Supplementary Table S3. Luciferase assay and qRT-PCR primers. The PCR primers for amplifying sequences containing Gli2 binding motif in SE peak of Irs1 and IRS1 for luciferase assay, and primers for qRT-PCR assay.

Supplementary Table S2. shRNA and sgRNA oligonucleotides. Sequences of shRNA oligonucleotides of Irs1, and sgRNA oligonucleotides of Irs1 SE, Irs1 promoter, Rhbdd1 promoter, and Stat3.

Supplementary Table S1. PCR primers for NGS. The primer sequences for amplifying sgRNA sequences from genome DNA for NGS assays.

Abstract Single-cell RNA sequencing has rapidly expanded the scale of skin transcriptomic data, yet these datasets remain fragmented across studies spanning different species, diseases and experimental manipulations. An up-to-date, comprehensive, and queryable single-cell cross-species repository for skin is still lacking. Here, we present scSAID (skin-scsaid.com), a single-cell database with an interactive web portal offering a broad suite of in-depth analyses for human and mouse skin. It integrates more than 1.2 million high-quality cells collected from 252 samples, establishing a unified reference for cell-type annotation, cross-species comparison and pathological studies. Using psoriasis as a case study, we demonstrate how scSAID can be used to evaluate how faithfully mouse models reproduce human pathology. Systematic comparison with the imiquimod-induced mouse model revealed numerous species-specific molecular signatures of psoriasis, including human-specific NFKB1 activation and STAT1 involvement, indicating that the current mouse model captures only limited aspects of the disease. We further introduce psoSpotter, a disease-biomarker-selection algorithm that, coupled with in silico perturbation using scSAID data, uncovers PPIA as a novel psoriasis drug target, illustrating the potential of scSAID for identifying therapeutic approaches. Overall, scSAID delivers a large-scale, cross-species skin single-cell resource and analysis platform, opening new opportunities for the discovery of disease-relevant targets in skin diseases.

The PDF file includes Supplementary Figures S1-S15, Figure Legends, and Table Legends

The remodeling of mammary glands during pregnancy is essential for initiating lactation. In dairy animals, the overlap of pregnancy and mammary involution triggers a unique process, regenerative remodeling, which is critical for extending lactation duration and enhancing milk production. Unlike the complete regression of lobuloalveolar structures during involution, the regenerative remodeling preserves alveolar structures and promotes rapid mammary gland renewal. However, the cellular and molecular mechanisms underlying such process remain elusive. Here, taking dairy goats (Capra hircus) as a ruminant model, we identified four luminal cell populations through single-cell RNA-sequencing and found a significant reduction in luminal hormone-responsive (LumHR) cells and an increase in luminal secretory precursors (LumSecP) during regenerative remodeling. A reduction of LumHR cells during regenerative remodeling is essential for promoting the accumulation of LumSecP. Goat mammary organoids and in vivo genetic ablation assays suggested that LumHR cells function as a crucial switch for the differentiation of LumSecP to LumSec cells through the prolactin receptor pathway. Furthermore, high levels of IRF1 inhibited while downregulation of IRF1 stimulated the proliferation of LumHR cells. We showed that IRF1 regulated the dynamics of LumHR cells through hormonal signaling targets, including ESRRB. Our findings identified a key cell type responsible for the dynamics of luminal lineages during regenerative remodeling in large mammals and highlighted the potential for accelerating tissue regeneration through targeted modulation of lineage stage-specific regulators.

Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer, known for its early onset, strong metastatic tendencies, and poor prognosis. Conventional treatments, including chemotherapy and immunotherapy, often face challenges such as limited efficacy, adverse side effects, and high recurrence rates. To address these limitations, a family of tri-block chimeric proteins, cysteine-tagged silk-elastin-like proteins (cSELPs), is designed to form responsive in situ hydrogels for treating late-stage and metastatic TNBC. These cSELPs are de novo designed to integrate multiple functional protein motifs, including a photothermal agent binding motif, silk-inspired crosslinking motifs, and elastin-like thermo-responsive motifs. This unique sequence design enables the cSELP hydrogels to exhibit in situ gelation, photothermal responsive release of chemotherapeutic agent doxorubicin and immune checkpoint inhibitor anti-PD-L1, and antibacterial properties, leading to effective tumor microenvironment remodeling. By promoting immunogenic cell death and stimulating immune activation, this approach converts immunosuppressive "cold" tumors into immunologically active "hot" tumors. The cSELP hydrogel system demonstrates potent therapeutic efficacy against both primary and metastatic TNBC while maintaining excellent biocompatibility and long-term safety. This protein material platform offers an innovative strategy to reshape the tumor microenvironment and combine multimodal treatments into a single biocompatible system, highlighting its potential for clinical translation.

Merkel cells (MCs) are specialized mechanoreceptors crucial for tactile sensation, yet their developmental investigation remains challenging, particularly in humans, due to the lack of validated in vitro culture system. Here, we establish novel approaches, including short-term ex vivo vibrissae explants, innovative mouse skin organoids (mSKOs), and human pluripotent stem cell-derived skin organoids (hSKOs), to monitor MC development. We demonstrate that Polycomb repressive complex inhibitors (PRCis) efficiently promote MC generation in these culture systems. Through single-cell and spatial transcriptomics analysis, together with pharmacological screening, we identify IGF1R as a potential regulator of MC formation, which likely exerts its effects through the AKT pathway. Furthermore, we validate the role of FGFR2 signaling in MC generation. These systems constitute a versatile platform that harnesses complementary strengths to not only advance MC biology and skin development but also enable stem cell research, supporting organoid-based disease modeling, therapeutic compound screening, and regenerative medicine.

The electrochemical reduction of nitrates (NO3RR) for ammonia synthesis at room temperature holds immense potential. One key challenge is the adsorption and activation of NO3-, along with the provision of sufficient active hydrogen to accelerate the hydrogenation process. Here, the study prepares N-doped TiO2-x supported by Zr single atoms (Zr-TiON) with rich oxygen vacancies (Ov), in which unsaturated Zr (Lewis acidic, LA) sites together with oxygen atoms around Ov (Lewis base, LB) form frustrated Lewis acid-base pairs (FLPs). At -60 mA cm(-2), NH3 Faradaic efficiency reaches 94.8%, corresponding to the production rate of 663.15 mu mol h-1 mgcat-1. The yield rate is up to 26.16 mmol h(-1)mg(cat)(-1) at -1 A cm(-2) in flowing electrolyzer. Theoretical calculations and in situ spectroscopy analysis reveal that the interaction between LA and LB sites in FLPs plays a crucial role in facilitating adsorption and activation of electron-rich NO3- and electron-deficient *H. The presence of enhanced FLPs significantly reduces the energy barrier for H2O dissociation, lowering it to 0.20 eV, which facilitates subsequent hydrogenation reactions. The abundance of *H accelerates hydrogenation process, thereby enhancing the activity of NO3RR. This FLP design offers a promising approach for paving the way for the development of highly efficient NO3RR catalysts.

ObjectivePancreatic ductal adenocarcinoma (PDAC) stands as one of the most lethal cancers, marked by its lethality and limited treatment options, including the utilisation of checkpoint blockade (ICB) immunotherapy. Epigenetic dysregulation is a defining feature of tumourigenesis that is implicated in immune surveillance, but remains elusive in PDAC.DesignTo identify the factors that modulate immune surveillance, we employedin vivoepigenetic-focused CRISPR-Cas9 screen in mouse PDAC tumour models engrafted in either immunocompetent or immunodeficient mice.ResultsHere, we identified MED12 as a top hit, emerging as a potent negative modulator of immune tumour microenviroment (TME) in PDAC. Loss ofMed12significantly promoted infiltration and cytotoxicity of immune cells including CD8+T cells, natural killer (NK) and NK1.1+T cells in tumours, thereby heightening the sensitivity of ICB treatment in a mouse model of PDAC. Mechanistically, MED12 stabilised heterochromatin protein HP1A to repress H3K9me3-marked endogenous retroelements. The derepression of retrotransposons induced byMED12loss triggered cytosolic nucleic acid sensing and subsequent activation of type I interferon pathways, ultimately leading to robust inflamed TME . Moreover, we uncovered a negative correlation between MED12 expression and immune resposne pathways, retrotransposon levels as well as the prognosis of patients with PDAC undergoing ICB therapy.ConclusionIn summary, our findings underscore the pivotal role of MED12 in remodelling immnue TME through the epigenetic silencing of retrotransposons, offering a potential therapeutic target for enhancing tumour immunogenicity and overcoming immunotherapy resistance in PDAC.

