keyword
https://read.qxmd.com/read/38509111/allele-specific-transcriptional-effects-of-subclonal-copy-number-alterations-enable-genotype-phenotype-mapping-in-cancer-cells
#21
JOURNAL ARTICLE
Hongyu Shi, Marc J Williams, Gryte Satas, Adam C Weiner, Andrew McPherson, Sohrab P Shah
Subclonal copy number alterations are a prevalent feature in tumors with high chromosomal instability and result in heterogeneous cancer cell populations with distinct phenotypes. However, the extent to which subclonal copy number alterations contribute to clone-specific phenotypes remains poorly understood. We develop TreeAlign, which computationally integrates independently sampled single-cell DNA and RNA sequencing data from the same cell population. TreeAlign accurately encodes dosage effects from subclonal copy number alterations, the impact of allelic imbalance on allele-specific transcription, and obviates the need to define genotypic clones from a phylogeny a priori, leading to highly granular definitions of clones with distinct expression programs...
March 20, 2024: Nature Communications
https://read.qxmd.com/read/38508940/prostatic-adenocarcinoma-molecular-underpinnings-and-treatment-related-options
#22
REVIEW
Divyangi Paralkar, Amir Akbari, Manju Aron
Prostate cancer is heterogeneous with varied pathologic features and presents with a wide spectrum of clinical manifestations from indolent to advanced cancer. Interrogation of the molecular landscape of prostate cancer has unveiled the complex genomic alterations in these tumors, which significantly impacts tumor biology. The documented array of chromosomal alterations, gene fusions, and epigenetic changes not only play a crucial role in oncogenesis and disease progression, but also impacts response and resistance to various therapeutic modalities...
March 19, 2024: Urologic Oncology
https://read.qxmd.com/read/38506240/integration-of-hepatitis-b-virus-into-patients-sperm-genome-and-its-clinical-risks
#23
JOURNAL ARTICLE
Ting-Ting Han, Ji-Hua Huang, Ling-Xiao Li, Xue Liao, Xiang-Qian Meng, Zi-Na Wen, Qian Sun, Jian Ma, Tian-Hua Huang
BACKGROUND: Like the coronavirus disease 2019, the hepatitis B virus is also wreaking havoc worldwide, which has infected over 2 billion people globally. Using an experimental animal model, our previous research observed that the hepatitis B virus genes integrated into human spermatozoa can replicate and express after being transmitted to embryos. However, as of now, this phenomenon has not been confirmed in clinical data from patients. OBJECTIVES: To explore the integration of the hepatitis B virus into patients' sperm genome and its potential clinical risks...
March 20, 2024: Andrology
https://read.qxmd.com/read/38504345/epigenetic-mlh1-silencing-concurs-with-mismatch-repair-deficiency-in-sporadic-naturally-occurring-colorectal-cancer-in-rhesus-macaques
#24
JOURNAL ARTICLE
Simon Deycmar, Brendan J Johnson, Karina Ray, George W Schaaf, Declan Patrick Ryan, Cassandra Cullin, Brandy L Dozier, Betsy Ferguson, Benjamin N Bimber, John D Olson, David L Caudell, Christopher T Whitlow, Kiran Kumar Solingapuram Sai, Emily C Romero, Francois J Villinger, Armando G Burgos, Hannah C Ainsworth, Lance D Miller, Gregory A Hawkins, Jeff W Chou, Bruno Gomes, Michael Hettich, Maurizio Ceppi, Jehad Charo, J Mark Cline
BACKGROUND: Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers. METHODS: We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP)...
