Tag: TP53

Vincerx Pharma Announces Compelling Clinical Efficacy of Enitociclib in Combination with Venetoclax and Prednisone in Lymphoma

Vincerx Pharma, Inc. Investigators from the National Institutes of Health (NIH) report 2 partial responses (PR) in 3 peripheral T-cell lymphoma (PTCL) patients and 1 PR in 2 double-hit diffuse large b-cell lymphoma (DH-DLBCL) patients in ongoing dose-escalation trial of enitociclib in combination with venetoclax and prednisone Vincerx remains on…

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cfDNA Extraction Sensitivity Controls – cfDNA Extraction Sensitivity Controls

Does your cfDNA extraction process affect the Limit of Detection (LOD) of a particular gene target? Our new products, cfDNA Extraction Sensitivity Panels and Extraction Low Positive Controls, can help your research and development for liquid biopsy assays. NEW PRODUCTS: cfDNA EXTRACTION SENSITIVITY PANELS &  CONTROLS The Extraction Sensitivity Controls…

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Identifying Prognostic Genes in Diffuse Large B-cell Lymphoma (DLBCL)

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma, a cancer that starts in cells called lymphocytes, which are part of the body’s immune system. Its progression and prognosis vary significantly among patients, making it crucial to identify prognostic factors that can help predict patient outcomes…

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Dostarlimab/Niraparib Improves PFS Outcomes in Advanced Endometrial Cancer

It was reported that the safety profile of dostarlimab combined with chemotherapy plus maintenance dostarlimab and niraparib in the phase 3 RUBY trial (NCT03981796) was found to be primarily consistent with the known profiles of each drug. Treatment with dostarlimab-gxly (Jemperli) plus carboplatin/paclitaxel followed by maintenance dostarlimab and niraparib (Zejula)…

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[Analysis of the feasibility and prognostic value of circulating tumor DNA monitoring in detecting gene mutations in patients with diffuse large B-cell lymphoma receiving chimeric antigen receptor T-cell therapy]

Objective: To explore the prognostic value of circulating tumor DNA (ctDNA) testing in patients with refractory/relapsed diffuse large B-cell lymphoma (R/R DLBCL) undergoing chimeric antigen receptor T-cell (CAR-T) therapy, and to guide the prevention and subsequent treatment of CAR-T-cell therapy failure. Methods: In this study, 48 patients with R/R DLBCL…

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NM_000546.6(TP53):c.743G>A (p.Arg248Gln) AND Lymphoma – ClinVar

NM_000546.6(TP53):c.743G>A (p.Arg248Gln) AND Lymphoma Based on: 1 submission [Details] Record status: current Accession: RCV000790860.7 Allele description NM_000546.6(TP53):c.743G>A (p.Arg248Gln) Gene: TP53:tumor protein p53 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 17p13.1 Genomic location: Preferred name: NM_000546.6(TP53):c.743G>A (p.Arg248Gln) Other names: p.R248Q:CGG>CAG HGVS: NC_000017.11:g.7674220C>T NG_017013.2:g.18331G>A NM_000546.6:c.743G>AMANE SELECT NM_001126112.3:c.743G>A…

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Extended Follow-up of ALPINE Randomized Phase 3 Study Confirms Sustained Superior Progression-free Survival of Zanubrutinib Versus Ibrutinib for Treatment of Relapsed/Refractory Chronic Lymphocytic Leukemia and Small Lymphocytic Lymphoma (R/R CLL/SLL)

Background ALPINE, a randomized, multinational phase 3 study (NCT03734016) in patients with R/R CLL/SLL, established the statistical and clinically meaningful superiority of zanubrutinib over ibrutinib on progression-free survival (PFS) and overall response rate (ORR) and confirmed the favorable safety/tolerability profile of zanubrutinib (Brown et al. NEJM; 2022). Now, with 3…

Continue Reading Extended Follow-up of ALPINE Randomized Phase 3 Study Confirms Sustained Superior Progression-free Survival of Zanubrutinib Versus Ibrutinib for Treatment of Relapsed/Refractory Chronic Lymphocytic Leukemia and Small Lymphocytic Lymphoma (R/R CLL/SLL)

A STING Operation in neuroendocrine neoplasms | NANETS2023 | NANETS 2023

1Huntsman Cancer Institute, University of Utah, Salt Lake City, UT; 2University of Minnesota, Minneapolis, MN; 3Caris Life Sciences, Phoenix, AZ; 4The Ohio State University, Columbus, OH; 5Fox Chase Cancer Center, Philadelphia, PA; 6Sylvester Cancer Center, University of Miami, Miami, FL; 7Brown University, Providence, RI Background: Significant advances have been made…

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MD Anderson Research Highlights for December

HOUSTON ― The University of Texas MD Anderson Cancer Center’s Research Highlights showcases the latest breakthroughs in cancer care, research and prevention. These advances are made possible through seamless collaboration between MD Anderson’s world-leading clinicians and scientists, bringing discoveries from the lab to the clinic and back. Recent developments at…

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Bioinformatics-based analysis of the relationship between disulfidptosis and prognosis and treatment response in pancreatic cancer

Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…

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Actinium Pharma Reports Results From Phase 3 SIERRA Trial Of Iomab-B – Quick Facts

(RTTNews) – Actinium Pharmaceuticals, Inc. reported results from the Phase 3 SIERRA trial of Iomab-B. The company said Iomab-B achieved the primary endpoint in the SIERRA trial of durable Complete Remission or dCR of at least 6 months with high statistical significance, with 22% of patients randomized to the Iomab-B…

