The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences

Abstract: Molecular profiling of breast cancer has enabled the development of more robust molecular prognostic signatures and therapeutic options for breast cancer patients. However, non-Caucasian populations remain understudied. Here, we present the mutational, transcriptional, and copy number profiles of 560 Malaysian breast tumours and a comparative analysis of breast cancers arising in Asian and Caucasian women. Compared to breast tumours in Caucasian women, we show an increased prevalence of HER2-enriched molecular subtypes and higher prevalence of TP53 somatic mutations in ER+ Asian breast tumours. We also observe elevated immune scores in Asian breast tumours, suggesting potential clinical response to immune checkpoint inhibitors. Whilst HER2-subtype and enriched immune score are associated with improved survival, presence of TP53 somatic mutations is associated with poorer survival in ER+ tumours. Taken together, these population differences unveil opportunities to improve the understanding of this disease and lay the foundation for precision medicine in different populations

The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences

Abstract: Molecular profiling of breast cancer has enabled the development of more robust molecular prognostic signatures and therapeutic options for breast cancer patients. However, non-Caucasian populations remain understudied. Here, we present the mutational, transcriptional, and copy number profiles of 560 Malaysian breast tumours and a comparative analysis of breast cancers arising in Asian and Caucasian women. Compared to breast tumours in Caucasian women, we show an increased prevalence of HER2-enriched molecular subtypes and higher prevalence of TP53 somatic mutations in ER+ Asian breast tumours. We also observe elevated immune scores in Asian breast tumours, suggesting potential clinical response to immune checkpoint inhibitors. Whilst HER2-subtype and enriched immune score are associated with improved survival, presence of TP53 somatic mutations is associated with poorer survival in ER+ tumours. Taken together, these population differences unveil opportunities to improve the understanding of this disease and lay the foundation for precision medicine in different populations

Enhancer-responsiveness and -specificity of Core Promoters in gene transcription

Differenzielle Genexpression ist entscheidend für die Entwicklung mehrzelliger Lebewesen wie Menschen und Tiere und muss daher streng kontrolliert werden. Gene werden beginnend von einer etwa 100 Basenpaare langen DNA Sequenz transkribiert. Diese Sequenz wird als Kernpromotor oder Core Promotor bezeichnet und umgibt den Transkriptionsstartpunkt (TSS), außerdem enthält sie die mindest-notwendigen DNA Sequenzelemente, welche für die Assemblierung des RNA-Polymerase II Komplexes nötig sind. Die zelltypspezifische Aktivierung der Transkription an den Core Promotoren ist jedoch von einer zweiten Klasse regulatorischer DNA Elemente im Genom, genannt transkriptionelle Enhancer, abhängig. Während meiner Doktorarbeit konzentrierte ich mich auf die Spezifität und das Ansprechverhalten von Core Promotoren in Bezug auf transkriptionelle Enhancer. Eine der offenen Fragen in der Transkriptionsforschung ist, ob Core Promotoren eine intrinsische Präferenz für bestimmte Enhancer besitzen. Um diese Frage zu beantworten, untersuchten wir Enhancerkandidaten auf deren Fähigkeit Core Promotoren zu aktivieren. Dabei testeten wir sowohl Core Promotoren, die sich an nicht-regulierten, konstitutiv exprimierten Genen, sogenannten Haushaltsgenen, befinden, als auch solche, die an entwicklungsspezifisch regulierten Genen liegen. Die zwei Core Promotor Typen weisen in Drosophila melanogaster unterschiedliche Präferenzen zu tausenden Enhancern auf. Enhancer, die Core Promotoren vom Haushaltstyp aktivieren, sind über mehrere Zelltypen hinweg aktiv, wohingegen Enhancer, welche entwicklungsspezifische Core Promotoren aktivieren, zelltypspezifische Aktivität aufweisen. Enhancer dieser zwei Klassen unterscheiden sich auch in ihrer Position innerhalb des Genoms, den Proteinen, die sie binden, und der Funktion ihrer Nachbargene. Core Promotoren weisen unterschiedliche Transkriptionslevel auf, Unterschiede, die bislang der weiten Bandbreite an Stärke der Enhancer zugeschrieben wurden. Über das intrinsische Ansprechverhalten von Core Promotoren auf bestimmte Enhancer ist bisher wenig bekannt. Wir verwendeten einzelne, definierte Enhancer, um dieses Ansprechverhalten von sämtlichen Core Promotor Kandidaten im Drosophila melanogaster Genom zu testen. Core Promotoren variieren stark im Enhancer-Ansprechverhalten, wobei wir Unterschiede von bis zu drei Größenordnungen feststellten. Die Unterschiede korrelieren mit bestimmten Sequenzeigenschaften und sind mit Genen verschiedener Funktionen assoziiert. Zusammenfassend zeigen die Ergebnisse meiner Doktorarbeit, dass Core Promotoren Präferenzen zu unterschiedlichen Enhancern aufweisen, was einen weiteren Mechanismus der Kommnunikation zwischen Enhancern und Core Promoter darstellt, und dass sich die tausenden Core Promotoren im Genom substantiell im Enhancer-Ansprechverhalten unterscheiden. Diese Erkenntnisse zeigen, dass Core Promotoren aktiv an der präzisen Regulation der Genexpression beteiligt sind, welche die Entwicklung höherer Organismen erst ermöglicht.Animal development is attributed to differential gene expression that is tightly regulated. Genes are transcribed from core promoters, sequences of around 100 base pairs (bp) surrounding the transcription start sites (TSSs) at which the RNA Polymerase II (Pol II) complex assembles. The cell-type specific transcriptional activities of core promoters are dependent on a second type of genomic regulatory element termed enhancers. During my PhD, I am interested in the specificity and responsiveness of core promoters towards enhancers. An open question in the study of transcription is whether core promoters display intrinsic preferences towards enhancers. To address this hypothesis, we tested genome-wide enhancer candidates for their ability to activate core promoters that represent the housekeeping or developmental transcription programs, respectively. In Drosophila melanogaster cell lines, the two core promoter types exhibit differential preferences towards thousands of enhancers. Housekeeping core promoters are activated by enhancers that are active across cell types, while developmental core promoters are activated by enhancers that are highly cell-type specific. These two enhancer classes also differ in their genomic location, the protein factors that they bind, and the function of the neighbouring genes. Different core promoters do not always support transcription at the same level, differences that have been mainly attributed to the wide range of enhancer strengths. Little is known about the intrinsic responsiveness of core promoters towards enhancers. We used single defined enhancers to test the enhancer-responsiveness of genome-wide core promoter candidates from Drosophila melanogaster. Core promoters vary widely in their enhancer-responsiveness, with differences up to three orders of magnitude. The differences correlate with sequence signatures and are associated with genes of different function. In summary, the results obtained during my PhD thesis project show that the preference of core promoters towards enhancers represent another mechanism of enhancer–core-promoter communication, and the thousands of core promoters in the genome vary substantially in their enhancer-responsiveness. These findings demonstrate that core promoters are actively involved in the precisely regulated gene expression that drives animal development

