigated MAVS-dependent gene expression alteration of tumor tissue following pulsed MPS1 treatment.

first: Nobunari

last: Sasaki

first: Mizuki

last: Homme