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Current Knowledge About The Impact Of Microgravity On Gene Regulation

The effects of a four-day RPM exposure on the human squamous non-small-cell lung cancer cell line CRL-5889 according to Dietz and co-workers [196] (A–D). (A) The RPM exposure leads to partial detachment of cells from the bottom of the flask and after 24 h to first aggregations (spheroid formation) that…

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Early Diagnosis of High-Grade Serous Ovarian Cancer Feasible

MONDAY, Dec. 11, 2023 (HealthDay News) — Early diagnosis of high-grade serous ovarian cancer (HGSOC) seems feasible through analysis of genomic alterations in DNA from Papanicolaou (Pap) test smears, according to a study published online Dec. 6 in Science Translational Medicine. Lara Paracchini, Ph.D., from Humanitas University in Milan, and…

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Actinium Announces Iomab-B Produces High Response Rates and Significant Improvement in Overall Survival in Relapsed Refractory AML Patients with Active Disease Overcoming TP53 Mutation

  Relapsed or refractory AML patients with TP53 mutation known to have dismal outcomes due to limited effective treatment options   Median Overall Survival of 5.49 months observed in patients with a TP53 mutation receiving an Iomab-B led allogeneic bone marrow transplant compared to 1.66…

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Liquid Biopsy Uses ctDNA to Predict Recurrence of Hodgkin Lymphoma

A Stanford Medicine-led, international study of hundreds of samples from patients with classic Hodgkin lymphoma (cHL) has shown that levels of tumor DNA circulating in the blood can identify those individuals who are responding well to treatment and those who are likely to experience a disease recurrence. The study results suggest…

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Zanubrutinib Showcases Sustained PFS Benefit Vs Ibrutinib in R/R CLL/SLL

Jennifer R. Brown, MD, PhD Zanubrutinib (Brukinsa) continued to demonstrate improved progression-free survival (PFS) benefit over ibrutinib (Imbruvica) in the treatment of patients with relapsed/refractory chronic lymphocytic leukemia (CLL) and small lymphocytic lymphoma (SLL), according to extended follow-up data from the phase 3 ALPINE trial (NCT03734016) presented at the 2023…

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Brukinsa Lengthens Time to Progression in Relapsed/Refractory CLL, SLL

Treatment with Brukinsa (zanubrutinib) led to better progression-free survival (PFS; time from treatment until disease worsening or death) compared with Imbruvica (ibrutinib) in patients with relapsed/refractory chronic lymphocytic leukemia (CLL) and small lymphocytic lymphoma (SLL), according to extended follow-up from the phase 3 ALPINE trial presented at the 2023 American…

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HER2 low expression breast cancer subtyping and their correlation with prognosis and immune landscape based on the histone modification related genes

Barzaman, K. et al. Breast cancer: Biology, biomarkers, and treatments. Int. Immunopharmacol. 84, 106535 (2020). Article  CAS  PubMed  Google Scholar  Siegel, R. L., Miller, K. D., Wagle, N. S. & Jemal, A. Cancer statistics, 2023. CA Cancer J. Clin. 73(1), 17–48 (2023). Article  PubMed  Google Scholar  Mueller, C., Haymond, A.,…

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NOTCH1 mutations predict superior outcomes, NSCLC

Introduction Lung cancer remains the leading cause of cancer-related mortality worldwide, and the majority are non-small-cell lung cancer (NSCLC).1,2 Genetic variation is a typical feature of NSCLC that drives cancer initiation and progression.3 Understanding the role of mutated genes in NSCLC is the basis of the development of novel treatment…

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Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq

Abstract Background: Alzheimer’s disease is the most common cause of dementia and is characterized by amyloid-β plaques, tau neurofibrillary tangles, and neuronal loss. Although neuronal loss is a primary hallmark of Alzheimer’s disease, it is known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis and neuronal health…

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Histologically Transformed MZL May Be Distinct Tumor Type

The clinicopathologic and genetic features of marginal zone lymphomas (MZL) with histologic transformation (HT-MZL) suggest that they may be a distinct tumor type from other MZLs. In addition, the higher rates of TBL1XR1 mutations in HT-MZL suggest this could be a predictor for transformation. The study, which was published in…

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Maintenance Selinexor Shows PFS in TP53 Wild-type Endometrial Cancer

Selinexor did not show a clinically meaningful improvement in the general study population. Maintenance selinexor (Xpovio) showed a significant progression-free survival (PFS) benefit compared with placebo in a subgroup of patients with TP53 wild-type advanced/recurrent endometrial cancer, according to findings from the phase 3 ENGOT-EN5/GOG-3055/SIENDO trial (NCT03555422).1,2 Data from the…

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Revisiting Reddy: A DLBCL Do-over

Abstract The 2017 study by Reddy et al described the comprehensive characterization of somatic drivers of diffuse large B-cell lymphoma using whole exome sequencing. After additional large studies relying on exome or whole genome sequencing were published, several oddities unique to the Reddy results have emerged. Seeking to explain the…

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Selinexor Maintenance Leads to PFS Benefit in TP53 Wild-Type Advanced/Recurrent Endometrial Cancer

Maintenance therapy with selinexor (Xpovio) improved progression-free survival (PFS) compared with placebo in patients with TP53 wild-type advanced or recurrent endometrial cancer, regardless of microsatellite instability (MSI) status, according to long-term follow-up data from the phase 3 ENGOT-EN5/GOG-3055/SIENDO trial (NCT03555422)presented at the 2023 IGCS Annual Global Meeting.1 At a median…

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Discovery from public data (GEO, SRA and more) using Ingenuity Pathway Analysis

