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Additional file 1: Figure S1a. Hi-C million read counts (left) and read percentage (right) per cell line. Figure S2a. Venn diagram showing overlap of differentially expressed genes (abs(L2FC) > 0.32, p-value < 0.05) between three B-ALL cell lines upon knockdown, decreased and increased genes (left and right respectively). b. Volcano plots demonstrating differentially expressed genes (abs(L2FC) > 0.32, p-value < 0.05) highlighted by compartment switch or shift (A to more A, B to A, B to less B, or stable). c. Scatterplot demonstrating compartments colored by concordance score (percentage of genes with that compartment switch or shift that change in the same direction). Figure S3a. Rate of concordance calculations represent the amount of upregulated and downregulated genes (abs(L2FC) > 0.32, p-value < 0.05) that can be explained by compartment switches and shifts. Figure S4a. Barplot showing number of subcompartment calls with SNIPER for each cell line at NSD2 Low and NSD2 High. b. Barplots presenting fraction of Cscore compartment calls (A or B) overlapping SNIPER subcompartment calls (A1, A2, B1, B2, and B3) c. Barplot showing number of subcompartment calls with SNIPER for each cell line at NSD2 Low and NSD2 High excluding B1 subcompartment calls. d. Barplot presenting number of subcompartment switches from A to B and from B to A from NS2D Low to NSD2 High in each of the cell lines. e. Barplots presenting fraction of SNIPER subcompartment calls overlapping cscore compartment switches and shifts. Figure S5a. Correlation boxplots of SNIPER subcompartments and gene expression changes (abs(L2FC) > 0.32, p-value 0.05) for each cell line from NSD2 Low to NSD2 High. b. Volcano plots demonstrate differentially expressed genes (abs(L2FC) > 0.32, p-value < 0.05) highlighted by subcompartment switches and shifts. Figure S6a. PCA of ATAC-seq peaks for each cell line identifies three distinct clusters which are cell line-specific. b. Heat map representation of ATAC-seq results generated with DiffBind. c. Venn Diagram showing overlap of differentially accessible regions between three B-ALL cell lines decreased and increased accessibility (left and right respectively; (FDR < 0.01, abs(log2(fold change)) > 1). d. Example of B to A compartment shift shared by all three cell lines at the NEO1 locus showing concordance with gene expression and chromatin accessibility. e. Example of B to A compartment shift specific to RS4;11 cell line at the PRDM8 locus showing concordance with gene expression and chromatin accessibility. Figure S7a. Heatmap representation of mean intra-TAD activity per cell line. b. Bar plot showing number of TAD activity changes per cell line (abs(L2FC) > 0.25, FDR < 0.01). c. Venn diagrams demonstrating significant overlap of patient NSD2-High upregulated genes and cell line NSD2-High upregulated genes and insignificant overlap of patient NSD2-High downregulated genes and cell line NSD2-High upregulated genes (one-tailed Fisher’s exact test). The last row presents insignificant overlap of genes upregulated in 9 matched D/R patient pairs with no NSD2 mutation (NSD2 Low) and cell line NSD2-High upregulated genes with a B to A compartment switch or shift. d. Table presenting percentage of patient NSD2-High upregulated genes overlapping a compartment switch/shift from any of the three cell lines. Figure S8a. Table presents patient information associated with the three matched diagnosis-relapse pairs acquired from COG. Figure S9a. Rate of concordance calculations present the number of genes upregulated in expression, increased in H3K36me2 ChIP-seq peaks, and B to A compartment shifts and switches for the RCH, RS4;11, and SEM cell lines. b. Association bar plots showing fraction of differential H3K36me2 chip-seq peaks (decreased, increased, and stable) that overlap changes in intra-TAD activity (increased, decreased, and stable TADs).

Additional file 14. Review history.

Oncogenic fusions formed through chromosome rearrangements are hallmarks of childhood cancer that define cancer subtype, can provide prognostic value, remain stable upon treatment or during clonal evolutionand have a high potential for serving as novel therapeutic vulnerabilities. However, mechanistic understanding of the etiology of oncogenic fusions in childhood cancers remains elusive. In order to better study these questions, we developed several methods,including neoversioner to study fusion version patterns, neosplicer to detect neosplicing sites for a given fusion, DNA breakpoint detection based onRNAseq dataand CRIPSR processing code. Prerequisitetools are listed in"manifest.docx" and and reference files can be generated following "download_reference.sh". Run command can refer README file and "example.sh". We also included all edited fastq files under CRISPR folder. All steps processing CRIPSR sequence data are included in file "CRISPR/cri-splicer.sh".All Figures included in the study and their according codes are available in folder "Figures/jobs.sh".&nbsp