BACKGROUND:This study evaluated the level of burden in pediatric and adolescent atopic dermatitis (AD) patients in Japan, the associated burden on caregivers/families, and whether this burden varied with age. METHODS:Data were drawn from the Adelphi Pediatric AD Disease Specific Programme (DSP)™, a cross-sectional survey of physicians and their patients conducted in Japan between July and December 2022. Physicians reported patient demographics, clinical characteristics, disease burden, and current/previous therapies. Patients and/or caregivers reported perceived disease severity and impact of AD, including the Children's Dermatology Life Quality Index (CDLQI) and Dermatitis Family Impact questionnaire (DFI). RESULTS:Overall, 55 physicians provided data for 537 AD patients aged ≤17. Mean (SD) overall scores for CDLQI, POEM, and DFI were 9.3 (6.3), 8.3 (6.8), and 11.7 (7.2), respectively. Age was associated with higher patient and/or caregiver-reported CDLQI scores, which increased by 0.543 points per year of age (P = 0.01). Patients with severe disease reported a more significant impact on quality of life factors compared with mild patients (P < 0.001). Age was associated with higher caregiver-reported burden, with DFI scores increasing by 0.325 per year (P = 0.01). Physician-reported impact on caregivers showed that age was significantly associated with increased burden on sleep, daily activities, work, and mood (P < 0.05), with disease severity associated with impact across all factors (P < 0.01). CONCLUSIONS:Both increasing age and disease severity were associated with the increased impact of AD on patients and their caregivers. Disease control/modification through appropriate therapeutic intervention at a younger age may relieve the burden of pediatric AD on patients and their families.

Traditional drug development is a long and expensive process with high rates of failure. This has prompted the pharmaceutical industry to seek more efficient drug development frameworks, driving the emergence of organ-on-a-chip (OOC) based on microfluidic technologies. Unlike traditional animal experiments, OOC systems provide a more accurate simulation of human organ microenvironments and physiological responses, therefore offering a cost-effective and efficient platform for biomedical research, particularly in the development of new medicines. Additionally, OOC systems enable quick and real-time analysis, high-throughput experimentation, and automation. These advantages have shown significant promise in enhancing the drug development process. The success of an OOC system hinges on the integration of specific designs, manufacturing techniques, and biosensors to meet the need for integrated multiparameter datasets. This review focuses on the manufacturing, design, sensing systems, and applications of OOC systems, highlighting their design and sensing capabilities, as well as the technical challenges they currently face.

Gallbladder cancer (GBC) is a highly aggressive malignancy lacking clinically available targeted therapeutic agents. Super-enhancers (SEs) are crucial epigenetic cis-regulatory elements whose extensive reprogramming drives aberrant transcription in cancers. To study SE in GBC, the genomic distribution of H3K27ac is profiled in multiple GBC tissue and cell line samples to establish the SE landscape and its associated core regulatory circuitry (CRC). The biliary lineage factor SOX9 and Wnt pathway effector TCF7L2, two master transcription factor (TF) candidates identified by CRC analysis, are verified to co-occupy each other's SE region, forming a mutually autoregulatory loop to drive oncogenic SE reprogramming in a subset of GBC. The SOX9/TCF7L2 double-high GBC cells are highly dependent on the two TFs and enriched of SE-associated gene signatures related to stemness, ErbB and Wnt pathways. Patients with more such GBC cells exhibited significantly worse prognosis. Furthermore, SOX9/TCF7L2 double-high GBC preclinical models are found to be susceptible to SE-targeted CDK7 inhibition therapy in vitro and in vivo. Together, this study provides novel insights into the epigenetic mechanisms underlying the oncogenesis of a subset of GBCs with poorer prognosis and illustrates promising prognostic stratification and therapeutic strategies for treating those GBC patients in future clinical trials.