March 19, 2024: Journal of Translational Medicine
https://read.qxmd.com/read/38502113/molecular-and-clinical-determinants-of-acquired-resistance-and-treatment-duration-for-targeted-therapies-in-colorectal-cancer
#25
JOURNAL ARTICLE
Emily Harrold, Fergus Keane, Henry Walch, Joanne F Chou, Jenna Sinopoli, Silvia Palladino, Duaa H Al-Rawi, Kalyani Chadalavada, Paolo Manca, Sree Chalasani, Jessica Yang, Andrea Cercek, Jinru Shia, Marinela Capanu, Samuel F Bakhoum, Nikolaus Schultz, Walid K Chatila, Rona Yaeger
PURPOSE: Targeted therapies have improved outcomes for patients with metastatic colorectal cancer, but their impact is limited by rapid emergence of resistance. We hypothesized that an understanding of the underlying genetic mechanisms and intrinsic tumor features that mediate resistance to therapy will guide new therapeutic strategies and ultimately allow the prevention of resistance. EXPERIMENTAL DESIGN: We assembled a series of 52 patients with paired pre-treatment and progression samples who received therapy targeting EGFR (n=17), BRAF V600E (n=17), KRAS G12C (n=15), or amplified HER2 (n=3) to identify molecular and clinical factors associated with time on treatment (TOT)...
March 19, 2024: Clinical Cancer Research
https://read.qxmd.com/read/38496700/clinical-translation-for-targeting-dna-damage-repair-in-non-small-cell-lung-cancer-a-review
#26
REVIEW
Xinru Mao, Nung Kion Lee, Shaban Eljali Saad, Isabel Lim Fong
Despite significant advancements in screening, diagnosis, and treatment of non-small cell lung cancer (NSCLC), it remains the primary cause of cancer-related deaths globally. DNA damage is caused by the exposure to exogenous and endogenous factors and the correct functioning of DNA damage repair (DDR) is essential to maintain of normal cell circulation. The presence of genomic instability, which results from defective DDR, is a critical characteristic of cancer. The changes promote the accumulation of mutations, which are implicated in cancer cells, but these may be exploited for anti-cancer therapies...
February 29, 2024: Translational Lung Cancer Research
https://read.qxmd.com/read/38492762/in-vivo-assessment-of-the-toxic-impact-of-exposure-to-magnetic-iron-oxide-nanoparticles-ionps-using-drosophila-melanogaster
#27
JOURNAL ARTICLE
Merve Güneş, Kemal Aktaş, Burçin Yalcın, Ayşen Yağmur Burgazlı, Meltem Asilturk, Ayca Erdem Ünşar, Bülent Kaya
Iron oxide nanoparticles (IONPs) have useful properties, such as strong magnetism and compatibility with living organisms which is preferable for medical applications such as drug delivery and imaging. However, increasing use of these materials, especially in medicine, has raised concerns regarding potential risks to human health. In this study, IONPs were coated with silicon dioxide (SiO2 ), citric acid (CA), and polyethylenimine (PEI) to enhance their dispersion and biocompatibility. Both coated and uncoated IONPs were assessed for genotoxic effects on Drosophila melanogaster...
March 14, 2024: Environmental Toxicology and Pharmacology
https://read.qxmd.com/read/38491408/integrative-multi-omics-characterization-reveals-sex-differences-in-glioblastoma
#28
JOURNAL ARTICLE
Byunghyun Jang, Dayoung Yoon, Ji Yoon Lee, Jiwon Kim, Jisoo Hong, Harim Koo, Jason K Sa
BACKGROUND: Glioblastoma (GBM) is the most common and lethal primary brain tumor in adults, with limited treatment modalities and poor prognosis. Recent studies have highlighted the importance of considering sex differences in cancer incidence, prognosis, molecular disparities, and treatment outcomes across various tumor types, including colorectal adenocarcinoma, lung adenocarcinoma, and GBM. METHODS: We performed comprehensive analyses of large-scale multi-omics data (genomic, transcriptomic, and proteomic data) from TCGA, GLASS, and CPTAC to investigate the genetic and molecular determinants that contribute to the unique clinical properties of male and female GBM patients...
