scholarly journals PolyG-DS: An ultrasensitive polyguanine tract–profiling method to detect clonal expansions and trace cell lineage

2021 ◽  
Vol 118 (31) ◽  
pp. e2023373118
Author(s):  
Yuezheng Zhang ◽  
Brendan F. Kohrn ◽  
Ming Yang ◽  
Daniela Nachmanson ◽  
T. Rinda Soong ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Precancerous Lesions ◽  
Cell Lineage ◽  
Low Frequency ◽  
Cost Effective ◽  
Lineage Tracing ◽  
Driver Mutations ◽  
Tumor Evolution ◽  
Somatic Evolution ◽  
Length Analysis

Polyguanine tracts (PolyGs) are short guanine homopolymer repeats that are prone to accumulating mutations when cells divide. This feature makes them especially suitable for cell lineage tracing, which has been exploited to detect and characterize precancerous and cancerous somatic evolution. PolyG genotyping, however, is challenging because of the inherent biochemical difficulties in amplifying and sequencing repetitive regions. To overcome this limitation, we developed PolyG-DS, a next-generation sequencing (NGS) method that combines the error-correction capabilities of duplex sequencing (DS) with enrichment of PolyG loci using CRISPR-Cas9–targeted genomic fragmentation. PolyG-DS markedly reduces technical artifacts by comparing the sequences derived from the complementary strands of each original DNA molecule. We demonstrate that PolyG-DS genotyping is accurate, reproducible, and highly sensitive, enabling the detection of low-frequency alleles (<0.01) in spike-in samples using a panel of only 19 PolyG markers. PolyG-DS replicated prior results based on PolyG fragment length analysis by capillary electrophoresis, and exhibited higher sensitivity for identifying clonal expansions in the nondysplastic colon of patients with ulcerative colitis. We illustrate the utility of this method for resolving the phylogenetic relationship among precancerous lesions in ulcerative colitis and for tracing the metastatic dissemination of ovarian cancer. PolyG-DS enables the study of tumor evolution without prior knowledge of tumor driver mutations and provides a tool to perform cost-effective and easily scalable ultra-accurate NGS-based PolyG genotyping for multiple applications in biology, genetics, and cancer research.

scholarly journals Cancer Risk and the Somatic Cell Lineage Tree

2020 ◽  
Author(s):  
Imre Derényi ◽  
Márton C. Demeter ◽  
Gergely J. Szöllősi
Keyword(s):  
Cancer Research ◽  
Analytical Formula ◽  
Cell Lineage ◽  
Driver Mutations ◽  
Cell Divisions ◽  
Somatic Evolution ◽  
Lineage Tree ◽  
Multicellular Organisms ◽  
Risk Of Cancer ◽  
Simple Analytical Formula

All the cells of a multicellular organism are the product of cell divisions that trace out a single binary tree, the so-called cell lineage tree. Because cell divisions are accompanied by replication errors, the shape of the cell lineage tree is one of the key determinants of how somatic evolution, which can potentially lead to cancer, proceeds. Cancer initiation usually requires the accumulation of a certain number of driver mutations. By mapping the accumulation of driver mutations into a graph theoretical problem, we show that in leading order of the mutation rate the probability of collecting a given number of driver mutations depends only on the distribution of the lineage lengths (irrespective of any other details of the cell lineage tree), and we derive a simple analytical formula for this probability. Our results are crucial in understanding how natural selection can shape the cell lineage trees of multicellular organisms in order to reduce their lifetime risk of cancer. In particular, our results highlight the significance of the longest cell lineages. Our analytical formula also provides a tool to quantify cancer susceptibility in theoretical models of tissue development and maintenance, as well as for empirical data on cell linage trees.Significance StatementA series of cell divisions starting from a single cell produce and maintain tissues of multicellular organisms. Somatic evolution, including the development of cancer, takes place along the cell lineage tree traced out by these cell divisions. A fundamental question in cancer research is how the lifetime risk of cancer depends on the properties of an arbitrary cell lineage tree. Here we show that for small mutation rates (which is the case in reality) the distribution of the lineage lengths alone determines cancer risk, and that this risk can be described by a simple analytical formula. Our results have far-reaching implications not only for cancer research, but also for evolutionary biology in general.

