Ingrid Cifola

My research activity focuses on human cancer genomics and application of high-throughput technologies, such as next-generation sequencing (NGS) and microarray platforms, to perform "-omics" analyses for translational medicine purposes. Working in close cooperation with hospital and university research groups, I used such technologies to perform genomic, transcriptomic and epigenetic analyses in several human cancer pathologies, among which renal cell carcinoma, cutaneous malignant melanoma, acute myeloid leukemia, acute lymphoblastic leukemia, myeloproliferative neoplasms and multiple myeloma. I used high-density microarray platforms to identify chromosomal aberrations, to analyse gene expression profiles and to study promoter methylation. Then, I applied NGS technologies for whole-exome sequencing (WES) or gene target sequencing to identify mutations and/or structural genomic rearrangements, for transcriptomic profiling and identification of particular transcripts, such as fusion transcripts, conjoined genes and circular RNAs (RNA-seq), for miRNA expression profiling in extracellular vesicles released by cancer cells (small RNA-seq), for single-cell transcriptomics analysis of tumor samples (single-cell RNA-seq). Moreover, I applied integrated approaches to combine different kind of omics data, e.g. genomic profile and gene expression data, aiming to obtain a more complete view of molecular mechanisms underlying tumorigenesis and to identify candidate crucial genes for tumor biology. The final goal of my studies is to contribute to improve the knowledge of the molecular mechanisms involved in malignant transformation and progression and to help the identification of novel candidate markers useful for early tumor diagnosis or prognostic prediction, or as molecular targets for new therapeutic strategies. A particular interest is addressed to "liquid biopsy" approaches for a non-invasive and early tumor diagnosis and post-therapy patient's monitoring. These are the basis to realize a "personalized medicine" that maximizes therapy efficacy and minimizes toxic side effects, thus improving life expectation and quality of cancer patients. I have been involved in many research projects funded by Italian MIUR, Cariplo and AIRC Foundations. My scientific activity is documented by 35 papers on peer-reviewed international journals (Scopus h 19).

Application of high-throughput technologies for molecular characterization of human cancer pathologies, among which renal cell carcinoma (RCC), cutaneous malignant melanoma, acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), myeloproliferative neoplasms (MPN), multiple myeloma (MM). Application of high-density microarray platforms for human DNA copy number profiling, gene and miRNA expression analysis, and promoter methylation analysis. Application of next-generation sequencing (NGS) for whole-exome or target sequencing and identification of single nucleotide variants (SNV) and copy number variants (CNV), for gene expression profiling and identification of fusion transcripts, conjoined genes and circular RNAs (RNA-seq), for miRNA expression profiling in extracellular vesicles released by cancer cells (small RNA-seq), for single-cell transcriptomics analysis of tumor samples (single-cell RNA-seq).

BL1391: an established cell line from a human malignant peripheral nerve sheath tumor with unique genomic features

Expression profiling of microRNAs and isomiRs in conventional central chondrosarcoma

Circulating miRNAs in Small Extracellular Vesicles Secreted by a Human Melanoma Xenograft in Mouse Brains

Disruption of redox homeostasis for combinatorial drug efficacy in K-Ras tumors as revealed by metabolic connectivity profiling

36-kDa Annexin A3 Isoform Negatively Modulates Lipid Storage in Clear Cell Renal Cell Carcinoma Cells

Linked read sequencing reveals new genetic variants in autism

Severe Heterotopic Ossification in the Skeletal Muscle and Endothelial Cells Recruitment to Chondrogenesis Are Enhanced by Monocyte/Macrophage Depletion

The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer

Nup153 Unlocks the Nuclear Pore Complex for HIV-1 Nuclear Translocation in Non-dividing Cells

Retroviral Scanning: Mapping MLV Integration Sites to Define Cell-specific Regulatory Regions.