Abstract Aberrant activation of the Hedgehog (Hh) signaling pathway plays important roles in oncogenesis and therapeutic resistance in several types of cancer. The clinical application of FDA-approved Hh-targeted smoothened inhibitors (SMOi) is hindered by the emergence of primary or acquired drug resistance. Epigenetic and transcriptional-targeted therapies represent a promising direction for developing improved anti-Hh therapies. In this study, we integrated epigenetic/transcriptional-targeted small-molecule library screening with CRISPR/Cas9 knockout library screening and identified CDK9 and CDK12, two transcription elongation regulators, as therapeutic targets for antagonizing aberrant Hh activation and overcoming SMOi resistance. Inhibition of CDK9 or CDK12 potently suppressed Hh signaling and tumor growth in various SMOi responsive or resistant Hh-driven tumor models. Systemic epigenomic profiling elucidated the Hh-driven super-enhancer (SE) landscape and identified IRS1, encoding a critical component and cytoplasmic adaptor protein of the insulin-like growth factor (IGF) pathway, as an oncogenic Hh-driven SE target gene and effective therapeutic target in Hh-driven tumor models. Collectively, this study identifies SE-driven transcriptional dependencies that represent promising therapeutic vulnerabilities for suppressing the Hh pathway and overcoming SMOi resistance. As CDK9 and IRS inhibitors have already entered human clinical trials for cancer treatment, these findings provide comprehensive preclinical support for developing trials for Hh-driven cancers. Significance: Dissecting transcriptional dependencies driven by super-enhancers uncovers therapeutic targets in Hedgehog-driven cancers and identifies strategies for overcoming resistance to smoothened inhibitors.

110 Background: Oxaliplatin-containing regimens (FOLFOX or CAPOX) are the most common adjuvant treatments after curative resection of colorectal cancer (CRC). However, real-world evidence (RWE) of treatment sequence/outcomes for patients with early recurrence CRC after receiving adjuvant chemotherapy are limited. Methods: This retrospective cohort study was based on an administrative database in Japan. The primary objective was to describe the treatment sequence for patients with early recurrence CRC and treated by combination of FOLFIRI and anti-angiogenesis inhibitors (AAIs) or anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (mAbs) after adjuvant FOLFOX or CAPOX therapy. The study included patients with CRC who underwent surgical resection, started adjuvant chemotherapy ≤3 months (mo) after the first surgery, had early recurrence of CRC (defined as initiation of FOLFIRI + AAIs/anti-EGFR mAbs second line [2L] regimen) within 1 year after adjuvant chemotherapy ended. Patient characteristics at baseline of 2L (60 days prior to 2L initiation) and treatment sequence were summarized descriptively; time to discontinuation (TTD) for adjuvant and 2L therapy were analyzed using Kaplan-Meier method. Cox proportional hazard model was used to identify risk factors associated with TTD of 2L regimen. Results: The cohort included 832 patients: median (range) age was 67 (24-86) years, 56.4% males, 65.5% with left-sided CRC. Most patients received CAPOX (71.3%) as adjuvant therapy. Median (95% CI) duration of adjuvant therapy was 5.4 mo (5.3-5.5). As 2L therapy, 72.5% and 27.5% of patients received FOLFIRI + AAIs (AAIs group) and FOLFIRI + anti-EGFR mAbs (anti-EGFR group), respectively. Median TTD (95% CI) of the AAIs and anti-EGFR groups in 2L were 6.2 mo (5.8-6.9) and 6.1 mo (5.2-7.4), respectively. Among patients with recurrence within 6 mo (72.6%), the median TTD (95% CI) for AAIs and anti-EGFR groups were 6.1 mo (5.5- 6.5) and 5.8 mo (5.1-7.8), respectively. Among patients with recurrence during 6 to 12 mo (27.4%), the median TTD (95% CI) of AAIs and anti-EGFR groups were 8.1 mo (6.1-9.2) and 6.2 mo (4.6-8.0), respectively. Age ≥70 years was negatively associated with TTD of 2L, HR = 1.19 (95% CI: 1.02-1.39); p=0.03. Conclusions: This is the first RWE based on administrative data on treatment sequence/ outcomes for patients with early recurrence CRC treated by FOLFIRI + AAIs/anti-EGFR mAbs after adjuvant FOLFOX/CAPOX therapy in Japan. The treatment outcomes for patients with early recurrence CRC were similar to previous clinical trials in 2L advanced CRC. The results suggested that these two 2L regimens had similar TTD; however, the timing of relapse may influence the efficacy of AAIs and anti-EGFR mAbs.