scholarly journals Clonal approaches to understanding the impact of mutations on hematologic disease development

Blood ◽  
2019 ◽  
Vol 133 (13) ◽  
pp. 1436-1445 ◽  
Author(s):  
Jyoti Nangalia ◽  
Emily Mitchell ◽  
Anthony R. Green
Keyword(s):  
Somatic Mutations ◽  
Clonal Selection ◽  
Single Cells ◽  
Driver Mutations ◽  
Great Promise ◽  
Tumor Evolution ◽  
Disease Development ◽  
Hematopoietic Tissue ◽  
The Impact

Abstract Interrogation of hematopoietic tissue at the clonal level has a rich history spanning over 50 years, and has provided critical insights into both normal and malignant hematopoiesis. Characterization of chromosomes identified some of the first genetic links to cancer with the discovery of chromosomal translocations in association with many hematological neoplasms. The unique accessibility of hematopoietic tissue and the ability to clonally expand hematopoietic progenitors in vitro has provided fundamental insights into the cellular hierarchy of normal hematopoiesis, as well as the functional impact of driver mutations in disease. Transplantation assays in murine models have enabled cellular assessment of the functional consequences of somatic mutations in vivo. Most recently, next-generation sequencing–based assays have shown great promise in allowing multi-“omic” characterization of single cells. Here, we review how clonal approaches have advanced our understanding of disease development, focusing on the acquisition of somatic mutations, clonal selection, driver mutation cooperation, and tumor evolution.

scholarly journals Loss-of-function of p53 isoform Δ113p53 accelerates brain aging in zebrafish

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Ting Zhao ◽  
Shengfan Ye ◽  
Zimu Tang ◽  
Liwei Guo ◽  
Zhipeng Ma ◽  
...  
Keyword(s):  
Replicative Senescence ◽  
Brain Aging ◽  
Ventricular Zone ◽  
Human Fibroblasts ◽  
Cell Lineage ◽  
Lineage Tracing ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Antioxidant Genes ◽  
Age Related

AbstractReactive oxygen species (ROS) stress has been demonstrated as potentially critical for induction and maintenance of cellular senescence, and been considered as a contributing factor in aging and in various neurological disorders including Alzheimer’s disease (AD) and amyotrophic lateral sclerosis (ALS). In response to low-level ROS stress, the expression of Δ133p53, a human p53 isoform, is upregulated to promote cell survival and protect cells from senescence by enhancing the expression of antioxidant genes. In normal conditions, the basal expression of Δ133p53 prevents human fibroblasts, T lymphocytes, and astrocytes from replicative senescence. It has been also found that brain tissues from AD and ALS patients showed decreased Δ133p53 expression. However, it is uncharacterized if Δ133p53 plays a role in brain aging. Here, we report that zebrafish Δ113p53, an ortholog of human Δ133p53, mainly expressed in some of the radial glial cells along the telencephalon ventricular zone in a full-length p53-dependent manner. EDU-labeling and cell lineage tracing showed that Δ113p53-positive cells underwent cell proliferation to contribute to the neuron renewal process. Importantly, Δ113p53M/M mutant telencephalon possessed less proliferation cells and more senescent cells compared to wild-type (WT) zebrafish telencephalon since 9-months old, which was associated with decreased antioxidant genes expression and increased level of ROS in the mutant telencephalon. More interestingly, unlike the mutant fish at 5-months old with cognition ability, Δ113p53M/M zebrafish, but not WT zebrafish, lost their learning and memory ability at 19-months old. The results demonstrate that Δ113p53 protects the brain from aging by its antioxidant function. Our finding provides evidence at the organism level to show that depletion of Δ113p53/Δ133p53 may result in long-term ROS stress, and finally lead to age-related diseases, such as AD and ALS in humans.