Per user feedback, we are hosting a comprehensive training on how to effectively use sample level public data and metadata from sources like GEO, SRA, TCGA, GTEx, Blueprint, CCLE and other sources through Ingenuity Pathway Analysis (IPA) and IPA Analysis Match Explorer feature. The trainer will walk through usecases in…

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Using Genomic Profiling to Provide Personalized Medicine in MDS

Myelodysplastic syndromes (MDS) is a group of clonal hematopoietic neoplasms characterized by the combination of persistent unexplained cytopenia (or cytopenias) and morphologic dysplasia and a propensity to progress to bone marrow failure or acute myeloid leukemia (AML).1 The treatment landscape for MDS is continually progressing and involves a multidisciplinary approach…

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10 Studies on InnoCare’s Oncology Pipelines Selected at the Upcoming 65th Annual Meeting of ASH

BEIJING, November 15, 2023–(BUSINESS WIRE)–InnoCare Pharma (HKEX: 09969; SSE: 688428), a leading biopharmaceutical company focusing on the treatment of cancer and autoimmune diseases, announced today that 10 studies from InnoCare’s oncology pipeline were selected for presentation at the 65th American Society of Hematology (ASH) Annual Meeting on December 9-12, 2023…

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Biomedicines | Free Full-Text | Association between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor Specimens: Data from Two Independent Molecularly-Characterized Cohorts

1. Introduction Pancreatic ductal adenocarcinoma (PDAC) has one of the highest case-specific mortality rates of all cancers [1]. Although resection remains the only curative therapy for PDAC, improvements in long-term survival are attributable to advances in systemic treatment [2,3,4,5]. Currently, 5-fluorouracil-based (i.e., with irinotecan and oxaliplatin as FOLFIRINOX) or gemcitabine-based…

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Pioneering study finds predictive biomarker in lung adenocarcinoma

In a recent study published in Nature Communications, researchers from the United States of America (USA) investigated the potential of the transcriptome of tumor-adjacent normal lung tissue in predicting the prognosis of lung cancer. They found that molecular profiling of the tumor-adjacent normal (TAN) lung tissue, rather than the tumor…

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Dr Baretti on the Mechanisms of Resistance Associated With FGFR2+ Cholangiocarcinoma

Marina Baretti, MD, assistant professor, oncology, Johns Hopkins Medicine, discusses innate and acquired mechanisms of resistance in patients with unresectable, advanced, or metastatic intrahepatic cholangiocarcinoma harboring FGFR2 gene fusions or rearrangements. Although previous data have demonstrated the efficacy of approved FGFR-targeted agents, such as pemigatinib (Pemazyre) and infigratinib (Truseltiq), in…

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The power and potential of mitochondria transfer

Roger, A. J., Muñoz-Gómez, S. A. & Kamikawa, R. The origin and diversification of mitochondria. Curr. Biol. 27, R1177–R1192 (2017). Article  CAS  PubMed  Google Scholar  Monzel, A. S., Enríquez, J. A. & Picard, M. Multifaceted mitochondria: moving mitochondrial science beyond function and dysfunction. Nat. Metab. 5, 546–562 (2023). Article  PubMed …

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Clonal Hematopoiesis and Cardiovascular Disease in Patients With Multiple Myeloma Undergoing Hematopoietic Cell Transplant | Cardiology | JAMA Cardiology

Key Points Question  Is clonal hematopoiesis of indeterminate potential (CHIP) detected at the time of hematopoietic stem transplant (HCT) associated with increased rates of cardiovascular disease (CVD) among patients with multiple myeloma (MM) following HCT? Finding  In this cohort study of patients with MM undergoing HCT, CHIP was highly prevalent…

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Adding median to Violin Plots ggplot2

Hello All, I want to make grouped violin plots from a table. I have a table of the following format: Cell_Id Cell_Type nox4_expr TP53 AAA1_AAACCCAAGGCCGCTT-1 Fibroblasts no_NOX4_Cells 0.42292722 AA1_AAACCCAGTATTTCGG-1 Smooth_Muscle_Cells no_NOX4_Cells -1.02533342 AAA1_AAACGAACAGGCTATT-1 Endothelial_Cells no_NOX4_Cells -1.23918040 AAA1_AAACGCTCACAAGTGG-1 Smooth_Muscle_Cells no_NOX4_Cells -0.30592846 AAA1_AAAGAACAGGAAAGGT-1 Smooth_Muscle_Cells no_NOX4_Cells -0.73323183 AAA1_AAAGGGCAGATGCCGA-1 Smooth_Muscle_Cells no_NOX4_Cells 0.75156034 AAA1_AAAGGTATCTGTCCCA-1 Endothelial_Cells…

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Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…

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Unveiling the transcriptomic and epigenetic secrets across 11 tumors

In a recent study published in Nature, researchers created a pan-tumor transcriptomic and epigenetic atlas using single-nucleus chromatin accessibility information and matched ribonucleic acid (RNA)-sequencing data. Study: Epigenetic regulation during cancer transitions across 11 tumour types. Image Credit: ART-ur/Shutterstock.com The researchers studied the spatiotemporal dynamics of chromatin decondensation and transcriptional…

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Patient-derived xenograft models of ALK+ ALCL reveal preclinical promise for therapy with brigatinib

. 2023 Sep;202(5):985-994. doi: 10.1111/bjh.18953. Epub 2023 Jun 25. Nina Prokoph  1 , Jamie D Matthews  1 , Ricky M Trigg  1 , Ivonne A Montes-Mojarro  2 , G A Amos Burke  3 , Falko Fend  2 , Olaf Merkel  4 , Lukas Kenner  4   5   6   7 , Birgit Geoerger  8   9 , Robert…

