Detailed Longitudinal Sampling of Glioma Stem Cells In Situ Reveals Chr7 Gain and Chr10 Loss As Repeated Events in Primary Tumor Formation and Recurrence
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE101114 | GEO | 2017/10/01
SECONDARY ACCESSION(S): PRJNA393726
REPOSITORIES: GEO
Similar Datasets
Project description:In this study, we developed an extensive dataset for a GBM case via the generation of polyclonal and monoclonal glioma stem cell lines from initial diagnosis, as well as from multiple sections of distant tumor locations of the deceased patient’s brain following tumor recurrence. Our analyses revealed the tissue-wide expansion of a new clone in the recurrent tumor as well as chromosome 7 gain and chromosome 10 loss as repeated genomic events in primary and recurrent disease. Moreover, chromosome 7 gain and chromosome 10 loss produced similar alterations in mRNA expression profiles in primary and recurrent tumors despite possessing other highly heterogeneous and divergent genomic alterations between the tumors. We identified ETV1 and CDK6 as putative candidate genes, and NFKB (complex), IL1B, IL6, Akt and VEGF as potential signaling regulators, as potentially central downstream effectors of chr7 gain and chr10 loss. Finally, the differences caused by the transcriptomic shift following gain of chromosome 7 and loss of chromosome 10 were consistent with those generally seen in GBM samples compared to normal brain in large-scale patient-tumor data sets.
2017-10-01 | GSE101113 | GEO
Project description:In this study, we developed an extensive dataset for a GBM case via the generation of polyclonal and monoclonal glioma stem cell lines from initial diagnosis, as well as from multiple sections of distant tumor locations of the deceased patient’s brain following tumor recurrence. Our analyses revealed the tissue-wide expansion of a new clone in the recurrent tumor as well as chromosome 7 gain and chromosome 10 loss as repeated genomic events in primary and recurrent disease. Moreover, chromosome 7 gain and chromosome 10 loss produced similar alterations in mRNA expression profiles in primary and recurrent tumors despite possessing other highly heterogeneous and divergent genomic alterations between the tumors. We identified ETV1 and CDK6 as putative candidate genes, and NFKB (complex), IL1B, IL6, Akt and VEGF as potential signaling regulators, as potentially central downstream effectors of chr7 gain and chr10 loss. Finally, the differences caused by the transcriptomic shift following gain of chromosome 7 and loss of chromosome 10 were consistent with those generally seen in GBM samples compared to normal brain in large-scale patient-tumor data sets.
2017-10-01 | GSE101110 | GEO
Project description:Detailed Longitudinal Sampling of Glioma Stem Cells In Situ Reveals Chr7 Gain and Chr10 Loss As Repeated Events in Primary Tumor Formation and Recurrence
| PRJNA393726 | ENA
Project description:We detail study design options that generalize case-control sampling when longitudinal outcome data are already collected as part of a primary cohort study, but new exposure data must be retrospectively processed for a secondary analysis. Furthermore, we assume that cost will limit the size of the subsample that can be evaluated. We describe a novel class of stratified outcome-dependent sampling designs for longitudinal binary response data where distinct strata are created for subjects who never, sometimes, and always experienced the event of interest during longitudinal follow-up. Individual designs within this class are differentiated by the stratum-specific sampling probabilities. We show for parameters associated with time-varying exposures, subjects who experience the event/outcome at some but not at all of the follow-up times (i.e., those who exhibit response variation) are highly informative. If the time-varying exposure varies exclusively within individuals (i.e., intraclass correlation coefficient is 0), then sampling all subjects with response variability can yield highly precise parameter estimates even when compared with an analysis of the original cohort. The flexibility of the designs and analysis procedures also permits estimation of parameters that correspond to time-fixed covariates, and we show that with an imputation-based estimation procedure, baseline covariate associations can be estimated with very high precision irrespective of the design. We demonstrate features of the designs and analysis procedures via a plasmode simulation using data from the Lung Health Study.
| S-EPMC5718932 | biostudies-literature
Project description:Mosquito-borne viruses are the cause of significant morbidity and mortality worldwide, especially in low- and middle-income countries. Assessing risk for viral transmission often involves characterization of the vector competence of vector-virus pairings. The most common determination of vector competence uses discreet, terminal time points, which cannot be used to investigate variation in transmission aspects, such as biting behavior, over time. Here, we present a novel method to longitudinally measure individual biting behavior and Zika virus (ZIKV) transmission. Individual mosquitoes were exposed to ZIKV, and from 9 to 24 days post-exposure, individuals were each offered a 180 μL bloodmeal every other day. Biting behavior was observed and characterized as either active probing, feeding, or no bite. The bloodmeal was then collected, spun down, serum collected, and tested for ZIKV RNA via qRT-PCR to determine individuals' vector competence over time. This included whether transmission to the bloodmeal was successful and the titer of expectorated virus. Additionally, serum was inoculated onto Vero cells in order to determine infectiousness of positive recovered sera. Results demonstrate heterogeneity in not only biting patterns but expectorated viral titers among individual mosquitoes over time. These findings demonstrate that the act of transmission is a complex process governed by mosquito behavior and mosquito-virus interaction, and herein we offer a method to investigate this phenomenon.