Does histological assessment accurately distinguish separate primary lung adenocarcinomas from intrapulmonary metastases? A study of paired resected lung nodules in 32 patients using a routine next-generation sequencing panel for driver mutations

2021 ◽  
pp. jclinpath-2021-207421
Author(s):  
Frido K Bruehl ◽  
Erika E Doxtader ◽  
Yu-Wei Cheng ◽  
Daniel H Farkas ◽  
Carol Farver ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Analysis ◽  
Low Frequency ◽  
Driver Mutations ◽  
Lung Nodules ◽  
Driver Gene ◽  
Next Generation ◽  
Histological Assessment ◽  
Lung Adenocarcinomas ◽  
Generation Sequencing

AimVarious approaches have been reported for distinguishing separate primary lung adenocarcinomas from intrapulmonary metastases in patients with two lung nodules. The aim of this study was to determine whether histological assessment is reliable and accurate in distinguishing separate primary lung adenocarcinomas from intrapulmonary metastases using routine molecular findings as an adjunct.MethodsWe studied resected tumour pairs from 32 patients with lung adenocarcinomas in different lobes. In 15 of 32 tumour pairs, next-generation sequencing (NGS) for common driver mutations was performed on both nodules. The remainder of tumour pairs underwent limited NGS, or EGFR genotyping. Tumour pairs with different drivers (or one driver/one wild-type) were classified as molecularly unrelated, while those with identical low-frequency drivers were classified as related. Three pathologists independently and blinded to the molecular results categorised tumour pairs as related or unrelated based on histological assessment.ResultsOf 32 pairs, 15 were classified as related by histological assessment, and 17 as unrelated. Of 15 classified as related by histology, 6 were classified as related by molecular analysis, 4 were unrelated and 5 were indeterminate. Of 17 classified as unrelated by histology, 14 were classified as unrelated by molecular analysis, none was related and 3 were indeterminate. Histological assessment of relatedness was inaccurate in 4/32 (12.5%) tumour pairs.ConclusionsA small but significant subset of two-nodule adenocarcinoma pairs is inaccurately judged as related by histological assessment, and can be proven to be unrelated by molecular analysis (driver gene mutations), leading to significant downstaging.

scholarly journals (P2-40) Patient Allocation to Hospitals During Mass-Casualty Incidents

2011 ◽  
Vol 26 (S1) ◽  
pp. s148-s149 ◽  
Author(s):  
K. Ruettger ◽  
W. Lenz
Keyword(s):  
Emergency Response ◽  
Operations Management ◽  
Low Frequency ◽  
Working Hours ◽  
Cost Effective ◽  
Mass Casualty ◽  
Rescue Service ◽  
Hospital Facility ◽  
State Register ◽  
Helicopter Landing

Due to the limited resources of specialized hospital departments, the allocation of patients to different hospitals according to severity is an extraordinarily complex and time-critical problem. The emergency capacity was determined for all medical centers (n = 135) in the State of Hessen, Germany, for patients of various triage categories (red, yellow, green) during normal working hours, and during weekends and nights and included logistic specifications of a potential helicopter landing. These data were entered into a state register. Using the data from the “acute-care-register”, a Ticket System was developed that allows operations management to assign patients according to the severity of their condition, urgency, and specialization requirements (e.g., neurosurgery, ophthalmology, pediatrics) to a hospital without exceeding the admission and/or treatment capacity of the hospital/facility. During a non-critical period, the order of allocations depending on the distance from the clinic is planned in advance so that no further modifications are necessary during the acute intervention phase of an emergency response. Additional notification of hospital capacities for severe casualties provided during the emergency response can be easily and immediately supplemented. Due to the relatively low frequency of such emergency responses, a cost-effective concept that is easily adaptable to the respective fields of application was decided upon. The system is a sticker set customized for the respective rescue teams. The sets will be carried permanently in the rescue equipment by the organization manager of the rescue service team. The equipment is not dependent on electronic components. The cost per sticker set is approximately US$50. Keeping track of the patient allocations is assured.

