Francesca Demichelis
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View article: Supplementary Figure 5 from Liquid Biopsy Identifies Taxane Resistance and Clonal Selection in Castration-Resistant Prostate Cancer
Supplementary Figure 5 from Liquid Biopsy Identifies Taxane Resistance and Clonal Selection in Castration-Resistant Prostate Cancer Open
Supplementary Figure 5
View article: Supplementary Figure 4 from Liquid Biopsy Identifies Taxane Resistance and Clonal Selection in Castration-Resistant Prostate Cancer
Supplementary Figure 4 from Liquid Biopsy Identifies Taxane Resistance and Clonal Selection in Castration-Resistant Prostate Cancer Open
Supplementary Figure 4
View article: Supplementary Figures S1-S5 from Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis
Supplementary Figures S1-S5 from Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis Open
The supplementary figure file includes Figures S1–S5. Descriptions of each figure are as follows: - Figure S1 shows the approach for editing the 7p14.3 locus in PC3 cells. - Figure S2 shows differential gene expression in bulk and in singl…
View article: Data from Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis
Data from Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis Open
The biological mechanisms underlying the cooperation between germline genetic variants and somatic mutations during carcinogenesis are rarely elucidated. In this study, characterizing isogenic prostate cancer cell lines, we dissected the i…
View article: Supplementary Tables S1-S12 from Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis
Supplementary Tables S1-S12 from Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis Open
The supplementary table file includes Supplementary Tables S1-S12. Descriptions of each table are as follows: - Supplementary Table 1: Study oligo sequences - Supplementary Table 2: Number of Off Targets calculated with Cas-OFFinder for th…
View article: MYC-driven gliosis impairs neuron-glia communication in amyotrophic lateral sclerosis
MYC-driven gliosis impairs neuron-glia communication in amyotrophic lateral sclerosis Open
Chronic activation of glial cells leads to the dysfunction and degeneration of motor and cortical neurons in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) with an unknown mechanism. To shed light on the molecular pa…
View article: Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis
Germline–Somatic Liaison Dictates Cancer Subtypes via <i>de novo</i> Steroid Biosynthesis Open
The biological mechanisms underlying the cooperation between germline genetic variants and somatic mutations during carcinogenesis are rarely elucidated. In this study, characterizing isogenic prostate cancer cell lines, we dissected the i…
View article: Extracellular vesicle heterogeneity through the lens of multiomics
Extracellular vesicle heterogeneity through the lens of multiomics Open
Extracellular vesicles (EVs) are heterogeneous in size, biogenesis, content, and function. Aggressive cancer cells release a distinct, poorly characterized, and particularly large EV subtype, namely large oncosomes (LOs). This study employ…
View article: EXaCT-2: An augmented and customizable oncology-focused whole exome sequencing platform
EXaCT-2: An augmented and customizable oncology-focused whole exome sequencing platform Open
With the rapid advances in cancer research, the list of variants and genes that drive human diseases is constantly expanding. Moreover, the FDA has approved more cancer therapies that incorporate a broader set of genomic features than simp…
View article: ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent transcription replication conflicts in triple negative breast cancer
ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent transcription replication conflicts in triple negative breast cancer Open
Oncogene-induced replicative stress (RS) drives tumor progression by disrupting genome stability, primarily through transcription-replication conflicts (TRCs), which promote R-loop accumulation and trigger the DNA damage response (DDR). In…
View article: PRODE recovers essential and context-essential genes through neighborhood-informed scores
PRODE recovers essential and context-essential genes through neighborhood-informed scores Open
View article: Mapping of Extracellular RNA from Human Biofluids Reveals &gt;17 Million Genomic Loci Covering &gt;18% of the Human Genome that Express Extracellular RNA
Mapping of Extracellular RNA from Human Biofluids Reveals >17 Million Genomic Loci Covering >18% of the Human Genome that Express Extracellular RNA Open
View article: CRISPR/Cas9 screens identify LIG1 as a sensitizer of PARP inhibitors in castration-resistant prostate cancer
CRISPR/Cas9 screens identify LIG1 as a sensitizer of PARP inhibitors in castration-resistant prostate cancer Open
PARP inhibitors (PARPi) have received regulatory approval for the treatment of several tumors, including prostate cancer (PCa), and demonstrate remarkable results in the treatment of castration-resistant prostate cancer (CRPC) patients cha…
View article: Liquid Biopsy in Progressing Prostate Cancer Patients Starting Docetaxel with or Without Enzalutamide: A Biomarker Study of the PRESIDE Phase 3b Trial
Liquid Biopsy in Progressing Prostate Cancer Patients Starting Docetaxel with or Without Enzalutamide: A Biomarker Study of the PRESIDE Phase 3b Trial Open
View article: Extracellular Vesicles heterogeneity through the lens of multiomics
Extracellular Vesicles heterogeneity through the lens of multiomics Open
Extracellular vesicles (EVs) are heterogenous in size, biogenesis, cargo and function. Beside small EVs, aggressive tumor cells release a population of particularly large EVs, namely large oncosomes (LO). This study provides the first reso…
View article: Sensitive tumor detection, accurate quantification, and cancer subtype classification using low-pass whole methylome sequencing of plasma DNA
