SCLC LCNEC FFPE LMD
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: Toshihide Nishimura
PROVIDER: PXD013583 | JPOST Repository | Tue May 14 00:00:00 BST 2019
REPOSITORIES: jPOST
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SMU003_T01_01.raw | Raw | |||
| SMU003_T01_02.raw | Raw | |||
| SMU003_T01_03.raw | Raw | |||
| SMU005_T01_01.raw | Raw | |||
| SMU005_T01_02.raw | Raw |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:Two prognostically significant subtypes of high-grade lung neuroendocrine tumors independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles. BACKGROUND: Classification of high-grade neuroendocrine tumors (HGNT) of the lung currently recognises large-cell neuroendocrine carcinoma (LCNEC) and small-cell lung carcinoma (SCLC) as distinct groups. However, a similarity in histology for these two carcinomas and uncertain clinical course have led to suggestions that a single HGNT classification would be more appropriate. Gene expression profiling, which can reproduce histopathological classification, and often defines new subclasses with prognostic significance, can be used to resolve HGNT classification. METHODS: We used cDNA microarrays with 40386 elements to analyze the gene expression profiles of 38 surgically resected samples of lung neuroendocrine tumors and 11 SCLC cell lines. Samples of large-cell carcinoma, adenocarcinoma, and normal lung were also included to give a total of 105 samples analyzed. The data were subjected to filtering to yield informative genes before unsupervised hierarchical clustering that identified relatedness of tumor samples. FINDINGS: Distinct groups for carcinoids, large-cell carcinoma, adenocarcinoma, and normal lung were readily identified. However, we were unable to distinguish LCNEC from SCLC by gene expression profiling. Three independent rounds of unsupervised hierarchical clustering consistently divided SCLC samples into two main groups with LCNEC samples largely integrated with these groups. Furthermore, patients in one of the groups identified by clustering had a significantly better clinical outcome than the other (83% vs 12% survived for 5 years; p=0.0094. None of the highly proliferative SCLC cell lines subsequently analyzed clustered with this good-prognosis group. INTERPRETATION: Our findings show that HGNT of the lung can be classified into two groups independent of SCLC and LCNEC. To this end, we have identified many genes, some of which encode well-characterized markers of cancer that distinguish the HGNT groups. These results have implications for the diagnosis, classification, and treatment of lung neuroendocrine tumors, and provide important insights into their underlying biology. Keywords: other
2004-02-10 | E-GEOD-1037 | biostudies-arrayexpress
Project description:PURPOSE The development of reliable gene expression profiling technology is having an increasing impact on our understanding of lung cancer biology. The present study aims to determine whether the phenotypic heterogeneity and genetic diversity of lung cancer are correlated. PATIENTS AND METHODS In this study, microarray analysis was performed in a set of 91 non-small cell lung cancer (NSCLC) samples in order to: establish gene signatures in primary adenocarcinomas and squamous-cell carcinomas; determine differentially expressed gene sequences at different stages of the disease; and identify sequences with biological significance for tumor progression. After microarray analysis, the expression level of 92 selected genes was validated by qPCR in an independent set of 70 samples. RESULTS Gene sequences were differentially expressed as a function of tumor type, stage, and differentiation grade. High upregulation was observed for KRT15 and PKP1, which may be good markers to distinguish squamous cell carcinoma samples. High downregulation was observed for DSG3 in stage IA adenocarcinomas. CONCLUSION Expression signatures in NSCLC distinguish tumor type, stage, and differentiation grade. Keywords: Tumor vs control comparative genomics study 91 samples studied, 46 tumors and 45 controls. All samples are paired except three.
