C. Caldas

Clustering of HR+/HER2- breast cancer in an Asian cohort is driven by immune phenotypes

This study identifies immune phenotype-driven clustering in HR+/HER2- breast cancer from an Asian cohort, deviating from the luminal A-luminal B classification seen in European populations.

Modelling drug responses and evolutionary dynamics using triple negative breast cancer patient-derived xenografts

This paper uses TNBC patient-derived xenografts to model drug responses and evolutionary dynamics, revealing a novel mechanism of olaparib response and synergistic effects with salinomycin.

Gene expression signature for predicting homologous recombination deficiency in triple-negative breast cancer

The paper develops a gene expression classifier to predict homologous recombination deficiency in triple-negative breast cancer using RNA-seq and WES data from a Malaysian cohort, achieving high accuracy in validation datasets.

Prediction of cancer treatment response from histopathology images through imputed transcriptomics

ENLIGHT-DeepPT predicts cancer treatment response from H&E slides by first imputing transcriptomics and then using that data to predict response across multiple therapies and cancer types.

The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure

The paper presents an infrastructure for high-throughput data and analysis of tumour and xenograft samples using multimodal imaging and molecular annotation.

Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

The paper identifies frequent allelic expression imbalance of PIK3CA mutations in breast cancer and links it to poor prognosis.

Somatic chromosomal number alterations affecting driver genes inform in-vitro and clinical drug response in high-grade serous ovarian cancer

This study shows that somatic copy number alterations in driver genes correlate with drug response in HGSOC spheroid models and clinical settings.

Transcriptional profiling reveals a subset of human breast tumors that retain wt TP53 but display mutant p53-associated features

The paper identifies a subset of human breast tumors with wild-type TP53 that exhibit gene expression and pathway patterns similar to TP53-mutated tumors, suggesting functional rewiring of p53.

Transcriptomically-inferred PI3K activity and stemness show a counterintuitive correlation with PIK3CA genotype in breast cancer

The paper finds a biphasic relationship between PIK3CA genotype and transcriptionally inferred PI3K activity and stemness in breast cancer, with mutant allele dosage affecting these traits differently.

Cancer-associated fibroblast compositions change with breast cancer progression linking S100A4 and PDPN ratios with clinical outcome

The paper tracks changes in cancer-associated fibroblast (CAF) subpopulations during breast cancer progression, linking their ratios to clinical outcomes and BRCA mutations.

Germline APOBEC3B deletion in Asian women increases somatic hypermutation in breast cancer that is associated with Her2 subtype, PIK3CA mutations, immune activation, and increased survival

Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures

The paper analyzes B cell receptor repertoires from COVID-19 patients to identify convergent immune signatures associated with disease outcome.

The Molecular Landscape of Asian Breast Cancers Reveals Clinically Relevant Population-Specific Differences

This study analyzes molecular profiles of 560 Asian breast tumors, revealing population-specific differences in subtypes, mutations, and immune scores compared to Caucasian populations.

The GATA3 X308_Splice breast cancer mutation is a hormone context-dependent oncogenic driver

The paper investigates the context-dependent oncogenic effects of the GATA3 X308_Splice mutation in breast cancer, showing its differential impact based on hormonal status.