| S-EPMC8065608 | biostudies-literature
Project description: Not available
| S-EPMC8567036 | biostudies-literature
Project description:Small scale study to asses the effects of taking multiple skinbiopts from individual mice in time. Results showed no influence on expression levels in time from older samplings on newer samplings. skin biopts from 4 individual mice in taken at 6 points in time
2014-09-01 | E-GEOD-51347 | biostudies-arrayexpress
Project description:Small scale study to asses the effects of taking multiple skinbiopts from individual mice in time. Results showed no influence on expression levels in time from older samplings on newer samplings.
2014-09-01 | GSE51347 | GEO
Project description:BACKGROUND:Anal cancer is a rare disease, which might be the reason for the "one size fits all" approach still used for radiotherapy target contouring. To refine and individualize future guidelines, detailed and contemporary pattern of recurrence studies are needed. METHODS:Consecutive anal cancer patients, all treated with curative intent intensity-modulated radiotherapy (IMRT), were retrospectively studied (n =?170). Data was extracted from medical records and radiological images. Radiotherapy planning CT's and treatment plans were reviewed, and recurrences were mapped and categorized according to radiation dose. RESULTS:The mean dose to the primary tumor was 59.0?Gy. With a median follow-up of 50?months (range 14-117?months), 5-year anal cancer specific survival was 86.1%. Only 1 of 20 local recurrences was located outside the high dose (CTVT) volume. More patients experienced a distant recurrence (n =?34; 20.0%) than a locoregional recurrence (n =?24; 14.1%). Seven patients (4.2%) had a common iliac and/or para-aortic (CI/PA) recurrence. External iliac lymph node involvement (P =?0.04), and metastases in ?3 inguinal or pelvic lymph node regions (P =?0.02) were associated with a 15-18% risk of CI/PA recurrence. Following chemoradiotherapy, 6 patients with recurrent or primary metastatic CI/PA lymph nodes were free of recurrence at last follow-up. The overall rate of ano-inguinal lymphatic drainage (AILD) recurrence was 2 of 170 (1.2%), and among patients with inguinal metastases at initial diagnosis it was 2 of 65 (3.1%). CONCLUSIONS:We conclude that other measures than increased margins around the primary tumor are needed to improve local control. Furthermore, metastatic CI/PA lymph nodes, either at initial diagnosis or in the recurrent setting, should be considered potentially curable. Patients with certain patterns of metastatic pelvic lymph nodes might be at an increased risk of harboring tumor cells also in the CI/PA lymph nodes.
| S-EPMC7251738 | biostudies-literature
Project description:Background The lymph node (LN) is one of the main sites of recurrence in patients with endometrial carcinoma (EC). Literature specifically analyzing LN recurrence (LNR) in EC remains limited in number. Methods Patients with EC undergoing surgery between 2006 and 2021 in Peking University People’s Hospital was included, clinicopathological data of whom were collected and analyzed retrospectively by R 4.0.3. Results A total of 792 patients were included, with 73 patients having recurrence, among whom 21 patients had LNR. Median recurrence-free survival (RFS) in patients with LNR was 16 [4–39] months. LNR was extensive, with pelvic LNs most commonly involved (9/21). There are various patterns of LNR, with 33.3% (7/21) LN-only recurrence. Multivariable analysis suggested advanced stage, larger tumor diameter and poor histology were independent risk factors for LNR. Patients with LN metastasis (LNM) diagnosed at initial treatment accounted for 47.6% (10/21) of cases with LNR, 60.0% (6/10) of whom had recurrent LNs beyond the region of LNM, 90.0% (9/10) of whom had recurrence nodes overlapping with the range of lymphadenectomy. Uni- and multi-variable analysis suggested lymphadenectomy was not a protective factor for LNR, with both the range and number of LNs harvested considered. Conclusions LNR is common in patients with EC, with an extensive range and various patterns of recurrence. The International Federation of Gynecology and Obstetrics (FIGO) stage, tumor diameter and histology were independent risk factors for LNR, but lymphadenectomy seemed not a protective factor for LNR.
| S-EPMC9372211 | biostudies-literature