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Bioinformatics analysis and experimental validation of tumorigenic role of PPIA in gastric cancer

Expression of PPIA in pan-cancer and prognostic value of PPIA in GC To assess the effects of PPIA on the genesis of human tumor, TCGA database was utilized to detect the mRNA levels of PPIA in 33 types of cancer. The findings demonstrated that the levels of PPIA were upregulated…

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Geron Corporation Eyes $3.5 Billion Opportunity in MDS and MF Treatment Market By Investing.com

© Reuters. Geron (NASDAQ:) Corporation (NASDAQ:GERN) has updated its progress and plans during its third quarter 2023 earnings conference call, highlighting the potential of its drug imetelstat for the treatment of lower-risk myelodysplastic syndromes (MDS) and myelofibrosis (MF). The company has submitted a New Drug Application (NDA) for imetelstat, which…

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Karyopharm Therapeutics Reports Q3 2023 Financial Results, Highlights Strong Position for Growth By Investing.com

© Reuters. Karyopharm Therapeutics (NASDAQ: NASDAQ:) has reported its financial results for the third quarter of 2023, noting a strong position for growth backed by its pipeline of innovative oral selective inhibitors and nuclear export. The company expects total revenues of $145 million to $160 million in 2023, and anticipates…

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CRISPR screening in hematology research: from bulk to single-cell level | Journal of Hematology & Oncology

Transcriptomics CROP-seq [46] Jurkat Poly-A CRISPRko Cas9 119 – 5798 (+ 1320 cells with NT gRNA) Lentiviral DROP-seq RNA Perturb-seq [43, 44] K562 Barcode CRISPRi dCas9-KRAB UPR epistasis screen: 9 triplet combinations UPR Perturb-seq experiment: 91 Up to 3 gRNAs in a single vector UPR epistasis screen: 15006 UPR Perturb-seq experiment:…

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Geron IMerge Phase 3 Presentations at Upcoming ASH Annual Meeting Reinforce Significant Durability and Breadth of Effect of Imetelstat in Lower Risk MDS

FOSTER CITY, Calif.–(BUSINESS WIRE)–Geron Corporation (Nasdaq: GERN), a late-stage clinical biopharmaceutical company, today announced the publication of abstracts from the IMerge Phase 3 clinical trial evaluating its first-in-class investigational telomerase inhibitor imetelstat in patients with lower risk myelodysplastic syndromes (MDS). Four abstracts have been accepted for presentation at the 65th…

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DIFFERENCES IN MUTATIONAL SIGNATURE OF DIFFUSE LARGE… : HemaSphere

Abstract Topic: 20. Lymphoma Biology & Translational Research Background: Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous entity. Recently, the updated World Health Organization classification and The International Consensus Classification have suggested a more subdivided categorization of DLBCL. Moreover, comprehensive molecular subtyping of DLBCL through genetic profiling has broadened…

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New blood test revolutionizes early cancer detection in Li-Fraumeni Syndrome patients

By Dr. Sushama R. Chaphalkar, PhD.Oct 29 2023Reviewed by Sophia Coveney In a study published in Cancer Discovery, researchers from Canada tested the use of a multimodal liquid biopsy assay based on cell-free DNA (cfDNA) for early cancer detection in patients with Li-Fraumeni syndrome. As early detection is associated with…

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Phase 2 GUIDANCE Trial of R-CHOP-X Meets Primary End Point in DLBCL

Red blood cells: © vipman4 – stock.adobe.com Rituximab (Rituxan), cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) alone or combined with targeted agents (R-CHOP-X) demonstrated efficacy and safety in patients with newly diagnosed, intermediate-risk, or high-risk diffuse large B-cell lymphoma (DLBCL), according to findings published in Cancer Cell.1 In the randomized, phase…

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What Factors Influence ALCL Cancer With Breast Implants?

What Factors Influence ALCL Cancer With Breast Implants? Skip To Main Content Home/Blog/ALCL update- findings from 248 cases Posted on October 24, 2023 This is out of the Aesthetic Journal. It was a retrospective study looking at 248 cases of BIA ALCL.  This isn’t adding a ton to what…

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Proteomics uncovers molecular features for relapse risk stratification in patients with diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid cancer, constituting approximately one third of all cases [1]. Although immunochemotherapy cures ~60–75% of patients, a significant proportion of patients still experience relapse [2, 3]. Relapsed DLBCL patients have poor outcomes, with a median overall survival of only 6.3 months…

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Liquid Biopsy Provides Earlier Detection of an Inherited Cancer

Credit: AlexRaths/iStock Researchers at the Hospital for Sick Children (SickKids), the Ontario Institute for Cancer Research (OICR), and the University Health Network (UHN) have developed a liquid biopsy that an initial study has shown provides earlier detection cancer in individuals with Li-Fraumeni syndrome (LFS) than existing methods. LFS is hereditary…

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Life with ‘an almost 100 per cent risk’ of getting cancer

Luana Locke has survived five different kinds of cancer. Her first diagnosis — breast cancer at age 25 while pregnant with her first child — triggered genetic testing that revealed she had a rare hereditary disorder that made it almost certain she would face the disease again in her lifetime….

