Rare renal tumours RNA
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001004323 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Rare renal tumours are by hard to classify and there is very little available information regarding prognosis and sensitivity to treatment. Here we endevour to understand their genomic properties in order to better understand their biology.
| EGAS00001004322 | EGA
Project description:Succinate dehydrogenase (SDH) deficient renal cancers are a rare and understudied subtype of renal cancer. As such they represent an unmet need in kidney cancer research. Here, we seek to describe the genomics and transcriptomics of SDH deficient renal cancers by sequencing five such tumours.
| EGAS00001004103 | EGA
Project description:Strong evidence supports the tumor immune landscape as a determinant of patient responses to immunotherapy. Readily available therapies, including radiation, are being investigated as modifying agents with immune checkpoint blockade. However, surprisingly little is known regarding radiotherapy’s impact within the tumor microenvironment and intratumoral T cell repertoires of patients, leaving critical gaps to guided design of clinical protocols. Here, samples from renal cell carcinoma (RCC) patients underwent high-throughput analysis to reveal transcriptional immune activation and increased clonality in irradiated tumors.
2020-09-08 | GSE153262 | GEO
Project description:BACKGROUND: Epstein-Barr Virus (EBV) associated lymphoproliferative disorders are encountered in immunodeficiency states. Amongst these, primary CNS lymphoma in HIV/AIDS patients is relatively rare and represents a therapeutic challenge. MATERIALS AND METHODS: This report was generated from patient's medical records throughout hospitalizations and outpatient visits. RESULTS: A 20-year-old female with congenitally acquired HIV and poor medication compliance presented with severe headaches and mild cranial nerve deficits. HIV viral load at presentation was 89,976/ml with CD4 count of 4/uL. Head MRI revealed 3-cm thick-walled ring-enhancing lesion in right basal ganglia. Serum titers for toxoplasmosis were negative. EBV DNA was detected by PCR in CSF without peripheral viremia. Imaging with thallium scan and MRI findings in combination with EBV PCR positive CSF allowed for the presumptive diagnosis of EBV-associated primary CNS lymphoma. Highly active anti-retroviral therapy (HAART) was reinitiated. Karnofsky score was 90%, thus chemotherapy was offered to optimize chance of cure. Agents of choice were high-dose Methotrexate for CNS penetration/anti-lymphoma activity and Rituximab. Within the next 5 months she received 8 cycles of alternating Methotrexate (4000 mg/m2/dose on Day 1) and Rituximab (375 mg/m2/dose on Day 8). Supportive care included leucovorin rescue and urine alkalinization. Therapy was tolerated well without sepsis episodes during neutropenia. Her headaches and neurological deficits resolved after the first cycle of therapy. Serial imaging demonstrated substantial and continuous regression of the lymphoma lesion. No adjunctive radiotherapy was administered. Patient remains in remission 18 months after diagnosis, despite fluctuating viral loads and CD4 counts due to the poor HAART compliance. No chronic hypogammaglobulinemia resulted from therapy to date. CONCLUSION: Given the observed results and acceptable toxicity profile, methotrexate and rituximab combination may be effective and should be considered in addition to HAART for treating EBV-associated CNS lymphoma in young patients with minimal comorbidities and underlying HIV/AIDS. INTRODUCTION: Pediatric pineal parenchymal tumors of intermediate differentiation (PPTID, WHO grade II or III) are extremely uncommon. Appropriate therapy has not been defined. We present three new cases of pediatric PPTID and 8 cases in patients under age 45 identified in a literature review. METHODS: This study utilized the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) (http://www.prisma-statement.org.). RESULTS: We diagnosed two children (female age 5 y, male age 14 y) with PPTID in the pineal region and negative work-up for metastases. Both underwent gross total resection (GTR). Pathologic evaluation was consistent with PPTID grade II in each. Both were treated with local radiation therapy via protons to 50.4 CGE. The first patient (case 1) is now 4 years since diagnosis with no evidence of disease (NED) and the second (case 2) is 8 months after surgery and NED. Our third case (male age 15 y) was diagnosed with PPTID grade III with drop metastases in the thecal sac (case 3). He was treated with craniospinal and boost radiation and multiagent chemotherapy but relapsed with leptomeningeal disease near the conus 2 years after diagnosis. Our literature review identified 8 cases of PPTID in patients under age 45, described in Table 1 (cases 4-11). There were broad treatment strategies from GTR only to craniospinal radiation and multiagent chemotherapy. While the therapy varied, the outcome for those with non-metastatic grade II tumors was good. Grade III tumors were associated with metastatic disease and a worse outcome. DISCUSSION: With very few cases, definitive recommendations for therapy are impossible. For PPTID grade II, GTR alone may be sufficient. PPTID grade III should be considered for more aggressive therapy.