2010-10-01 | E-GEOD-18842 | biostudies-arrayexpress
Project description:Two prognostically significant subtypes of high-grade lung neuroendocrine tumors independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles. BACKGROUND: Classification of high-grade neuroendocrine tumors (HGNT) of the lung currently recognises large-cell neuroendocrine carcinoma (LCNEC) and small-cell lung carcinoma (SCLC) as distinct groups. However, a similarity in histology for these two carcinomas and uncertain clinical course have led to suggestions that a single HGNT classification would be more appropriate. Gene expression profiling, which can reproduce histopathological classification, and often defines new subclasses with prognostic significance, can be used to resolve HGNT classification. METHODS: We used cDNA microarrays with 40386 elements to analyze the gene expression profiles of 38 surgically resected samples of lung neuroendocrine tumors and 11 SCLC cell lines. Samples of large-cell carcinoma, adenocarcinoma, and normal lung were also included to give a total of 105 samples analyzed. The data were subjected to filtering to yield informative genes before unsupervised hierarchical clustering that identified relatedness of tumor samples. FINDINGS: Distinct groups for carcinoids, large-cell carcinoma, adenocarcinoma, and normal lung were readily identified. However, we were unable to distinguish LCNEC from SCLC by gene expression profiling. Three independent rounds of unsupervised hierarchical clustering consistently divided SCLC samples into two main groups with LCNEC samples largely integrated with these groups. Furthermore, patients in one of the groups identified by clustering had a significantly better clinical outcome than the other (83% vs 12% survived for 5 years; p=0.0094. None of the highly proliferative SCLC cell lines subsequently analyzed clustered with this good-prognosis group. INTERPRETATION: Our findings show that HGNT of the lung can be classified into two groups independent of SCLC and LCNEC. To this end, we have identified many genes, some of which encode well-characterized markers of cancer that distinguish the HGNT groups. These results have implications for the diagnosis, classification, and treatment of lung neuroendocrine tumors, and provide important insights into their underlying biology. Keywords: other
2004-02-11 | GSE1037 | GEO
Project description:This study investigates the safety/toxicity and potential anti-tumor activity of sequential administration of nivolumab and escalating doses of the mTOR inhibitor ABI-009 in advanced Ewing’s sarcoma, PEComa, epithelioid sarcoma, desmoid tumor, chordoma, non-small cell lung cancer, small cell lung cancer, urethelial carcinoma, melanoma, renal cell carcinoma, squamous cell carcinoma of head and neck, hepatocellular carcinoma, classical Hodgkin’s lymphoma, MSI-H/dMMR metastatic colorectal cancer, and tumors with genetic mutations sensitive to mTOR inhibitors
| 2247222 | ecrin-mdr-crc
Project description:Here we describe novel murine models of High Grade Neuroendocrine Lung Carcinomas driven by the loss of four tumor suppressors: deletion of Rb, PTEN, and p53, in a Rbl1 null background, in a wide variety of lung epithelial cells produces Large Cell Neuroendocrine Carcinoma whereas inactivation of these genes exclusively in basal cells leads to the development of Small Cell Lung Carcinoma, showing that Keratin K5 expressing cells contribute to the development/act as cell of origin of Small Cell Lung Carcinoma differentially influencing the lung cancer type developed. Conditional ablation of Rb1, Trp53 and Pten in pulmonary cells was achieved by intratracheal administration of purified Ad5-CMVcre or Ad5-K5cre (Du Page et al, 2009) to Rb1F/F;Trp53F/F;PtenF/F;Rbl1−/− 8–10 week old mice. Mice were sacrificed 3 to 5 months after the Ad5-cre infection and tumors processed for whole transcriptome analysis. As control animals, RbF/F;p53F/F;PtenF/F;Rbl1−/− littermates were used.
2019-10-15 | GSE121574 | GEO
Project description:Twenty three small-cell lung carcinoma (SCLC) cell lines from ATCC profiled on 100K genotyping arrays Keywords: comparative genomic hybridization
2007-04-15 | GSE7068 | GEO
Project description:This phase II trial studies nivolumab and ipilimumab in treating patients with rare tumors. Immunotherapy with monoclonal antibodies, such as nivolumab and ipilimumab, may help the body’s immune system attack the cancer, and may interfere with the ability of tumor cells to grow and spread.