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Liquid Biopsy Detects Cancer Earlier in Patients with Inherited Disorder

Researchers at the Hospital for Sick Children (SickKids), the Ontario Institute for Cancer Research (OICR), and the University Health Network (UHN) have developed a method for analyzing blood samples that an initial study has shown can detect cancer in individuals with Li-Fraumeni syndrome (LFS) earlier than existing surveillance methods. LFS…

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Circulating Tumor DNA from Ascites as an alternative to tumor sampling for genomic profiling in ovarian cancer patients | Biomarker Research

To the editor, Genomic testing is crucial for the management of ovarian cancer (OC). Approximately 25% of high-grade OC have germline or somatic BRCA1 or BRCA2 mutations [1]. 50% of high-grade OC are homologous recombination deficient (HRD). HRD is defined by the detection of a BRCA1 or BRCA2 mutation, or…

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Genetic Testing for Breast Cancer

Genetic testing in breast cancer allows for personalized treatment that can improve patient outcomes, but it can be challenging to implement genetic testing in practice, according to experts.1-5 Genetic testing results can inform decisions about the extent of breast surgery, the optimal systemic treatment, and whether a patient should avoid…

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The role and impact of alternative polyadenylation and miRNA regulation on the expression of the multidrug resistance-associated protein 1 (MRP-1/ABCC1) in epithelial ovarian cancer

Domcke, S. et al. Evaluating cell lines as tumour models by comparison of genomic profiles. Nat. Commun. 4, 2126 (2013). Article  ADS  PubMed  Google Scholar  Köbel, M. et al. Ovarian carcinoma subtypes are different diseases: Implications for biomarker studies. PLoS Med. 5(12), e232 (2008). Article  PubMed  PubMed Central  Google Scholar …

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DLBCL News Briefs – Page 2 of 10

News Briefs » DLBCL News Briefs » Page 2 MicroRNA Sequencing May Detect DLBCL Biomarker Patterns MicroRNA sequencing can detect specific patterns in patients with diffuse large B-cell lymphoma (DLBCL) that could be used to guide diagnosis and treatment and assess prognosis, according to a recently published study in the journal…

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Bioconductor BulkRNAseq

Comment: deseq2 filter the low counts by Michael Love 40k You can’t filter the groups separately, you need to use a non-specific filter that doesn’t make use of information about which samples are … Comment: deseq2 filter the low counts by daiane.hemerichbrennan • 0 Hi Michael, I have another question…

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Scientists Discover How Genetics Helps Clarify Childhood Most Cancers

Scientists find how genetics can help clarify childhood cancer – Situations of India WASHINGTON: With an over-all survival fee of a lot more than 85% five several years right after prognosis, the quantity of kids most cancers survivors in the United States is climbing. Nevertheless, survivors could continue to be…

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Human endogenous retroviruses as epigenetic therapeutic targets in TP53-mutated diffuse large B-cell lymphoma

TP53 mutation (TP53mut) occurs in 10-20% of diffuse large B-cell lymphoma (DLBCL) cases and serves as an unfavorable biomarker of DLBCL progression. It confers resistance to immunochemotherapy, high-dose chemotherapy, autologous stem cell transplantation, and anti-CD19 chimeric antigen receptor T-cell therapy. Therapeutic targeting of TP53mut remains a significant challenge in DLBCL…

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The XRCC1 and TP53 gene polymorphisms are associated with advanced-stage disease and early distant metastasis at diagnosis in non-small cell lung cancer

Background: Studies on single nucleotide polymorphisms (SNPs) in non-small cell lung cancer (NSCLC) suggest that DNA repair capacity may have prognostic implications for disease recurrence and survival. However, there is no study investigating the relationship between SNPs and the risk of metastasis at the time of initial diagnosis in patients…

Continue Reading The XRCC1 and TP53 gene polymorphisms are associated with advanced-stage disease and early distant metastasis at diagnosis in non-small cell lung cancer

Diagnosing and monitoring pancreatic cancer through cell-free DNA methylation: progress and prospects | Biomarker Research

The exploration of methylated biomarkers in plasma for pancreatic cancer is still in its early stages, and the number of studies conducted to date for this purpose is limited. Analysis of cfDNA methylation patterns in pancreatic cancer has been approached both at the whole genome level and by identifying and…

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Childhood cancer survivors’ mortality risk

Researchers find genetic explanation for increased risk of developing second cancers. A high-magnification of the hydrogel (in blue) encapsulating T cell-activating platelets (in red) and nanoparticles that release a drug to inhibit tumor-boosting cells (in green). This gel inhibited the growth of cancer cells after surgical removal of different types…

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FDA Grants Marketing Authorization to First DNA Test to Assess Genetic Predisposition to Select Cancers

The FDA has granted de novo marketing authorization for the Invitae Common Hereditary Cancers Panel, an in vitro diagnostic test designed to detect genetic variants associated with an elevated risk of developing certain types of cancer.1 Additionally, the panel could also help identify potential cancer-associated variants in patients who have…

Continue Reading FDA Grants Marketing Authorization to First DNA Test to Assess Genetic Predisposition to Select Cancers

Host genetics helps explain childhood cancer survivors’ mortality risk from second cancers

Newswise — (MEMPHIS, Tenn. – October 02, 2023) The population of childhood cancer survivors in the U.S. is increasing, with an overall childhood cancer survival rate greater than 85% five years after diagnosis. However, survivors can still be at increased risk of various health conditions, including second cancers. Using data…

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PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology

Tissue samples A total of 84 analytic samples from surgical or biopsy specimens were collected from 84 patients who underwent radical surgery for CRC at Saitama Medical University International Medical Center between January and December 2016. One case was excluded because the specimen was too small; therefore, we used a…

Continue Reading PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology

Gilead Discontinues Phase 3 ENHANCE-2 Trial of Magrolimab Plus Azacitidine in TP53-Mutant AML