PATH-40. SPORADIC NF2 WILD-TYPE MULTIPLE MENINGIOMAS HARBOR DISTINCT DRIVER MUTATIONS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi124-vi124
Author(s):  
Insa Prilop ◽  
Thomas Pinzer ◽  
Daniel Cahill ◽  
Priscilla Brastianos ◽  
Gabriele Schackert ◽  
...  
Keyword(s):  
Hot Spot ◽  
Low Frequency ◽  
Neurofibromatosis Type ◽  
Driver Mutations ◽  
Wild Type ◽  
Driver Genes ◽  
Who Grade ◽  
Genetic Changes ◽  
Histologic Subtype ◽  
Multiple Meningiomas

Abstract OBJECTIVE Multiple meningiomas (MM) are rare and present a unique management challenge. While the mutational landscape of single meningiomas has been extensively studied, understanding the molecular pathogenesis of sporadic MM remains incomplete. The objective of this study is to elucidate the genetic features of sporadic MM. METHODS We identified nine patients with MM (n=19) defined as ≥2 spatially separated synchronous or metachronous meningiomas. We profiled genetic changes in these tumors using next-generation sequencing (NGS) assay that covers a large number of targetable and frequently mutated genes in meningiomas including AKT1, KLF4, NF2, PIK3CA/PIK3R1, POLR2A, SMARCB1, SMO, SUFU, TRAF7, and the TERT promoter. RESULTS Most of MM were WHO grade 1 (n= 16, 84.2%). Within individual patients, no driver mutation was shared between separate tumors. All but two cases harbored different hot spot mutations in known meningioma-driver genes like TRAF7 (n= 5), PIK3CA (n= 4), AKT1 (n= 3), POLR2A (n=1) and SMO (n= 1). Moreover, individual tumors differed in histologic subtype in 8/9 patients. The low frequency of NF2 mutations in our series stands in contrast to previous studies that included hereditary cases arising in the setting of neurofibromatosis type 2 (NF2). CONCLUSIONS Our findings provide evidence for genomic inter-tumor heterogeneity and an independent molecular origin of sporadic NF2 wild-type MM. Furthermore, these findings suggest that genetic characterization of each lesion is warranted in sporadic MM.

scholarly journals Mouse model of ulcerative colitis using trinitrobenzene sulfonic acid

2015 ◽  
Vol 10 (4) ◽  
pp. 860
Author(s):  
Irfan Ahmad Rather ◽  
Vivek K. Bajpai ◽  
Nam Gyeong-Jun
Keyword(s):  
Ulcerative Colitis ◽  
Inflammatory Bowel Disease ◽  
Mouse Model ◽  
Bowel Disease ◽  
Sulfonic Acid ◽  
Intestinal Inflammation ◽  
Cost Effective ◽  
Trinitrobenzene Sulfonic Acid ◽  
Clinical Presentations ◽  
Inflammatory Bowel

<p>Animal model of intestinal inflammation is of paramount significance that aids in discerning the pathologies underlying ulcerative colitis and Crohn’s disease, the two clinical presentations of inflammatory bowel disease. The 2,4,6-trinitrobenzene sulfonic acid (TNBS) colitis model represents one such intestinal inflammation-prototype that is generated in susceptible strains of mice through intra-rectal instillation of compound TNBS. In this paper, we demonstrate the experimental induction of TNBS-mediated colitis in a susceptible strain of ICR mice. This can be done by the following steps: a) acclimation, b) induction and c) observation. TNBS-mouse model provides the information in shortest possible time and simultaneously represents a cost effective and highly reproducible model method of studying the pathogenesis of inflammatory bowel disease.</p><p><strong>Video Clips</strong></p><p><a href="https://youtube.com/v/6MsuIGzH3uA">Acclimation and induction of TNBS</a>:          4.5 min</p><p><a href="https://youtube.com/v/ya66SNwoVag">Observation and drug administration</a>:      1.5 min</p>

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