Human epidermal growth factor receptor-2 (HER2)-enriched breast cancer is characterized by strong invasiveness, high recurrence rate, and poor prognosis. HER2-specific imaging can help screening right patients for appropriate HER2-targeted therapies. Previously, we have developed a 99mTc-labeled HER2-targeted H6 peptide for SPECT imaging of breast cancer. However, the poor metabolic stability and high gallbladder uptake hamper its clinical application. In this study, a retro-inverso D-peptide of H6 (RDH6) was designed to increase the metabolic stability. PEGylation was used to improve its water solubility and in vivo pharmacokinetics. The results showed that the D-amino acids in 99mTc-PEG4-RDH6 brought better metabolic stability than 99mTc-PEG4-H6, thus achieving higher tumor uptake. As the length of the PEG chain increases, the hydrophilicity of the probes gradually increased, which may also be the main cause for the decreased liver uptake. Compared with radiotracers modified by PEG4 and PEG12, 99mTc-PEG24-RDH6 had a comparable tumor uptake and the lowest liver radioactivity. The SPECT imaging demonstrated that 99mTc-PEG24-RDH6 could specifically distinguish HER2-positive tumors from HER2-negative tumors with better imaging contrast, which thus has the potential for clinical screening of HER2-positive breast patients.

Additional file1. Supplementary methods.

Additional file2. Supplementary figures.

Additional file 1: Fig. S1. The scatter plots between chronological age and epigenetic age based on four epigenetic clocks. Fig. S2. QQ plots of EAA GWAS based on four epigenetic clocks. Fig. S3. Distribution of intrinsic epigenetic age acceleration (IEAA) across five quintiles of polygenic risk score (PRS) for IEAA. Fig. S4. Molecular mechanism for associations between rs732314, chest/abdominal/pelvic-RT and EAA-Horvath. Table S1. SNPs (except the top one) significantly associated with EAA-Horvath and EAA-Hannum among survivors (SJLIFE1, SJLIFE2) and controls. Table S2. Single nucleotide polymorphisms (SNPs) with significant associations with IEAA-Horvath and EEAA-Hannum among survivors (SJLIFE1, SJLIFE2) and controls. Table S3. Differentially methylated regions (DMR) between the SJLIFE1 data set of survivors and controls overlapping with rs28366133 (+/- 500 kb) in HLA region. Table S4. Multivariable linear regression models for the two top SNPs. Table S5. Estimated SNP heritability of EAA based on each of four clock methods using single-trait LD Score Regression of the GWAS of the SJLIFE1 data set. Table S6. Estimated genetic correlation between EAA-Horvath and other traits using LD Score Regression of the GWAS of the SJLIFE1 data set (P

Childhood cancer is a major cause of child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is known about genetic interactions in childhood cancer. We apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological explanation of most candidates points to either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting genetic interaction test results., Josephine Daub, Saman Amini, et al. developed a genetic interaction map of childhood cancers by analyzing over 2,500 tumors from 23 types of childhood cancer. Their results provide a valuable resource for investigating the biological underpinnings of pediatric cancer.

Colorectal cancer is a common malignant tumour with a low 5-year survival rate. A combination therapy with high selectivity and easy controllability is a pressing need for the effective treatment of such cancer. In this study, an indocyanine green derivative (Cy7)-conjugated lipid with a terminal carboxyl group was synthesized, which could self-assemble with a cerasome-forming lipid (CFL) into nanoparticles (NPs) by encapsulating doxorubicin (DOX) to achieve combined photothermal chemotherapy. The resulting Gly@Cy7-Si-DOX NPs with a surface covalent silicate framework showed excellent morphological stability and colloidal stability. Specifically, the conjugated Cy7 was covalently conjugated in the liposomal bilayer, resulting in high drug loading content, high photostability, and high photothermal conversion efficiency, which enabled the resulting nanoparticles to be an effective platform for photothermal therapy. Meanwhile, the encapsulated DOX leaked only slightly under physiological conditions due to the silicate surface of Gly@Cy7-Si-DOX NPs and exhibited controlled release in a weakly acidic environment or under near-infrared (NIR) light irradiation for chemotherapy. Gly@Cy7-Si-DOX NPs were efficiently taken up by tumour cells. Upon light irradiation, the released DOX entered the nuclei of tumour cells, as observed by confocal microscopy and flow cytometry. In vitro cell experiments indicated that both healthy cells and tumour cells were viable under treatment with only Gly@Cy7-Si-DOX NPs, indicating the encapsulated DOX was stably confined to the NPs, and cells were significantly killed when treated with both Gly@Cy7-Si-DOX NPs and NIR laser irradiation. After i.v. administration, Gly@Cy7-Si-DOX NPs accumulated at the tumour site, as monitored by near-infrared fluorescence imaging. A significant tumour inhibition rate (95.8%) was also achieved in a HT-29 colorectal cancer model when treated with Gly@Cy7-Si-DOX NPs plus irradiation. Therefore, the Gly@Cy7-Si-DOX NPs hold great promise for controllable combined colorectal cancer photothermal chemotherapy.