March 16, 2024: Biology of Sex Differences
https://read.qxmd.com/read/38491202/usp24-i-101-targeting-of-usp24-activates-autophagy-to-inhibit-drug-resistance-acquired-during-cancer-therapy
#29
JOURNAL ARTICLE
Ming-Jer Young, Shao-An Wang, Yung-Ching Chen, Chia-Yu Liu, Kai-Cheng Hsu, Sin-Wei Tang, Yau-Lin Tseng, Yi-Ching Wang, Shih-Min Lin, Jan-Jong Hung
Drug resistance in cancer therapy is the major reason for poor prognosis. Addressing this clinically unmet issue is important and urgent. In this study, we found that targeting USP24 by the specific USP24 inhibitors, USP24-i and its analogues, dramatically activated autophagy in the interphase and mitotic periods of lung cancer cells by inhibiting E2F4 and TRAF6, respectively. USP24 functional knockout, USP24C1695A , or targeting USP24 by USP24-i-101 inhibited drug resistance and activated autophagy in gefitinib-induced drug-resistant mice with doxycycline-induced EGFRL858R lung cancer, but this effect was abolished after inhibition of autophagy, indicating that targeting USP24-mediated induction of autophagy is required for inhibition of drug resistance...
March 15, 2024: Cell Death and Differentiation
https://read.qxmd.com/read/38489090/a-case-of-bloom-syndrome-manifesting-with-therapy-related-myelodysplastic-syndromes-harboring-a-novel-blm-gene-variant
#30
JOURNAL ARTICLE
Takuma Ohashi, Hiroyoshi Kunimoto, Jun Nukui, Haruka Teshigawara, Satoshi Koyama, Takuya Miyazaki, Maki Hagihara, Kenji Matsumoto, Eriko Koshimizu, Naomi Tsuchida, Haruka Hamanoue, Satoko Miyatake, Akihiro Yachie, Naomichi Matsumoto, Hideaki Nakajima
Bloom syndrome (BS) is an autosomal recessive genetic disorder caused by variants in the BLM gene. BS is characterized by distinct facial features, elongated limbs, and various dermatological complications including photosensitivity, poikiloderma, and telangiectatic erythema. The BLM gene encodes a RecQ helicase critical for genome maintenance, stability, and repair, and a deficiency in functional BLM protein leads to genomic instability and high predisposition to various types of cancers, particularly hematological and gastrointestinal malignancies...
March 15, 2024: International Journal of Hematology
https://read.qxmd.com/read/38488661/wrnip1-prevents-transcription-associated-genomic-instability
#31
JOURNAL ARTICLE
Pasquale Valenzisi, Veronica Marabitti, Pietro Pichierri, Annapaola Franchitto
R-loops are non-canonical DNA structures that form during transcription and play diverse roles in various physiological processes. Disruption of R-loop homeostasis can lead to genomic instability and replication impairment, contributing to several human diseases, including cancer. Although the molecular mechanisms that protect cells against such events are not fully understood, recent research has identified fork protection factors and DNA damage response proteins as regulators of R-loop dynamics. In this study, we identify the Werner helicase-interacting protein 1 (WRNIP1) as a novel factor that counteracts transcription-associated DNA damage upon replication perturbation...
March 15, 2024: ELife
https://read.qxmd.com/read/38486992/metal-nanoparticles-for-cancer-therapy-precision-targeting-of-dna-damage
#32
REVIEW
Qian Chen, Chunyan Fang, Fan Xia, Qiyue Wang, Fangyuan Li, Daishun Ling
Cancer, a complex and heterogeneous disease, arises from genomic instability. Currently, DNA damage-based cancer treatments, including radiotherapy and chemotherapy, are employed in clinical practice. However, the efficacy and safety of these therapies are constrained by various factors, limiting their ability to meet current clinical demands. Metal nanoparticles present promising avenues for enhancing each critical aspect of DNA damage-based cancer therapy. Their customizable physicochemical properties enable the development of targeted and personalized treatment platforms...