Gilead Discontinues Phase 3 ENHANCE-2 Trial | Image Credit: ©freshidea – stock.adobe.com The phase 3 ENHANCE-2 trial (NCT04778397) examining the frontline combination of magrolimab and azacitidine (Vidaza) vs physician’s choice of venetoclax (Venclexta) with azacitidine or intensive chemotherapy in patients with acute myeloid leukemia and TP53 mutations has been discontinued,…

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Genes Linked to Aggressive Prostate Cancer

Researchers say they have identified genes that should be considered for gene panel testing in prostate cancer. The researchers found evidence to suggest that variants in BRCA2, ATM, NBN, MSH2, XRCC2, and MRE11A are associated with aggressive prostate cancer. These findings were published in JAMA Oncology. For this study, researchers…

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Inhibition of PLK4 remodels histone methylation and activates immune response via cGAS-STING pathway in TP53 mutated AML | Blood

Citation Cheuk Him Man, Wing Lam, Chee Chean Dang, Xiao-yuan Zeng, Li-Chuan Zheng, Natalie Nok-Man Chan, Nelson K. L. Ng, Koon-Chuen Chan, Tsz-Ho Kwok, Timothy Chi-Chun Ng, Wing Yan Leung, Michael Huen, Carmen Chak-Lui Wong, Chi Wai Eric So, Zhixun Dou, Susumu Goyama, Mark Robert Bray, Tak Wah Mak, Anskar…

Continue Reading Inhibition of PLK4 remodels histone methylation and activates immune response via cGAS-STING pathway in TP53 mutated AML | Blood

Leukemic Presentation and Progressive Genomic Alterations of MCD/C5 Diffuse Large B-cell Lymphoma (DLBCL)

Diffuse large B-cell lymphoma (DLBCL) is a very heterogenous group, subdivided into germinal-center (GC)-derived and activated B-cell (ABC) types. Advances in molecular methodologies, including whole exome sequencing (WES) and chromosomal microarrays (CMA), have fostered molecular subclassification of DLBCL, while improving our understanding of their pathogenic mechanisms and resistance to therapy….

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I need to retrieve a set of protein and mRNA sequences

Using EntrezDirect: $ esearch -db gene -query ‘7157’ | elink -db gene -target nuccore -name gene_nuccore_refseqrna | efetch -format fasta | grep “>” >NR_176326.1 Homo sapiens tumor protein p53 (TP53), transcript variant 14, non-coding RNA >NM_001407264.1 Homo sapiens tumor protein p53 (TP53), transcript variant 10, mRNA >NM_001407263.1 Homo sapiens tumor…

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median survival time doesn’t match plot

maftools – median survival time doesn’t match plot 0 Hello all, I’m using maftools in R to plot some basic survival curves based on gene mutation, for example: mafSurvival(maf = TCGA_maf, genes = “TP53”, time = “overall_survival”, Status = “deceased”) I get the following output plot: The output text from…

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Real world evidence reveals improved survival outcomes in biliary tract cancer through molecular matched targeted treatment

Patient characteristics In our analysis, we included patients with biliary tract cancer and available comprehensive molecular characterization data from five Austrian cancer centers. The data cut-off date was September 2022 (Fig. 1). Figure 1 Trial design: Flow chart depicting patient allocation. In total, the molecular profile of 159 patients with biliary…

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Despite Early Success, Karyopharm’s Selinexor Faces Uncertain Path to Expansion

Pictured: a bone marrow slide showing multiple myeloma/iStock, Md Saiful Islam Khan Ever since Karyopharm Therapeutics gained accelerated FDA approval for selinexor combined with dexamethasone in relapsed or refractory multiple myeloma, the Massachusetts–based company has been conducting clinical trials with an eye toward increasing its market share, primarily in the…

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A biobank of pediatric patient-derived-xenograft models in cancer precision medicine trial MAPPYACTS for relapsed and refractory tumors

Patient characteristics and PDX establishment Between February 2016 and July 2020, 787 pediatric, adolescent and young adult patients with recurrent or refractory malignancies were enrolled in the MAPPYACTS trial;2 756 (96%) patients and their parents consented to the optional ancillary study of preclinical model development (Fig. 1a). 744 patients had a…

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Differences in mutational signature of diffuse large B-cell lymphomas according to the primary organ

Background: Comprehensive molecular subtyping of diffuse large B-cell lymphoma (DLBCL) through genetic profiling has broadened our understanding of DLBCL biology. In this study, we investigated whether DLBCL, not otherwise specified (NOS) shows differences in mutational patterns depending on the primary organ. Patients and methods: Panel-based next-generation sequencing was performed on…

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Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA

Diagnosing post-transplant lymphoproliferative disorder (PTLD) is challenging and often requires invasive procedures. Analyses of cell-free DNA (cfDNA) isolated from plasma is minimally invasive and highly effective for genomic profiling of tumors. We studied the feasibility of using cfDNA to profile PTLD and explore its potential to serve as a screening…

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The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer

Genomic analysis and cohort description We generated whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data from tumors and blood samples from 27 advanced urothelial cancer patients treated with anti-PD-1/PD-L1 ICIs at Hospital del Mar (Fig. 1a). WES data was obtained from the tumors before treatment as well as from blood samples,…

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DNA/RNA Sequencing Aids Subsequent Treatment Selection in HCC/H-CCK Post Atezolizumab/Bevacizumab