Doxorubicin (DOX) has been clinically used as a broad-spectrum chemotherapeutic agent for decades, but its clinical application is hindered by the lack of tumour specificity, severe cardiotoxicity and haematotoxicity. Pre-targeted strategies are highly tumour-specific, therapeutic approaches. Herein, a novel pre-targeted system was constructed, aiming to enhance anticancer efficacy of DOX and maximally reduce its side effects. Methods: The DOX prodrug (bDOX) was first synthesized by conjugating DOX with mini-PEGylated (mPEGylated) biotin through a pH-sensitive bond. During the pre-targeted treatment, avidin was first administrated. After an optimized interval, bDOX was second administrated. The nontoxic prodrug bDOX was eventually transformed into the toxic anticancer form (DOX) by a pH-triggered cleavage specifically in tumour cells. The drug efficacy and side effect of the two-step, pre-targeted treatment were fully compared with free DOX in vitro and in vivo. Results: The prodrug bDOX was quite stable under neutral conditions and nearly nontoxic, but was immediately transformed into the toxic anticancer form (DOX) under acidic conditions. Compared to free DOX, the pre-targeted bDOX exhibited a higher cellular uptake by human colorectal tumour cells (LS180 and HT-29 cells). In vivo evaluation performed on LS180 xenograft animal model demonstrated that the pre-targeted bDOX achieved a much more significant tumour inhibition than free DOX. The largely decreased, unwanted bystander toxicity was demonstrated by changes in body weight, cardiomyocyte apoptosis, blood routine examination and splenic pathological changes. Conclusion: The high therapeutic efficacy, together with the minimal side effects, of this easily synthesized, pre-targeted system exhibited immense potentiality for the clinical application of DOX delivery.

Additional file 1: Supplementary Figure S1. Minimal sample effect for calculating error rates for flow cells. Supplementary Figure S2. Flow cell-level error rate of all sequencers analyzed in this study. Supplementary Figure S3. Physical location pattern of tile-level error rates across flow cells in an outlier sequencer. Supplementary Figure S4. Prevalence of outlier tiles at flow cell level. Supplementary Figure S5. Positional pattern of problematic tiles. Supplementary Figure S6. Comparison of sequencers by using a common reference DNA library. Supplementary Figure S7. Effect of removing outlier tiles on the overall sequencing error rate. Supplementary Figure S8. Effect of removing outlier tiles evaluated by fold change. Supplementary Figure S9. Benchmarking SequencErr with FastQC. Supplementary Figure S10. Effect of DNA sequencing features on sequencer error rate. Supplementary Figure S11. Comparison of SequencErr with error correction methods. Supplementary Figure S12. Application of SequencErr on non-human dataset (SARS-CoV-2). Supplementary Note 1. Illustration of flowcell architecture. Supplementary Note 2. Manually checking read name information from NCBI SRA. Supplementary Note 3. Manually checking NCBI SRA database for the suitability of public datasets for our analysis. Supplementary Note 4. Flow cell layout of HiSeq. Supplementary Note 5. Flow cell layout of NextSeq. Supplementary Note 6. Flow cell layout of NovaSeq.

Additional file 16: Review history.