MYC-containing amplicons in acute myeloid leukemia: Genomic structures, evolution, and transcriptional consequences

The glucose and lipid metabolism reprogramming is grade-dependent in clear cell renal cell carcinoma primary cultures and is targetable to modulate cell viability and proliferation

Biological and prognostic impact of APOBEC-induced mutations in the spectrum of plasma cell dyscrasias and multiple myeloma cell lines.

Integrative transcriptomic and protein analysis of human bronchial BEAS-2B exposed to seasonal urban particulate matter.

Major Action of Endogenous Lysyl Oxidase in Clear Cell Renal Cell Carcinoma Progression and Collagen Stiffness Revealed by Primary Cell Cultures

Characterization and identification of hidden rare variants in the human genome

Three novel fusion transcripts of the paired box 5 gene in B-cell precursor acute lymphoblastic leukemia.

Whole-exome sequencing of primary plasma cell leukemia discloses heterogeneous mutational patterns

A compendium of DIS3 mutations and associated transcriptional signatures in plasma cell dyscrasias.

Structural Variations Identified By Whole Transcriptome Sequencing (RNA-Seq) in Childhood ALL with Different Response to Therapy

Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro e87680

Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro

Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer

Health Risk Assessment for Air Pollutants: Alterations in Lung and Cardiac Gene Expression in Mice Exposed to Milano Winter Fine Particulate Matter (PM2.5)

Gene expression profiling of human bronchial epithelial cells exposed to seasonal Milan particulate matter

Novel Chimeric Transcripts Involving PAX5 in B-Cell Precursor ALL

Comprehensive Genomic Characterization of Cutaneous Malignant Melanoma Cell Lines Derived from Metastatic Lesions by Whole-Exome Sequencing and SNP Array Profiling

Chronic Resveratrol Treatment Ameliorates Cell Adhesion and Mitigates the Inflammatory Phenotype in Senescent Human Fibroblasts

EXCAVATOR: Detecting copy number variants from whole-exome sequencing data

Genome-wide analysis of promoter and enhancer usage in hematopoietic stem cell differentiation.

Renal cell carcinoma primary cultures maintain genomic and phenotypic profile of parental tumor tissues.

Molecular Portrait of Clear Cell Renal Cell Carcinoma: An Integrative Analysis of Gene Expression Profiling and Genomic Copy Number

Integration of gene and miRNA expression profiles in clear cell renal carcinoma cell lines and relationship with VHL gene status

An integrated in vitro kinetical model of human monocyte reactivity during inflammation

DNA copy-number abnormalities do not occur in infant ALL with t(4;11)/MLL-AF4

Primary Cell Cultures from Human Renal Cortex and Renal-Cell Carcinoma Evidence a Differential Expression of Two Spliced Isoforms of Annexin A3

A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets.

LAL INFANT INTRODUCES A NEW SPECIFIC GENOMIC PROFILE

Renal cell carcinoma primary cultures as in vitro model to study genomic profile of parental tumor tissues

Infant ALL patients carrying t(4;11) have a different genotypic profile than older ALL children

Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile

Simultaneous occurrence of acute myeloid leukaemia with mutated nucleophosmin (NPM1) in the same famil

Infant ALL patients carrying t(4;11) have a different genotypic profile than older ALL children

Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile

Applications of Fuzzy Sets Theory

Applications of Fuzzy Sets Theory

Assessment of common regions and specific footprints of DNA copy number aberrations across multiple affymetrix SNP mapping Arrays

Locally adaptive statistical procedures for the integrative analysis on genomic and transcriptional data

Infant ALL Patients Carrying (4;11) Have A Different Genotypic Profile Than Older ALL Children

Integration of genome wide molecular analysis and subcellular proteomics for renal cell carcinoma biomarker identification

Reconstitution of human telomerase reverse transcriptase expression rescues colorectal carcinoma cells from in vitro senescence: Evidence against immortality as a constitutive trait of tumor cells

Reconstitution of hTERT expression allows successful immortalization of short-lived primary cultures of colorectal carcinoma: A new tool for the efficient generation of colorectal carcinoma cell lines.