Tissue- and blood-based molecular analysis could help match patients with advanced hepatocellular carcinoma (HCC) or hepatocholangiocarcinoma (H-CCK) following disease progression on frontline atezolizumab (Tecentriq) and bevacizumab (Avastin) to targeted therapy or another TKI based on identified genomic alterations, according to retrospective findings from a single-center study presented at the 2023…

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Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA | Journal of Hematology & Oncology

The median age of the patients was 55 years (range 13–74). Median time between SOT and PTLD was 95 months (range 2–338). Most patients had stage IV disease (n = 13, 76%) with a median metabolic tumor volume (MTV) of 302 mL (range 5–2070 mL). Lactate dehydrogenase (LDH) levels ranged from 210 to 5068 (Additional file…

Continue Reading Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA | Journal of Hematology & Oncology

Genetic Cancer Hereditary Cancer Mutations Susceptibility To Cancer Genetic Changes

Genetic Cancers: Welcome back to “The Science Of Health”, ABP Live’s health column. Last time, in the health column, we discussed the difference between small cell lung cancers and non-small cell lung cancers, and explained why small cell lung cancers are less common than non-small cell lung cancers, despite the…

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Cell-free DNA chromosome copy number variations predict outcomes in plasma cell myeloma

Testing for measurable residual disease (MRD) in persons with plasma cell myeloma (PCM) after therapy correlates with therapy outcomes including progression-free survival (PFS) and survival (reviewed in refs. [1, 2]). Most MRD-testing in this setting uses multi-parameter flow cytometry (MPFC) but prediction accuracy is imperfect with C-statistics of only about…

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Challenging interpretation of germline TP53 variants based on the experience of a national comprehensive cancer centre

Subjects TP53 gene was investigated in 880 consecutive oncology patients referred for molecular genetic testing at our national centres (Department of Laboratory Medicine, Semmelweis University and Department of Molecular Genetics, National Institute of Oncology) between 2021 and 2022. This cohort consisted of patients with potential hereditary tumour predisposition. Their genetic…

Continue Reading Challenging interpretation of germline TP53 variants based on the experience of a national comprehensive cancer centre

Allogeneic HCT Improves Survival Rates for TP53-Mutated MDS

This article was originally published by Targeted Oncology. This version has been edited. Allogeneic hematopoietic cell transplantation (HCT) improved overall survival (OS) vs non-HCT treatment in patients with myelodysplastic syndrome (MDS) harboring TP53 mutations.1 The findings come from a study performed at Dana-Farber Cancer Institute and published in the Journal…

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Similarities Found Among Bladder Cancer Affecting Cats, Dogs, People

Bladder cancer affecting cats and dogs could serve as a model for the disease among humans, a new study finds. Researchers from the Wellcome Sanger Institute, the University of Guelph in Ontario, and elsewhere performed whole-exome sequencing on 87 urothelial carcinomas from dogs and 23 from cats. Urothelial carcinomas affecting…

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Multiparameter prediction of myeloid neoplasia risk

Data acquisition UKB is a large-scale biomedical database and research resource containing genetic, lifestyle and health information from half a million UK participants. UKB has approval from the North West Multicentre Research Ethics Committee (11/NW/0382) and all participants provided written informed consent. The present study has been conducted under approved…

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Screening Market Poised for Remarkable 12.4% CAGR Surge, Projected to Reach US$ 4.32 Billion by 2033 | FMI

  The global Carrier Screening Market is expected to record a CAGR of 12.4% between 2023 and 2033, with a size estimated in 2023 at US$ 1,343.40 million. The market’s value is expected to rise to US$ 4,323.84 million by 2033. As a result of increased funding from the public and…

Continue Reading Screening Market Poised for Remarkable 12.4% CAGR Surge, Projected to Reach US$ 4.32 Billion by 2033 | FMI

High-Risk MDS Patients May Benefit from Allogenic Transplants

Study Title: Allogeneic Hematopoietic Cell Transplantation Improves Outcome in MDS across High-Risk genetic subgroups: Genetic analysis of the BMT CTN 1102 study Publication: Journal of Clinical Oncology, Click here for link Dana-Farber Authors: Jurjen Versluis, MD; Christopher J. Gibson, MD; Corey Cutler, MD, MPH, FRCPC; R. Coleman Lindsley, MD, PhD…

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Common variants of eNOS and XRCC1 genes may predict acute skin toxicity in breast cancer patients receiving radiotherapy after breast conserving surgery

Purpose: To evaluate the impact of functional polymorphisms in genes related to DNA repair mechanisms (XRCC1, TP53, MSH2, MSH3, XPD), oxidative stress response (GSTP1, GSTA1, eNOS, SOD2) and fibroblast proliferation (TGFb1) on the risk of acute skin toxicity in breast cancer patients receiving radiotherapy. Material and methods: Skin toxicity was…

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AlloSCT leads to long-term remissions in TP53-mutated MCL

Key clinical point: Allogeneic stem cell transplantation (alloSCT) results in long-term disease control in patients with mantle cell lymphoma (MCL), including those with TP53-mutated disease, and should be considered for earlier use in these high-risk patients who are unresponsive to conventional chemoimmunotherapy. Major finding: The estimated overall survival rates were…

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What is the best way to combine machine learning algorithms for feature selection such as Variable importance in Random Forest with differential expression analysis?

