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CTCF/cohesin-binding sites are frequently mutated in cancer

Katainen, Riku ; Dave, Kashyap ; Pitkänen, Esa ; [et al.]

Springer Science and Business Media LLC ; 2015

In: Nature Genetics Vol. 47, No. 7 ( 2015-7), p. 818-821

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 47, No. 7 ( 2015-7), p. 818-821

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/ng.3335

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2015

detail.hit.zdb_id: 1494946-5

SSG: 12

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Abstract 3156: New candidate oncogenes discovered in microsatellite unstable colorectal cancer.

Gylfe, Alexandra E. ; Kondelin, Johanna ; Turunen, Mikko ; [et al.]

American Association for Cancer Research (AACR) ; 2013

In: Cancer Research Vol. 73, No. 8_Supplement ( 2013-04-15), p. 3156-3156

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In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 3156-3156

Abstract: Around 15% of colorectal cancers (CRCs) show microsatellite instability (MSI). A characteristic high passenger mutation load has discouraged systematic mutation screens in MSI CRCs. To systematically search for novel MSI CRC oncogenes, the exomes of 25 MSI CRC-normal pairs were sequenced as the discovery set. Observed hot spots were confirmed by Sanger sequencing and further validated in a set of 86 MSI CRCs. Mutational hot spots were confirmed in 15 genes and three genes showed additional hot spot mutations in the validation set. These three sites were highly conserved across species. The hot spot sites of these three genes were screened in 75 microsatellite stable CRCs and 12 MSI CRC cell lines with negative results. Next, we analyzed the subcellular localization of wild-type and mutant proteins. The findings of this study support the idea that cancer genomes are heterogeneous and characterized by few, frequently mutated “mountains” (e.g. BRAF and KRAS) and numerous, less frequently mutated “hills”. The identified mutational hot spots may prove important in developing personalized tumor profiling and therapy. Citation Format: Alexandra E. Gylfe, Johanna Kondelin, Mikko Turunen, Heikki Ristolainen, Riku Katainen, Esa Pitkänen, Eevi Kaasinen, Ville Rantanen, Tomas Tanskanen, Heli J. Lehtonen, Kimmo Palin, Minna Taipale, Jussi Taipale, Laura Renkonen-Sinisalo, Heikki Järvinen, Jan Böhm, Jukka-Pekka Mecklin, Ari Ristimäki, Sari Tuupanen, Auli Karhu, Outi Kilpivaara, Pia Vahteristo, Lauri A. Aaltonen. New candidate oncogenes discovered in microsatellite unstable colorectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3156. doi:10.1158/1538-7445.AM2013-3156

Type of Medium: Online Resource

ISSN: 0008-5472 , 1538-7445

URL: Article

DOI: 10.1158/1538-7445.AM2013-3156

RVK:

XA 36000

RVK:

XA 10000

Language: English

Publisher: American Association for Cancer Research (AACR)

Publication Date: 2013

detail.hit.zdb_id: 2036785-5

detail.hit.zdb_id: 1432-1

detail.hit.zdb_id: 410466-3

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Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Kondelin, Johanna ; Gylfe, Alexandra E. ; Lundgren, Sofie ; [et al.]

American Association for Cancer Research (AACR) ; 2017

In: Cancer Research Vol. 77, No. 15 ( 2017-08-01), p. 4078-4088

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In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 15 ( 2017-08-01), p. 4078-4088

Abstract: Approximately 15% of colorectal cancers exhibit microsatellite instability (MSI), which leads to accumulation of large numbers of small insertions and deletions (indels). Genes that provide growth advantage to cells via loss-of-function mutations in microsatellites are called MSI target genes. Several criteria to define these genes have been suggested, one of them being simple mutation frequency. Microsatellite mutation rate, however, depends on the length and nucleotide context of the microsatellite. Therefore, assessing the general impact of mismatch repair deficiency on the likelihood of mutation events is paramount when following this approach. To identify MSI target genes, we developed a statistical model for the somatic background indel mutation rate of microsatellites to assess mutation significance. Exome sequencing data of 24 MSI colorectal cancers revealed indels at 54 million mononucleotide microsatellites of three or more nucleotides in length. The top 105 microsatellites from 71 genes were further analyzed in 93 additional MSI colorectal cancers. Mutation significance and estimated clonality of mutations determined the most likely MSI target genes to be the aminoadipate-semialdehyde dehydrogenase AASDH and the solute transporter SLC9A8. Our findings offer a systematic profiling of the somatic background mutation rate in protein-coding mononucleotide microsatellites, allowing a full cataloging of the true targets of MSI in colorectal cancer. Cancer Res; 77(15); 4078–88. ©2017 AACR.