| S-EPMC4046297 | biostudies-literature
Project description:Long non-coding RNA (lncRNA) play an important role in several biological processes including some renal diseases. Nevertheless, little is known on lncRNAs that are expressed in healthy kidney and involved in renal cell homeostasis and development and even less is known about lncRNA involved in the maintenance of human adult renal stem/progenitor cells (ARPCs). ARPCs have been shown to be very important for renal homeostasis and repair processes thanks to their self-renewal and differentiative ability as well as their capacity to secrete different reparative factors depending on the type of damage. Through a whole genome transcriptome screening, we found that the HOTAIR lncRNA is highly expressed in renal progenitors and potentially involved cell cycle and senescence biological processes. We then generated HOTAIR knock-out ARPC lines by CRISPR/Cas9 genome editing and showed that this lncRNA limits the apoptotic process of ARPCs and sustains their proliferative capacity, thus resulting responsible of their self-renewal properties. In addition, we found that the knockout of HOTAIR led to the ARPC senescence and to a significant decrease of the CD133 stem cell marker expression that is an inverse marker of ARPC senescence and can regulate renal tubular repair after the damage. Moreover, we found that ARPCs expressed high levels of the α-Klotho anti-aging protein and especially 2.6 fold higher levels compared to that secreted by RPTECs. The HOTAIR knockout in ARPCs leads to lower α-Klotho levels, comparable to that of RPTECs. Finnally we showed that HOTAIR induces epigenetic silencing of the cell cycle inhibitor p15 through the trimethylation of the histone H3K27. Altogether, these results shed new light on these important renal cells and may support the future development of precision therapies for kidney diseases.
2023-01-06 | E-MTAB-11451 | biostudies-arrayexpress
Project description:Succinate dehydrogenase (SDH) deficient renal cancers are a rare and understudied subtype of renal cancer. As such they represent an unmet need in kidney cancer research. Here, we seek to describe the genomics and transcriptomics of SDH deficient renal cancers by sequencing five such tumours. We document their mutational burden, define driver mutations, demonstrate typical patterns of structural variants, and estimate the cell of origin and cellular composition.
| EGAS00001004102 | EGA
Project description:Despite a growing body of knowledge regarding the pathogenesis of urinary tract infection, the mechanisms of renal scaring associated with acute pyelonephritis (APN) are poorly understood. Limited data available regarding histopathology, immune cell recruitment and gene expression changes during APN severely restricts the development of therapies to prevent renal scars. Here, we address this knowledge gap using inbred, immunocompetent mice with vesicoureteral reflux. Transurethral inoculation of uropathogenic Escherichia coli leads to renal mucosal injury, tubulointerstitial nephritis, and interstitial fibrosis – all histopathologic features of human APN. Interstitial fibrosis correlates most significantly with inflammation 7 and 28 days post infection. Flow cytometry identifies recruitment of neutrophils, macrophages, and lymphocytes to infected kidneys. Renal transcriptional analysis reveals molecular signatures associated with renal ischemia-reperfusion injury, immune cell chemotaxis, and leukocyte activation. Thus, C3H/HeOuJ mice with APN comprise a novel model of renal fibrosis that recapitulates the human condition of acquired renal scarring in an immunocompetent setting. The integration of organ pathology, quantitative cellular immune influx, and transcriptional analyses begin, for the first time, to define mechanisms of tissue injury during APN in the context of an intact immune response. The strong relationship between pro-inflammatory cell recruitment and fibrosis supports the hypothesis that renal scarring arises as a consequence of excessive host inflammation. Our studies suggest that immunomodulatory therapies should be investigated to reduce renal scarring in patients with APN.
2016-12-29 | GSE76469 | GEO
Project description:Genetic Testing to Understand and Address Renal Disease Disparities (GUARDD)
| PRJNA475646 | ENA
Project description:Genetic Testing to Understand and Address Renal Disease Disparities (GUARDD)
| PRJNA475647 | ENA
Project description:Renal tumors with complex morphology require extensive workup for accurate classification. Chromosomal aberrations that define subtypes of renal epithelial neoplasms have been reported. We explored if whole-genome chromosome copy number and loss-of-heterozygosity analysis with single nucleotide polymorphism (SNP) arrays can be used to identify these aberrations in cases where morphology was unable to definitively classify these tumors. Experiment Overall Design: We analyzed 50 paraffin-embedded tissues representing tumors with classic morphology from clear cell renal cell carcinoma (RCC), papillary RCC, chromophobe RCC, and oncocytoma with Affymetrix GeneChip 10K 2.0 Mapping arrays. We then analyzed 25 tumors that could not be classified by morphology and classified them based on the presence of defining chromosomal anomalies identified in the "classic" cohort.
2008-11-13 | E-GEOD-11447 | biostudies-arrayexpress