Biology subjects

Peng, W. C.

Publications and source records attributed to Peng, W. C..

4 recordsLinked to original sources

bioRxiv2023

Complex structural variation is prevalent and highly pathogenic in pediatric solid tumors

BackgroundIn pediatric cancer, structural variants (SVs) and copy number alterations can contribute to cancer initiation and progression, and hence aid diagnosis and treatment stratification. The few studies into complex rearrangements have found associations with tumor aggressiveness or poor outcome. Yet, their prevalence and biological relevance across pediatric solid tumors remains unknown. ResultsIn a cohort of 120 primary tumors, we systematically characterized patterns of extrachromosomal DNA, chromoplexy and chromothripsis across five pediatric solid cancer types: neuroblastoma, Ewing sarcoma, Wilms tumor, hepatoblastoma and rhabdomyosarcoma. Complex SVs were identified in 56 tumors (47%) and different classes occurred across multiple cancer types. Recurrently mutated regions tend to be cancer-type specific and overlap with cancer genes, suggesting that selection contributes to shaping the SV landscape. In total, we identified potentially pathogenic complex SVs in 42 tumors that affect cancer driver genes or result in unfavorable chromosomal alterations. Half of which were known drivers, e.g. MYCN amplifications due to ecDNA and EWSR1::FLI1 fusions due to chromoplexy. Recurrent novel candidate complex events include chromoplexy in WT1 in Wilms tumors, focal chromothripsis with 1p loss in hepatoblastomas and complex MDM2 amplifications in rhabdomyosarcomas. ConclusionsComplex SVs are prevalent and pathogenic in pediatric solid tumors. They represent a type of genomic variation which currently remains unexplored. Moreover, carrying complex SVs seems to be associated with adverse clinical events. Our study highlights the potential for complex SVs to be incorporated in risk stratification or exploited for targeted treatments.

cancer biology↗

bioRxiv2023

Multi-dimensional profiling of hepatoblastomas and patient-derived tumor organoids uncovers tumor subpopulations with divergent WNT activation profiles and identifies pan-hepatoblastoma drug sensitivities

Hepatoblastoma, the most prevalent pediatric liver cancer, almost always carries a WNT-activating CTNNB1 mutation, yet exhibits notable molecular heterogeneity. To characterize this heterogeneity and identify novel targeted therapies, we performed comprehensive analysis of hepatoblastomas and tumor-derived organoids using single-cell RNA-seq, spatial transcriptomics, single-cell ATAC-seq and high throughput drug profiling. We identified two distinct tumor epithelial signatures: hepatic fetal-like and WNT-high embryonal-like signatures, displaying divergent WNT signaling patterns. The liver-specific WNT targets were enriched in the fetal-like group, while the embryonal-like group was enriched in canonical WNT target genes. Gene regulatory network analysis revealed enrichment of regulons related to hepatic function such as bile acid, lipid and xenobiotic metabolism in the fetal-like subgroup but not in the embryonal-like subgroup. In addition, the dichotomous expression pattern of the transcription factors HNF4A and LEF1 allowed for a clear distinction between the fetal- and embryonal-like tumors. We also performed high-throughput drug screening using patient-derived tumor organoids and identified sensitivity to multiple inhibitor classes, most notably HDAC inhibitors. Intriguingly, embryonal-like tumor organoids, but not fetal-like tumor organoids, were sensitive to FGFR inhibitor treatments, suggesting a dependency on FGFR signaling. In summary, our data uncover the molecular and drug sensitivity landscapes of hepatoblastoma and pave the way for the development of targeted therapies.

cancer biology↗

bioRxiv2023

Hepatoblastoma exhibits a predominantly myeloid immune landscape and reveals opportunities for macrophage targeted immunotherapy

Background & AimsHepatoblastoma (HB) is a rare form of pediatric liver cancer which is currently treated with chemotherapy and surgery. The side effects of chemotherapy pose a major problem in HB and underline the need for an alternative treatment option. We aimed to characterize the immune landscape of HB to improve our understanding of the immunologic contribution to this disease and explore immunotherapeutic options. MethodsAn imaging mass cytometry panel of 36 antibodies was used on tissue of treatment-naive HB (n=5), and chemotherapy-treated HB (n=3), with paired distal normal liver tissue. Immunofluorescence was used to stain HB and normal liver tissue for Kupffer cell marker MARCO. A public single-cell RNA-sequencing (scRNA-seq) dataset was analyzed consisting of 9 chemotherapy-treated HB and paired normal liver tissue. ResultsHB showed a heterogeneous immune landscape predominantly comprising macrophages and monocytes with high expression of immune checkpoints CD47, SIRP, and VISTA, whereas T cells were limited. Chemotherapy increased influx of macrophages and CD8+ T cells in HB. Transcriptome profiling demonstrated an early activated phenotype of CD8+ T cells in chemotherapy-treated HB and absence of an exhaustion signature and immune checkpoint expression. Furthermore, tumor-associated macrophages had low MARCO expression, upregulated inflammatory markers and a high liver tissue residency score while expressing other Kupffer cell markers, such as CD5L, to a variable degree. ConclusionsThe absence of immune checkpoints and exhaustion markers in CD8+ T cells prohibits T cell-targeting by immune checkpoint blockade in HB patients. Instead, HB tumors contain a large myeloid compartment which provide opportunities for macrophage targeting, thereby paving the way for the development of improved treatment strategies for HB patients. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/546852v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@3748e2org.highwire.dtl.DTLVardef@191f9d9org.highwire.dtl.DTLVardef@aa4172org.highwire.dtl.DTLVardef@1aed5f9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS

BackgroundGene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products, but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions. ResultsWe developed Fusion-sq to detect tumor-specific gene fusions by integrating and "fusing" evidence from RNA-seq and whole genome sequencing (WGS) using intron-exon gene structure. In a pediatric pan-cancer cohort of 130 patients, we identified 165 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions, and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterised by underlying SVs or expression changes indicative of activating or disruptive effects. ConclusionsOur results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific fusions for future clinical decision making.

genomics↗