Oxaliplatin-containing adjuvant regimens (folinic acid, fluorouracil, and oxaliplatin/capecitabine and oxaliplatin [FOLFOX/CAPOX]) are used after curative resection of colorectal cancer (CRC). However, real-world evidence regarding treatment sequences and outcomes in patients with early recurrence CRC after adjuvant chemotherapy is limited. We aimed to describe the patient characteristics, treatment sequence, and overall duration of second-line (2L) therapy in patients with early recurrence CRC who received adjuvant chemotherapy (FOLFOX/CAPOX) followed by folinic acid, fluorouracil, and irinotecan (FOLFIRI) + anti-angiogenesis drugs (AA) or FOLFIRI + anti-epidermal growth factor receptor (EGFR) antibodies. This retrospective study analyzed Japanese administrative data from November 2014 to March 2023 of adult patients who underwent CRC resection surgery, started FOLFOX/CAPOX ≤3 months (mo) after surgery, and had early CRC recurrence. Early recurrence was defined as initiation of FOLFIRI+AA or FOLFIRI+anti-EGFR antibodies as 2L therapy, ≤12 mo of discontinuing adjuvant chemotherapy. Patient characteristics, treatment sequence, median time to treatment discontinuation (mTTD), i.e., duration between the start and end dates of 2L therapy (Kaplan–Meier method), and factors associated with 2L time to treatment discontinuation constituted the study outcomes (Cox regression model). Subgroup analyses were performed for timing of early CRC recurrence (≤6 mo and 6–12 mo) and tumor sidedness. Among the 832 selected patients (median age [minimum–maximum] 67 (24–86) years, 56.4

Chronic lymphocytic leukemia (CLL) is a rare form of lymphoma in Japan. This study aimed to explore hematologists’ motivations and considerations in making treatment decisions for CLL. Responses from hematologists treating CLL, obtained through an online survey, were descriptively analyzed. Subgroup analyses by preferred first-line (1L) treatment, years of clinical experience, and level of interest in CLL were conducted. Out of 107 hematologists surveyed, 82.2

In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, there lacks specific evaluation of correction efficacy for varying contamination levels. Here, we show that DecontX and CellBender under-correct highly contaminating genes, while SoupX and scAR over-correct lowly/non-contaminating genes. Here, we develop scCDC as the first method to detect the contamination-causing genes and only correct expression levels of these genes, some of which are cell-type markers. Compared with existing decontamination methods, scCDC excels in decontaminating highly contaminating genes while avoiding over-correction of other genes.

Supplementary Figure from HMGN5 Escorts Oncogenic STAT3 Signaling by Regulating the Chromatin Landscape in Breast Cancer Tumorigenesis

The covalent Bruton tyrosine kinase inhibitor (cBTKi), ibrutinib (IBR), and B-cell lymphoma-2 inhibitor (BCL-2i), venetoclax, were recently approved in Japan for the treatment of chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL). Treatment options following cBTKi are limited. This study investigated characteristics, treatment patterns, and outcomes of patients with CLL/SLL following cBTKi exposure using a Japanese real-world database.