In this study, we reported a 99mTc-labeled integrin α6-targeted peptide as the molecular imaging probe for tumor imaging by single-photon emission computed tomography (SPECT). We found that replacing Cys-Cys cyclized RWY peptide (sequence: cCRWYDENAC) with lactam-bridged cyclic cKiE peptide (sequence: cKRWYDENAisoE) did not sacrifice the integrin α6-binding affinity and specificity of cKiE radiotracer. To further improve the radiotracer's tumor targeting capability, the dimerized cKiE peptide (termed cKiE2) was designed, and the corresponding radiotracer 99mTc-cKiE2 was evaluated for tumor uptake and in vivo pharmacokinetics properties in tumor models. We found that cKiE2 showed higher binding affinity to integrin α6 than did monomeric RWY or cKiE peptide. The biodistribution results showed that the tumor uptake of 99mTc-cKiE2 was twice higher than that of 99mTc-RWY (3.20 ± 0.12 vs 1.26 ± 0.06 %ID/g, P < 0.001) at 0.5 h postinjection. The tumor to nontargeting tissue ratios were also enhanced in most normal organs. Specificity of 99mTc-cKiE2 for integrin α6 was demonstrated by competitive blocking of tumor uptake with excess cold peptide (3.20 ± 0.24 to 1.38 ± 0.23 %ID/g, P < 0.001). The integrin α6-positive tumors were clearly visualized by 99mTc-cKiE2/SPECT with low background except with a relatively high kidney uptake. The tumor uptake of 99mTc-cKiE2 correlates well with the tumor integrin α6 expression levels in a linear fashion (R2 = 0.9623). We also compared 99mTc-cKiE2 with an integrin αvβ3-targeted radiotracer 99mTc-3PRGD2 in the orthotopic hepatocellular carcinoma tumor models. We found that the orthotopic tumor was clearly visualized with 99mTc-cKiE2. 99mTc-3PRGD2 imaging did not show tumor contours in situ as clearly as 99mTc-cKiE2. The tumor-to-liver ratios of 99mTc-cKiE2 and 99mTc-3PRGD2 were 2.20 ± 0.17 and 0.85 ± 0.20. In conclusion, 99mTc-cKiE2 is an improved SPECT radiotracer for imaging integrin α6-positive tumors and has great potential for further clinical application.

Sonodynamic therapy (SDT) is a prospective therapy for many tumors by activation of sonosensitizers to produce reactive oxygen species (ROS) by ultrasound (US). However, limited generation of ROS and low drug delivery efficiency of sonosensitizers to the tumor tissue still hinder the application of SDT. Herein, an amphiphilic rose bengal (ARB) conjugate was designed to fabricate rose bengal microbubbles (RB-MBs) with high drug-loading contents (∼6.8%) and excellent contrast enhancement capability for US imaging, well suited for detecting tumor location and size. More importantly, RB-MBs could be successfully converted into RB-NPs by local US exposure, resulting in ∼7.5 times higher drug accumulation at the tumor tissue through the sonoporation effect as compared to RB-NPs and RB-MBs without US sonication. Meanwhile, using RB as the MB shell facilitated US energy transfer by the US mediated collapse of MBs through either a sonoluminescence or pyrolysis process; thus, the ROS generation efficiency could be greatly enhanced, resulting in a significantly higher tumor inhibition rate for the RB-MBs + US (∼76.5%) in the HT-29 tumor model as compared to conventional MBs + US and RB-NPs + US (∼23.8% and ∼49.2%), respectively. All these results suggested that this novel sonosensitizer delivery system of RB-MBs combined with US is a powerful strategy for remarkably enhancing SDT therapeutic efficacy with minimal side effects, showing great potential in cancer theranostics.

Despite the good prognosis of the low-risk thyroid cancer, there are no truly effective treatments for radioactive iodine-refractory thyroid cancer. Herein, a novel theranostic nanoplatform, as well as a smart doxorubucin (DOX) delivery system is fabricated. Gelatin-stabilized polypyrrole nanoparticles are reported for the first time. The combination of gelatin-stabilized polypyrrole and cyclodextrin-DOX complexes enabling three-stimuli-controlled drug delivery, including the enzyme-sensitive, pH-sensitive and photothermal-sensitive drug release, exhibiting a new way to equip photothermal agents with precisely controlled drug delivery. Anti-galectin-3 antibodies are utilized as the targeting molecules of nanoparticles in the first time, which surprisingly increase intracellular DOX uptake by enhanced clathrin-mediated endocytosis, showing galectin-3 can be employed as a highly efficient target of drug delivery systems. The nanoparticles achieve excellent photoacoustic imaging effect, enabled chemo-photothermal combined therapy with pinpointed drug delivery. Compared to free DOX, these multifunctional nanoparticles decrease the heart damage, but greatly increase the tumor/heart ratio of DOX concentration by 12.9-fold. The tumors are completely eradicated without any recurrence after the in vivo combined therapy. To the best of the authors' knowledge, this is also the first report to apply photoacoustic imaging-guided chemo-photothermal therapy for thyroid cancer, showing great potential to solve the dilemma in thyroid cancer therapy.