Identification of four-jointed box 1 as a potential oncogene in nasopharyngeal carcinoma / Muhammad Mamduh bin Ahmad Zabidi

Nasopharyngeal carcinoma (NPC) is a highly metastatic cancer that is endemic in South East Asia and Southern China. Despite the gravity of the disease, the current knowledge on its molecular pathogenesis is still inadequate to improve the disease management. The present study seeks to understand the molecular mechanism of NPC, with an aim to identify potential therapeutic targets or biomarkers. From a previous expression microarray study, Four – Jointed Box 1 (FJX1) gene was found to be upregulated in NPC compared to non-cancerous controls with negligible expression in 5 vital normal human organs. Human FJX1 is a Drosophila orthologue of four-jointed (fj) gene which codes for a Golgi-resident kinase that phosphorylates specific cadherin domains and functions downstream of the Notch and Hippo signaling pathways. The overexpression of FJX1 in primary NPC tissues was confirmed at both mRNA and protein levels, while its low expression was validated in 16 normal human organs. Both overexpression and knockdown experiments showed that FJX1 increased the aggressiveness of NPC cells by promoting cell proliferation, invasion and anchorageindependent growth. Concomitant change of Cyclins D1 and E1 levels were observed with FJX1 level, suggesting FJX1 enhances cell proliferation through cell cycle regulation. The results of the present study demonstrate for the first time the overexpression of FJX1 in NPC as a putative oncogene, and it represents an attractive therapeutic target for NPC

Characterisation of PALB2 tumours through whole-exome and whole-transcriptomic analyses.

Rare protein-truncating variants (PTVs) in PALB2 confer increased risk to breast cancer, but relatively few studies have reported the characteristics of tumours with PALB2 PTVs. In this study, we describe molecular characteristics of tumours with either germline or somatic alterations in PALB2. DNA from fresh frozen tumour tissues and matched peripheral blood lymphocytes for 560 breast cancer patients was subjected for whole-exome sequencing (WES), and RNA from tumour tissues was subjected to RNA sequencing (RNA-seq). We found six cases with germline and three with somatic protein-truncating variants in PALB2. The characteristics of tumours in patients with PALB2 PTVs were similar to those with BRCA1 and BRCA2 PTVs, having significantly more somatic alterations, and a high proportion of the mutational signature and genomic scar scores characteristic of deficiencies in homologous recombination (HR), compared to tumours arising in non-carriers. Unlike tumours arising in patients with BRCA1 and BRCA2 PTVs, PALB2 tumours did not have high prevalence of TP53 somatic alterations or an enriched immune microenvironment. In summary, PALB2 tumours show the homologous recombination deficiencies characteristic of BRCA1 and BRCA2 tumours, and highlight the potential clinical relevance of PALB2 mutational status in guiding therapeutic choices

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

Funder: Charitable funds from Yayasan PETRONAS, Yayasan Sime Darby, Vistage Malaysia, Scientex Foundation, Estee Lauder CompaniesFunder: Cancer Research UK (CRUK); doi: https://doi.org/10.13039/501100000289Triple-negative breast cancers (TNBCs) are a subset of breast cancers that have remained difficult to treat. A proportion of TNBCs arising in non-carriers of BRCA pathogenic variants have genomic features that are similar to BRCA carriers and may also benefit from PARP inhibitor treatment. Using genomic data from 129 TNBC samples from the Malaysian Breast Cancer (MyBrCa) cohort, we developed a gene expression-based machine learning classifier for homologous recombination deficiency (HRD) in TNBCs. The classifier identified samples with HRD mutational signature at an AUROC of 0.93 in MyBrCa validation datasets and 0.84 in TCGA TNBCs. Additionally, the classifier strongly segregated HRD-associated genomic features in TNBCs from TCGA, METABRIC, and ICGC. Thus, our gene expression classifier may identify triple-negative breast cancer patients with homologous recombination deficiency, suggesting an alternative method to identify individuals who may benefit from treatment with PARP inhibitors or platinum chemotherapy