This trial enrolls participants for the following cohorts based on condition:
1. Epithelial tumors of nasal cavity, sinuses, nasopharynx: A) Squamous cell carcinoma with variants of nasal cavity, sinuses, and nasopharynx and trachea (excluding laryngeal, nasopharyngeal cancer [NPC], and squamous cell carcinoma of the head and neck [SCCHN]) B) Adenocarcinoma and variants of nasal cavity, sinuses, and nasopharynx (closed to accrual 07/27/2018)
2. Epithelial tumors of major salivary glands (closed to accrual 03/20/2018)
3. Salivary gland type tumors of head and neck, lip, esophagus, stomach, trachea and lung, breast and other location (closed to accrual)
4. Undifferentiated carcinoma of gastrointestinal (GI) tract
5. Adenocarcinoma with variants of small intestine (closed to accrual 05/10/2018)
6. Squamous cell carcinoma with variants of GI tract (stomach small intestine, colon, rectum, pancreas) (closed to accrual 10/17/2018)
7. Fibromixoma and low grade mucinous adenocarcinoma (pseudomixoma peritonei) of the appendix and ovary (closed to accrual 03/20/2018)
8. Rare pancreatic tumors including acinar cell carcinoma, mucinous cystadenocarcinoma or serous cystadenocarcinoma. Pancreatic adenocarcinoma is not eligible (closed to accrual)
9. Intrahepatic cholangiocarcinoma (closed to accrual 03/20/2018)
10. Extrahepatic cholangiocarcinoma and bile duct tumors (closed to accrual 03/20/2018)
11. Sarcomatoid carcinoma of lung
12. Bronchoalveolar carcinoma lung. This condition is now also referred to as adenocarcinoma in situ, minimally invasive adenocarcinoma, lepidic predominant adenocarcinoma, or invasive mucinous adenocarcinoma
13. Non-epithelial tumors of the ovary: A) Germ cell tumor of ovary B) Mullerian mixed tumor and adenosarcoma (closed to accrual 03/30/2018)
14. Trophoblastic tumor: A) Choriocarcinoma (closed to accrual)
15. Transitional cell carcinoma other than that of the renal, pelvis, ureter, or bladder (closed to accrual)
16. Cell tumor of the testes and extragonadal germ tumors: A) Seminoma and testicular sex cord cancer B) Non seminomatous tumor C) Teratoma with malignant transformation (closed to accrual)
17. Epithelial tumors of penis - squamous adenocarcinoma cell carcinoma with variants of penis (closed to accrual)
18. Squamous cell carcinoma variants of the genitourinary (GU) system
19. Spindle cell carcinoma of kidney, pelvis, ureter
20. Adenocarcinoma with variants of GU system (excluding prostate cancer) (closed to accrual 07/27/2018)
21. Odontogenic malignant tumors
22. Pancreatic neuroendocrine tumor (PNET) (formerly named: Endocrine carcinoma of pancreas and digestive tract.) (closed to accrual)
23. Neuroendocrine carcinoma including carcinoid of the lung (closed to accrual 12/19/2017)
24. Pheochromocytoma, malignant (closed to accrual)
25. Paraganglioma (closed to accrual 11/29/2018)
26. Carcinomas of pituitary gland, thyroid gland parathyroid gland and adrenal cortex (closed to accrual)
27. Desmoid tumors
28. Peripheral nerve sheath tumors and NF1-related tumors (closed to accrual 09/19/2018)
29. Malignant giant cell tumors
30. Chordoma (closed to accrual 11/29/2018)
31. Adrenal cortical tumors (closed to accrual 06/27/2018)
32. Tumor of unknown primary (Cancer of Unknown Primary; CuP) (closed to accrual 12/22/2017)
33. Not Otherwise Categorized (NOC) Rare Tumors [To obtain permission to enroll in the NOC cohort, contact: S1609SC@swog.org] (closed to accrual 03/15/2019)
34. Adenoid cystic carcinoma (closed to accrual 02/06/2018)
35. Vulvar cancer (closed to accrual)
36. MetaPLASTIC carcinoma (of the breast) (closed to accrual)
37. Gastrointestinal stromal tumor (GIST) (closed to accrual 09/26/2018)
38. Perivascular epithelioid cell tumor (PEComa)
39. Apocrine tumors/extramammary Paget’s disease (closed to accrual)
40. Peritoneal mesothelioma
41. Basal cell carcinoma (temporarily closed to accrual 04/29/2020)
42. Clear cell cervical cancer
43. Esthenioneuroblastoma (closed to accrual)