NB – this answer has been updated January 28th, 2020 Update: It is important to point out that the assumptions of RandomForest® differ from those of, e.g., a regression model. So, RandomForest® and other classification algorithms certainly must be considered. Just use my general pointers here as just that, i.e.,…

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Ex vivo expansion of lung cancer-derived disseminated cancer cells from lymph nodes identifies cells associated with metastatic progression

doi: 10.1002/ijc.34658. Online ahead of print. Steffi Treitschke  1 , Kathrin Weidele  1 , Adithi Ravikumar Varadarajan  1 , Giancarlo Feliciello  1 , Jens Warfsmann  1 , Sybille Vorbeck  1 , Bernhard Polzer  1 , Catherine Botteron  1 , Martin Hoffmann  1 , Vadim Dechand  1 , Tobias Mederer  2 , Florian Weber  1   3 , Melanie Werner-Klein  2 , Tobias Robold …

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PhD / Doctoral position in Biomedical Data Sciences & Bioinformatics for studying the role of mutant TP53 in cancer development and progression

The start date is as early as possible or by agreement. The position is available for three years. The University of Konstanz is one of the eleven Excellence Universities in Germany. Since 2007 it has been successful in the German Excellence Initiative and its follow-up programme, the Excellence Strategy. This…

Continue Reading PhD / Doctoral position in Biomedical Data Sciences & Bioinformatics for studying the role of mutant TP53 in cancer development and progression

Low-dose radiation induces unstable gene expression in developing human iPSC-derived retinal ganglion organoids

RGCs from human iPSCs for genomic analysis We developed neuronal organoids, including RGCs from human iPSCs, to assess the effects of low-dose irradiation. Phase-contrast microscopy (Supple Fig. S1a) indicated time-dependent morphological changes in the embryonal body formed from human iPSCs, which corresponded to previous reports14, 15. Retinal development was evaluated…

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Myeloid Cancer Panel cfDNA Reference Standard

The Myeloid Cancer Panel cfDNA reference standard is a well-characterized cell line-derived control which contains 15 clinically-relevant variants across 14 genes. This cell-free DNA reference material allows labs to perform reliable and cost-effective validations of myeloid cancer liquid biopsy assays. QC pipelines are supported by controls manufactured under ISO:13485 with…

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2023-08-02 | NDAQ:KPTI | Press Release

– Achieved Second Quarter 2023 Total Revenue of $37.6 Million and U.S. XPOVIO® (selinexor) Net Product Revenue of $28.5 Million – – Maintains Full Year 2023 Total Revenue Guidance of $145 Million to $160 Million, Including U.S. XPOVIO Net Product Revenue Guidance of $110 Million to $125 Million – –…

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Selinexor Maintenance Improves PFS in TP53 Wild-Type Endometrial Cancer

Patients with TP53 wild-type endometrial cancer had longer progression-free survival (PFS) when they received selinexor maintenance in a phase 3 trial. The PFS benefit was even more pronounced among patients with microsatellite stable (MSS) disease. However, selinexor maintenance did not improve PFS among patients with TP53-mutant endometrial cancer. These results,…

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Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics | Cancer Research

We observed a total of 4,510 true somatic mutations in 3,391 genes in the 146 primary breast tumors (Supplementary Table S2). The number of mutations per individual varied from 2 to 225. Using MutSigCV, we found that mutations in PIK3CA, TP53, GATA3, MAP3K1, CDH1, CBFB, PTEN, and RUNX1 were significant…

Continue Reading Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics | Cancer Research

SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response

SF3B1 MUT cells show selective sensitivity to PARP inhibitors To identify candidate therapeutic targets for cancers with SF3B1 hotspot mutations, we utilized the leukemia K562K700E (SF3B1K700E) and parental (SF3B1WT) isogenic cells1, to model one of the most prevalent SF3B1 hotspot mutations seen in patients8,19,20 (Fig. 1a,b and Supplementary Fig. 1a)….

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Analysis Helps Distinguish the Molecular Profile of Intraductal Carcinoma of the Prostate

Patients with intraductal carcinoma of the prostate harbored several alterations in DNA damage repair (DDR) genes that may be clinically actionable, and they had high frequency of alterations associated with poor disease prognosis, according to a molecular analysis presented at the 2023 ASCO Annual Meeting. Better understanding the genetic profile…

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DNA Sequencing: Another Weapon Against Cancer

Gene mutations and dysregulation of cellular pathways lead to the creation of cancer cells and potentially to tumour formation. Usually, the genes involved in tumour formation are oncogenes and tumour suppressor genes. Most oncogenes begin as proto-oncogenes. Proto-oncogenes are normally regulating cell proliferation, growth and differentiation and they control cell…

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Annual Clinical Update on MDS Sees Hope in Precision Medicine, Use of Oral Therapy

The Annual Clinical Update in Hematological Malignancies, appearing online in early June and now publishing in the August issue of the American Journal of Hematology (AJH), includes an update on myelodysplastic syndromes by Guillermo Garcia-Manero, MD, who leads the MDS Section in the Department of Leukemia at The University of…

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Selinexor Maintenance Demonstrates Efficacy in TP53 Wild-Type Advanced Endometrial Cancer Following Frontline Chemotherapy

Compared with placebo, selinexor (Xpovio) maintenance therapy garnered superior progression-free survival (PFS) in patients with TP53 wild-type advanced or recurrent endometrial cancer who had received chemotherapy as frontline treatment, according to updated data from a prespecified subgroup analysis of the phase 3 SIENDO trial (NCT03555422).1 Long-term findings presented at the 2023 ASCO…

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microRNA sequencing for biomarker detection in the diagnosis, classification and prognosis of Diffuse Large B Cell Lymphoma

In this study, we identified new signatures of miRNAs of relevance in DLBCL with potential to improve diagnosis, subtype characterization and treatment response through small RNA sequencing. To our knowledge, few reports exist in which miRNA sequencing were used to identify miRNA signatures in cancer, and only one which analyzed…

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