March 2024: Acta Pharmaceutica Sinica. B
https://read.qxmd.com/read/38484940/single-cell-and-bulk-rna-sequencing-identifies-tumor-microenvironment-subtypes-and-chemoresistance-related-igf1-cancer-associated-fibroblast-in-gastric-cancer
#33
JOURNAL ARTICLE
Xiya Jia, Ziteng Li, Runye Zhou, Wanjing Feng, Lixia Yi, Hena Zhang, Bing Chen, Qin Li, Shenglin Huang, Xiaodong Zhu
BACKGROUND: The tumor microenvironment (TME) significantly influences prognosis and drug resistance in various tumors, yet its heterogeneity and the mechanisms affecting therapeutic response remain unclear in gastric cancer (GC). METHODS: The heterogenous TME were explored with single-cell RNA-sequencing (scRNA-seq) data of 50 primary GC samples. We then identified four GC TME subtypes with nonnegative matrix factorization (NMF) and constructed a pearson nearest-centroid classifier based on subtype-specific upregulated genes...
March 12, 2024: Biochimica et Biophysica Acta. Molecular Basis of Disease
https://read.qxmd.com/read/38482965/molecular-pathological-approach-to-cancer-epigenomics-and-its-clinical-application
#34
REVIEW
Yae Kanai
Careful microscopic observation of histopathological specimens, accumulation of large numbers of high-quality tissue specimens, and analysis of molecular pathology in relation to morphological features are considered to yield realistic data on the nature of multistage carcinogenesis. Since the morphological hallmark of cancer is disruption of the normal histological structure maintained through cell-cell adhesiveness and cellular polarity, attempts have been made to investigate abnormalities of the cadherin-catenin cell adhesion system in human cancer cells...
March 14, 2024: Pathology International
https://read.qxmd.com/read/38482738/patterns-of-structural-variants-within-tp53-introns-and-relocation-of-the-tp53-promoter-a-commentary-%C3%A2
#35
JOURNAL ARTICLE
Hannah C Beird, Dimitri Lin, Alexander J Lazar, P Andrew Futreal
Gene disruption from double-strand DNA breaks within introns is a mechanism of inactivating the tumor suppressor TP53. This occurs more frequently in osteosarcoma and biliary adenocarcinoma compared with other cancer types. The patterns of intron breakpoints within TP53 do not correlate with prevalence, intron length, or overall genome-wide levels of rearrangements. Therefore, these breakpoints appear to be selected for reasons other than to disrupt TP53. A recent article published by Saba et al in The Journal of Pathology illustrates a benefit to having breakpoints within intron 1 using high-quality matched genomic and transcriptomic osteosarcoma sequencing data as well as in vitro validation...
March 14, 2024: Journal of Pathology
https://read.qxmd.com/read/38482597/implementing-mychoice%C3%A2-cdx-hrd-testing-for-the-nordics-lessons-from-2021-to-2023
#36
JOURNAL ARTICLE
Lea Milling Korsholm, Verena Broecker, Mansoor Raza Mirza, Maria Rossing
BACKGROUND: Assessment of homologous recombinant deficient (HRD) phenotypes is key for managing Poly (ADP-ribose) polymerase inhibitor (PARPi) treatment. To accommodate the need for a validated HRD platform and enhance targeted treatment of ovarian cancer patients, a Nordic core facility for the myChoice® CDx platform was established in Denmark. MATERIALS AND METHODS: Comparative calculations and statistics are based on information from test requisitions and results (Genome Instability Score [GIS], BRCA status and combined HRD status) obtained from ovarian and breast cancer samples submitted for HRD-testing by myChoice® CDx through the Nordic core facility in the 2-year period...