44. Endometrial carcinosarcoma (malignant mixed Mullerian tumors) (closed to accrual)
45. Clear cell endometrial cancer
46. Clear cell ovarian cancer (closed to accrual)
47. Gestational trophoblastic disease (GTD)
48. Gallbladder cancer
49. Small cell carcinoma of the ovary, hypercalcemic type
50. PD-L1 amplified tumors
51. Angiosarcoma
52. High-grade neuroendocrine carcinoma (pancreatic neuroendocrine tumor [PNET] should be enrolled in Cohort 22; prostatic neuroendocrine carcinomas should be enrolled into Cohort 53). Small cell lung cancer is not eligible (closed to accrual)
53. Treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC)
| 2219879 | ecrin-mdr-crc
Project description:PURPOSE The development of reliable gene expression profiling technology is having an increasing impact on our understanding of lung cancer biology. The present study aims to determine whether the phenotypic heterogeneity and genetic diversity of lung cancer are correlated. PATIENTS AND METHODS In this study, microarray analysis was performed in a set of 91 non-small cell lung cancer (NSCLC) samples in order to: establish gene signatures in primary adenocarcinomas and squamous-cell carcinomas; determine differentially expressed gene sequences at different stages of the disease; and identify sequences with biological significance for tumor progression. After microarray analysis, the expression level of 92 selected genes was validated by qPCR in an independent set of 70 samples. RESULTS Gene sequences were differentially expressed as a function of tumor type, stage, and differentiation grade. High upregulation was observed for KRT15 and PKP1, which may be good markers to distinguish squamous cell carcinoma samples. High downregulation was observed for DSG3 in stage IA adenocarcinomas. CONCLUSION Expression signatures in NSCLC distinguish tumor type, stage, and differentiation grade. Keywords: Tumor vs control comparative genomics study
2010-10-01 | GSE18842 | GEO
Project description:Small cell lung carcinoma (SCLC) and large cell neuroendocrine carcinoma (LCNEC) are high-grade pulmonary neuroendocrine tumors. The neural basic helix-loop-helix (bHLH) transcription factors ASCL1 and NEUROD1 have been shown to play crucial roles in promoting the malignant behavior and survival of human SCLC cell lines. In this study, we find ASCL1 and NEUROD1 identify distinct neuroendocrine tumors, bind distinct genomic loci, and regulate mostly distinct genes. ASCL1 and NEUROD1 are often bound in super-enhancers that are associated with highly expressed genes in their respective SCLC cell lines suggesting different cell lineage of origin for these tumors. ASCL1 targets oncogenic genes such as MYCL1, RET, and NFIB, while NEUROD1 targets the oncogenic gene MYC. Although ASCL1 and NEUROD1 regulate different genes, many of these gene targets commonly contribute to neuroendocrine and cell migration function. ASCL1 in particular also regulates genes in the NOTCH pathway and genes important in cell-cycle dynamics. Finally, we demonstrate ASCL1 but not NEUROD1 is required for SCLC and LCNEC tumor formation in current in vivo genetic mouse models of pulmonary neuroendocrine tumors RNA-seq analysis performed on two ASCL1high and two NEUROD1high human SCLC cell lines to identify gene expression patterns in these cells. Also, we performed RNA-seq in mouse neuroendocrine lung tumors obtained from Trp53;Rb1;Rbl2 triple knockout model mice treated with Adeno-CMVCRE intratracheally.
2016-07-21 | E-GEOD-69393 | biostudies-arrayexpress
Project description:This series contain 36 samples obtained from human lung tissue and includes the following: 7 Adenocarcinoma samples. 16 Squamous cell carcinoma samples. 1 AdenoSquamous sample. 2 Renal Metastasis. 1 Colon metastasis. 7 normal lung tissue adjacent to the tumors. 2 commercial normal lung RNA. Keywords = Lung Keywords = Non Small Cell Lung Cancer Keywords = Adenocarcinoma Keywords = Squamous Cell Carcinoma Keywords = Normal Lung. Keywords: other
2005-07-20 | GSE1987 | GEO