Maria Teresa Landi

Examining the Role of Extrachromosomal DNA in Lung Cancer

This study examines ecDNA in lung cancer, finding it in 18.9% of patients and associating it with worse survival and genomic instability.

Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression

The paper presents an isoform-level lung cell atlas using single-cell long-read RNA-sequencing, revealing genetic effects on isoform regulation that improve cell-type classification and identify novel variants associated with lung cancer risk.

Single-cell lung eQTL dataset of Asian never-smokers highlights the roles of alveolar cells in lung cancer etiology

The paper constructs a single-cell eQTL dataset from Asian never-smokers, identifying alveolar cell-specific genes linked to lung cancer susceptibility.

Integrative screening identifies functional variants and VNTRs underlying GWAS signals at the 5p15.33 multi-cancer susceptibility locus

The paper identifies functional variants and VNTRs at the 5p15.33 locus using fine-mapping, MPRA, and CRISPRi screens, revealing their role in cancer susceptibility through antagonistic pleiotropy.

Functional characterization of the 9q34.13 locus identifies RAPGEF1 as modulating risk for melanoma and nevi via RAS activation

This study identifies RAPGEF1 as a gene modulating melanoma and nevi risk through RAS activation, using fine-mapping, expression data, and functional assays.

Genomic Characterization of Lung Cancer in Never-Smokers Using Deep Learning

This paper develops a deep learning model to predict molecular alterations in never-smoker lung adenocarcinomas from histological images, achieving high accuracy for most features.

Functional characterization of a multi-cancer risk locus on chromosome band 2q33.1 near CASP8

The paper identifies rs3769823 as a functional variant near CASP8 influencing its expression in a cell-type specific manner and associated with multiple cancers.

Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma

This study identifies three distinct evolutionary trajectories in lung adenocarcinomas using whole-genome sequencing, revealing that some never-smoking tumors follow smoking-like paths driven by KRAS mutations.

Identifying High-Dimensional Genomic Factors Modulating Biological Networks Across Multi-Omics Data

GFBioNet identifies genomic factors modulating trait-trait relationships in multi-omics data, revealing host genetics, microbial taxa, and mutations affecting biological networks.

Stratifying Lung Adenocarcinoma Risk with Multi-ancestry Polygenic Risk Scores in East Asian Never-Smokers

The paper develops and validates multi-ancestry polygenic risk scores for LUAD in East Asian never-smokers, showing improved risk prediction compared to East Asian-only models.

A prognostic signature for lung adenocarcinoma in people who have never smoked

The paper identifies three subtypes of NS-LUAD using RNA-seq data and develops a 60-gene signature that predicts survival across subgroups.

Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition

This study analyzes 1024 lung adenocarcinomas to identify evolutionary patterns and mutational mechanisms, revealing distinct trajectories linked to smoking, ancestry, and retrotransposition.

Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis-regulation

The paper identifies candidate causal variants and genes at melanoma risk loci using capture-HiC and integrates multi-omics data to prioritize cis-regulatory interactions.

Context-aware single-cell multiome approach identified cell-type specific lung cancer susceptibility genes

The paper identifies cell-type specific lung cancer susceptibility genes by integrating single-cell multi-omics data with GWAS loci.

APOBEC shapes tumor evolution and age at onset of lung cancer in smokers

The paper identifies two lung cancer subtypes defined by APOBEC mutagenesis levels and shows their association with different genetic mutations, aging, and immune responses.

A real-world pan-cancer catalogue of mutational signatures from 111,711 tumors

This paper introduces SATS, a framework for mutational signature analysis in targeted sequencing data, and presents a pan-cancer catalogue of mutational signatures from 111,711 tumors.

Time to first cigarette and its impact on lung tumorigenesis

This study shows that time to first cigarette strongly influences lung tumor mutational burden, signatures, and survival in smokers.

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

SigProfilerExtractor is a tool for de novo mutational signature extraction that outperforms existing methods and identifies four novel signatures, including one linked to tobacco smoking.

SUITOR: selecting the number of mutational signatures through cross-validation

SUITOR selects the optimal number of mutational signatures using cross-validation, improving accuracy over existing methods in cancer genomics.

A UVB-responsive common variant at chr7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor gene (AHR)

This paper identifies rs117132860 as a functional variant at 7p21.1 that regulates AHR expression in response to UVB, contributing to melanoma risk and tanning ability.

Cell type-specific meQTL extends melanoma GWAS annotation beyond eQTL and informs melanocyte gene regulatory mechanisms

The paper identifies cell-type-specific meQTLs in melanocytes and melanomas, enhancing GWAS annotation and revealing regulatory mechanisms involving IRF4.

Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family

The paper identifies a novel NRAS variant in a melanoma-prone family and shows it impairs MAPK/AKT signaling while enhancing PI3K signaling.

Expanding the Genetic Architecture of Nicotine Dependence and its Shared Genetics with Multiple Traits: Findings from the Nicotine Dependence GenOmics (iNDiGO) Consortium

The paper identifies novel genetic loci associated with nicotine dependence and shows genetic correlations with other smoking traits and comorbidities using genome-wide association studies.

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

This study examines intratumor heterogeneity and clonal evolution in papillary renal cell carcinomas using whole-genome sequencing and DNA methylation data, revealing distinct patterns of genomic and epigenomic evolution across subtypes.

Genetic and Epigenetic Intratumor Heterogeneity Impacts Prognosis of Lung Adenocarcinoma

This study quantifies genetic and epigenetic intratumor heterogeneity in lung adenocarcinoma and links it to poor prognosis.

Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility

The paper identifies genetic links between impaired pulmonary function and increased lung cancer risk, showing causal relationships through Mendelian randomization and highlighting immune-related pathways.