March 14, 2024: Acta Oncologica
https://read.qxmd.com/read/38482443/comprehensive-analysis-of-the-effects-of-the-cuprotosis-associated-gene-slc31a1-on-patient-prognosis-and-tumor-microenvironment-in-human-cancer
#37
JOURNAL ARTICLE
Guiqian Zhang, Ning Wang, Shixun Ma, Pengxian Tao, Hui Cai
BACKGROUND: Solute carrier family 31 (copper transporter), member 1 ( SLC31A1 ) is a key factor in maintaining intracellular copper concentration and an important factor affecting cancer energy metabolism. Therefore, exploring the potential biological function and value of SLC31A1 could provide a new direction for the targeted therapy of tumors. METHODS: This study assessed gene expression levels, survival, clinicopathology, gene mutations, methylation levels, the tumor mutational burden (TMB), microsatellite instability (MSI), and the immune cell infiltration of SLC31A1 in pan-cancer using the Tumor Immune Estimation Resource 2...
February 29, 2024: Translational Cancer Research
https://read.qxmd.com/read/38482423/-nf2-is-a-candidate-diagnosis-prognostic-and-immunotherapeutic-biomarker-a-systematic-pan-cancer-analysis
#38
JOURNAL ARTICLE
Honglu Zhang, Jiyong Liu
BACKGROUND: Neurofibromin 2 ( NF2 ) regulates diverse cellular events such as transcription, translation, ubiquitination, and micro-RNA biosynthesis. Previous evidence revealed that aberrant expression of NF2 contributes to tumorigenesis in mesothelioma, meningioma, and breast cancer. However, there is no comprehensive pan-cancer analysis to explore NF2 's function in cancer diagnosis, prognosis, and immunological prediction. METHODS: By extensive use of data profiles from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) project, Cancer Cell Line Encyclopedia (CCLE), CIBERSORT, Human Protein Atlas (HPA), and cBioPortal, we employed various bioinformatics methods to explore the role of NF2 in pan-cancer, including analyzing the association between NF2 and tumor diagnosis, prognosis, immune cell infiltration, tumor mutational burden (TMB), and microsatellite instability (MSI)...
February 29, 2024: Translational Cancer Research
https://read.qxmd.com/read/38482233/the-prognostic-value-and-potential-immunotherapeutic-efficacy-of-acvr1-in-treating-gastric-cancer
#39
JOURNAL ARTICLE
Hui Zhang, Ruiqi Liu, Yanrong Chen, Ruicong Ma, Qiang Xue, Arvind Sahu, Xiaodi Yan, Hongmei Gu
BACKGROUND: The discovery of biomarkers has facilitated the treatment of cancer. At present, the relationship between activin A receptor type-1 ( ACVR1 ) and gastric cancer is gradually discovered. The aim of this study was to explore the expression of ACVR1 in gastric cancer and its clinical significance, to study the relationship between ACVR1 and tumor microenvironment (TME) for the prognosis of gastric cancer, and to further identify new targets for immunotherapy in gastric cancer...
February 29, 2024: Journal of Gastrointestinal Oncology
https://read.qxmd.com/read/38481813/tubule-specific-cyclin-dependent-kinase-12-knockdown-potentiates-kidney-injury-through-transcriptional-elongation-defects
#40
JOURNAL ARTICLE
Yi-Lin Zhang, Tao-Tao Tang, Wei-Jie Ni, Zhong-Tang Li, Liang-Yun-Zi Jiang, Yao Wang, Xuan Zhou, Jing-Yuan Cao, Qing Yin, Wei Jiang, Ya-Jie Zhao, Wei-Hua Gan, Ai-Qing Zhang, Zuo-Lin Li, Yi Wen, Lin-Li Lv, Bi-Cheng Liu, Bin Wang
Direct tubular injury caused by several medications, especially chemotherapeutic drugs, is a common cause of AKI. Inhibition or loss of cyclin-dependent kinase 12 (CDK12) triggers a transcriptional elongation defect that results in deficiencies in DNA damage repair, producing genomic instability in a variety of cancers. Notably, 10-25% of individuals developed AKI after treatment with a CDK12 inhibitor, and the potential mechanism is not well understood. Here, we found that CDK12 was downregulated in the renal tubular epithelial cells in both patients with AKI and murine AKI models...
2024: International Journal of Biological Sciences
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