Type of Medium: Online Resource

ISSN: 0008-5472 , 1538-7445

URL: Article

DOI: 10.1158/0008-5472.CAN-17-0682

RVK:

XA 36000

RVK:

XA 10000

Language: English

Publisher: American Association for Cancer Research (AACR)

Publication Date: 2017

detail.hit.zdb_id: 2036785-5

detail.hit.zdb_id: 1432-1

detail.hit.zdb_id: 410466-3

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Identification of Candidate Oncogenes in Human Colorectal Cancers With Microsatellite Instability

Gylfe, Alexandra E. ; Kondelin, Johanna ; Turunen, Mikko ; [et al.]

Elsevier BV ; 2013

In: Gastroenterology Vol. 145, No. 3 ( 2013-09), p. 540-543.e22

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In: Gastroenterology, Elsevier BV, Vol. 145, No. 3 ( 2013-09), p. 540-543.e22

Type of Medium: Online Resource

ISSN: 0016-5085

URL: Article

DOI: 10.1053/j.gastro.2013.05.015

RVK:

XA 44500

Language: English

Publisher: Elsevier BV

Publication Date: 2013

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Obese people benefit from lumbar spinal stenosis surgery as much as people of normal weight

Myllykangas, Henni ; Ristolainen, Leena ; Hurri, Heikki ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Journal of Orthopaedic Surgery and Research Vol. 16, No. 1 ( 2021-12)

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In: Journal of Orthopaedic Surgery and Research, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2021-12)

Abstract: Lumbar spinal stenosis (LSS) is a common degenerative condition of the spine that causes back pain radiating to the lower extremity. Surgical treatment is indicated to treat progressive radical symptoms. Obesity has been associated with inferior results in the domains of quality of life (QoL) following an LSS operation, but the research findings have been limited. This paper aims to identify whether obesity affects QoL due to back pain among patients who underwent an operation for LSS. Methods This study is based on a series of patients operated on for LSS between 2012 and 2018. Operated patients who returned for follow-up forms within the first or second years were included. A total of 359 patients were selected, 163 males (45%) and 196 females (55%). The mean age was 68.9 years. The EuroQol five-dimension scale (EQ-5D) questionnaire was chosen to measure QoL and the Oswestry Disability Index (ODI) for functional disability. Results QoL, as measured by EQ-5D, was preoperatively lower in those patients with a BMI ≥ 30. One year after the operation, all groups had a similar trend of improved QoL. At the second year, the results in all groups levelled off even though there was no statistical difference in clinical outcomes ( p = 0.92). The ODI was preoperatively statistically higher in patients with a BMI ≥ 30 ( p 〈 0.001). Two years after the surgery, all groups had improved ODI scores, but there was no statistical difference in ODI between the BMI groups ( p = 0.54). Conclusion Surgical intervention for debilitating or longstanding symptoms of LSS should be considered as a treatment option for suitable patients in spite of an elevated BMI.

Type of Medium: Online Resource

ISSN: 1749-799X

URL: Article

DOI: 10.1186/s13018-021-02692-z

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2252548-8

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Abstract 105: Characterizing the exomic profile of MSI colorectal cancer

Kondelin, Johanna K. ; Gylfe, Alexandra ; Tuupanen, Sari ; [et al.]

