Publications by authors named "Kelsey Zhu"

Approximately 30% of early-stage lung adenocarcinoma patients present with disease progression after successful surgical resection. Despite efforts of mapping the genetic landscape, there has been limited success in discovering predictive biomarkers of disease outcomes. Here we performed a systematic multi-omic assessment of 143 tumors and matched tumor-adjacent, histologically-normal lung tissue with long-term patient follow-up.

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Background: Cancer immunotherapies including immune checkpoint inhibitors and Chimeric Antigen Receptor (CAR) T-cell therapy have shown variable response rates in paediatric patients highlighting the need to establish robust biomarkers for patient selection. While the tumour microenvironment in adults has been widely studied to delineate determinants of immune response, the immune composition of paediatric solid tumours remains relatively uncharacterized calling for investigations to identify potential immune biomarkers.

Methods: To inform immunotherapy approaches in paediatric cancers with embryonal origin, we performed an immunogenomic analysis of RNA-seq data from 925 treatment-naïve paediatric nervous system tumours (pedNST) spanning 12 cancer types from three publicly available data sets.

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Article Synopsis
  • International cancer registries, like AACR Project GENIE, provide access to genomic and clinical data from over 130,000 cancer patients, but analyzing this combined data can be tricky.
  • The cBioPortal for Cancer Genomics has improved its features to help visualize and analyze longitudinal clinical and genomic data, allowing users to see how treatment impacts patient outcomes over time.
  • These enhancements enable researchers and clinicians to explore complex datasets, fostering discoveries on how specific genomic changes affect cancer prognosis and treatment effectiveness.
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There is currently no targeted therapy to treat NF1-mutant melanomas. In this study, we compared the genomic and transcriptomic signatures of NF1-mutant and NF1 wild-type melanoma to reveal potential treatment targets for this subset of patients. Genomic alterations were verified using qPCR, and differentially expressed genes were independently validated using The Cancer Genome Atlas data and immunohistochemistry.

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Chordoid meningioma is a morphological variant of meningioma designated as WHO grade 2. However, the recurrence rates varied widely in different case series, and to date, a unifying molecular genetic signature has not been identified. Among 1897 meningiomas resected at our institution, we identified 12 primary chordoid meningiomas from 12 patients.

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Purpose: Adult granulosa cell tumor (AGCT) is characterized by the somatic FOXL2 p.C134W mutation, and recurrences have been associated with TERT promoter and KMT2D-truncating mutations. Conversely, the molecular underpinnings of the rare juvenile granulosa cell tumor (JGCT) have not been well elucidated.

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Serial circulating tumor DNA (ctDNA) monitoring is emerging as a non-invasive strategy to predict and monitor immune checkpoint blockade (ICB) therapeutic efficacy across cancer types. Yet, limited data exist to show the relationship between ctDNA dynamics and tumor genome and immune microenvironment in patients receiving ICB. Here, we present an in-depth analysis of clinical, whole-exome, transcriptome, and ctDNA profiles of 73 patients with advanced solid tumors, across 30 cancer types, from a phase II basket clinical trial of pembrolizumab (NCT02644369) and report changes in genomic and immune landscapes (primary outcomes).

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Primary mucinous cystadenocarcinoma of the breast is a rare neoplasm with few reports in the literature. Here, we report for the first time a comprehensive genetic profile of a primary mucinous cystadenocarcinoma of the breast, using next-generation sequencing 580 cancer-associated gene panel. Mutations in TP53, RB1, and BAP1 were identified.

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Soft tissue tumors can be categorized molecularly into two categories: tumors which are known to have recurrent molecular alterations and tumors which do not have consistent recurrent molecular alterations or translocations. These "nontranslocation" associated sarcomas are clinically more aggressive than their more stable counterparts. However, recent advances in RNA sequencing have discovered recurrent novel fusions within the latter group, namely TERT-TRIO fusions.

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Article Synopsis
  • Malignant rhabdoid tumors (MRTs) are rare and lethal childhood cancers primarily found in the kidney and brain, driven by the loss of the SMARCB1 gene.
  • To better understand these tumors, researchers conducted extensive genomic analyses using various sequencing techniques and histone modification profiling.
  • The study identified different gene expression and methylation subsets, highlighting dysregulated pathways crucial for neural crest development.
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  • Recent studies reveal that A-to-I RNA editing in microRNAs impacts tumor growth and metastasis, but its effects in melanoma are unclear.
  • Evidence shows that low expression of ADAR1 in metastatic melanoma is linked to CREB, and re-introduction of ADAR1 suppresses tumor growth and metastasis.
  • The miRNA miR-455-5p, which has A-to-I editing sites, functions differently when edited; the unedited form promotes melanoma metastasis, while the edited version inhibits it, highlighting the role of RNA editing in cancer progression.
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