Sensitive tumor detection, accurate quantification, and cancer subtype classification using low-pass whole methylome sequencing of plasma DNA Open
The analysis of circulating tumor DNA (ctDNA) is increasingly used for monitoring disease in patients with metastatic cancer. Here, we introduce a robust and reproducible strategy combining low-pass whole methylome sequencing of plasma DNA…
View article: Correction: PaCBAM: fast and scalable processing of whole exome and targeted sequencing data
Correction: PaCBAM: fast and scalable processing of whole exome and targeted sequencing data Open
View article: ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent Transcription Replication Conflicts in Triple Negative Breast Cancer
ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent Transcription Replication Conflicts in Triple Negative Breast Cancer Open
Oncogene-induced replicative stress (RS) plays a central role in tumor progression, leading to genomic instability by eliciting transcription replication conflicts (TRCs), which represent the major source of R-loops, that ultimately favors…
View article: Supplementary Tables S1-S10 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation
Supplementary Tables S1-S10 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation Open
S1: Motif enrichment results around differentially methylated sites in CRPC-NE vs CRPC-Adeno solid tissue biopsy eRRBS data (Beltran2016) S2A: PSA and treatment timepoints for the PRIME cohort S2BPSA and treatment timepoints for the Wu2020…
View article: Supplementary Figures S1-S7 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation
Supplementary Figures S1-S7 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation Open
Supp. Fig. 1 Differential methylation across prostate cancer disease states Supp. Fig. 2 NEMO panel design Supp. Fig. 3 Tumor content estimation with a minimal set of informative regions Supp. Fig. 4 Scoring CRPC-NE in circulation with the…
View article: Data from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation
Data from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation Open
Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive therapy response and outcome differences. Histologic transformation to castration-resistant neuroendocrine prostate cance…
View article: Supplementary Tables S1-S10 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation
Supplementary Tables S1-S10 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation Open
S1: Motif enrichment results around differentially methylated sites in CRPC-NE vs CRPC-Adeno solid tissue biopsy eRRBS data (Beltran2016) S2A: PSA and treatment timepoints for the PRIME cohort S2BPSA and treatment timepoints for the Wu2020…
View article: Supplementary Figures S1-S7 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation
Supplementary Figures S1-S7 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation Open
Supp. Fig. 1 Differential methylation across prostate cancer disease states Supp. Fig. 2 NEMO panel design Supp. Fig. 3 Tumor content estimation with a minimal set of informative regions Supp. Fig. 4 Scoring CRPC-NE in circulation with the…
View article: Data from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation
Data from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation Open
Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive therapy response and outcome differences. Histologic transformation to castration-resistant neuroendocrine prostate cance…
View article: Sterile inflammation via TRPM8 RNA-dependent TLR3-NF-kB/IRF3 activation promotes antitumor immunity in prostate cancer
Sterile inflammation via TRPM8 RNA-dependent TLR3-NF-kB/IRF3 activation promotes antitumor immunity in prostate cancer Open
Inflammation is a common condition of prostate tissue, whose impact on carcinogenesis is highly debated. Microbial colonization is a well-documented cause of a small percentage of prostatitis cases, but it remains unclear what underlies th…
View article: International Society for Extracellular Vesicles workshop. QuantitatEVs: Multiscale analyses, from bulk to single extracellular vesicle
International Society for Extracellular Vesicles workshop. QuantitatEVs: Multiscale analyses, from bulk to single extracellular vesicle Open
The “QuantitatEVs: multiscale analyses, from bulk to single vesicle” workshop aimed to discuss quantitative strategies and harmonized wet and computational approaches toward the comprehensive analysis of extracellular vesicles (EVs) from b…
View article: Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation
Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation Open
Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive therapy response and outcome differences. Histologic transformation to castration-resistant neuroendocrine prostate cance…
View article: Establishment and application of patient-derived organoids as a functional system to assess therapy response in bladder cancer
Establishment and application of patient-derived organoids as a functional system to assess therapy response in bladder cancer Open
View article: 1809P Dynamics of plasma tumour DNA and copy number alterations in advanced metastatic castration-resistant prostate cancer (mCRPC) patients treated with cabazitaxel: A prospective biomarker trial
1809P Dynamics of plasma tumour DNA and copy number alterations in advanced metastatic castration-resistant prostate cancer (mCRPC) patients treated with cabazitaxel: A prospective biomarker trial Open
View article: Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients
Integrating extracellular vesicle and circulating cell‐free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients Open
Multi‐analyte liquid biopsies represent an emerging opportunity for non‐invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell‐free DNA (c…