American Association for Cancer Research (AACR) ; 2012

In: Cancer Research Vol. 72, No. 8_Supplement ( 2012-04-15), p. 105-105

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In: Cancer Research, American Association for Cancer Research (AACR), Vol. 72, No. 8_Supplement ( 2012-04-15), p. 105-105

Abstract: Colorectal cancer (CRC) is the third most common cancer in Western countries. Of all CRC tumors, 15% display microsatellite instability (MSI) caused by defective cellular mismatch repair. Cells displaying MSI accumulate a high number of mutations throughout the genome, especially in short repeat areas called microsatellites. Also point mutations occur in excess in these tumors. Sporadic MSI CRCs are caused by biallelic inactivation of the MLH1 gene, usually by promoter hypermethylation. The MSI tumors have a genetic and clinopathological profile that significantly differs from microsatellite stable (MSS) CRC. Overall, MSI tumors have been studied much less than MSS tumors, mainly due to the high number of mutations in MSI tumors, which makes data analysis and identification of relevant mutations challenging. To date, several genes have been proposed as MSI target genes based on targeted searches of their mutation frequency in microsatellite areas. A few systematic sequencing studies on colorectal cancer have been published, but none of them focus on MSI tumors, making this study first of a kind. In this study, the exome of 25 sporadic MSI tumors and corresponding normal samples are sequenced to identify changes of somatic origin. Bioinformatical tools are used to rank the genes and identify true driver genes based on clustering of missense mutations. The most interesting findings will be validated by direct Sanger sequencing. In addition to corresponding normal specimens, samples from healthy Finnish blood donors as well as data from other ongoing sequencing projects and sequence databases are used as controls to exclude polymorphisms. The data of all the 25 tumors has been analyzed and validation of the potential clusters of missense mutations is in process. The pathological nature of the changes will be confirmed by possible functional studies. This way we wish to identify new driver genes in MSI CRC. A detailed understanding of the molecular background of this tumor type is important for the development of more efficient screening methods and personalized treatments. By characterizing changes typical for different MSI tumors, we wish to identify subtypes within the MSI tumor category that could be exploited in treatment. Such understanding of MSI tumors could improve the treatment and hence prognosis of patients diagnosed with MSI type CRC. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 105. doi:1538-7445.AM2012-105

Type of Medium: Online Resource

ISSN: 0008-5472 , 1538-7445

URL: Article

DOI: 10.1158/1538-7445.AM2012-105

RVK:

XA 36000

RVK:

XA 10000

Language: English

Publisher: American Association for Cancer Research (AACR)

Publication Date: 2012

detail.hit.zdb_id: 2036785-5

detail.hit.zdb_id: 1432-1

detail.hit.zdb_id: 410466-3

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Abstract 5193: Novel candidate oncogenes with mutation hot spots in microsatellite unstable colorectal cancer

Gylfe, Alexandra E. ; Tuupanen, Sari ; Hänninen, Ulrika ; [et al.]

American Association for Cancer Research (AACR) ; 2014

In: Cancer Research Vol. 74, No. 19_Supplement ( 2014-10-01), p. 5193-5193

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In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 5193-5193

Abstract: Around 15% of colorectal cancers (CRCs) show microsatellite instability (MSI). MSI CRCs are prone to repeat mutations due to defective mismatch repair. The high background mutation frequency has discouraged systematic mutations screens in this tumor type. However, these tumors might form a sensitive system for generation and selection of oncogenic mutation hot spots. The aim of this study is to identify novel oncogenes with mutation hot spots that drive MSI CRC tumorigenesis. The exomes of 25 MSI tumors and respective healthy tissues were sequenced as the discovery set. The exome data was searched for mutation hot spots, with recurrent somatic missense mutations in at least two tumors. Potential mutation hot spots were observed in 43 genes and among these were the following known oncogenes: BRAF (V600E), CTNNB1 (T41A) and PIK3CA (H1047R). Novel potential mutation hot spots were identified in 40 genes and these were validated by Sanger sequencing. Mutation hot spots in 33 genes were confirmed and these were further screened in a validation set of 254 MSI CRCs. Fourteen genes displayed hotspot mutations also in the validation set with a total hot spot mutation frequency of 1.1-3.6 %. Many of the validated genes encode for known cancer-related proteins and for proteins with molecular and cellular functions relevant to cancer development and progression. Further work is needed to clarify the functional role of the identified hot spot mutations in MSI CRC tumorigenesis. The novel mutation hotspots may be utilized to develop personalized tumor profiling and therapy. Citation Format: Alexandra E. Gylfe, Sari Tuupanen, Ulrika Hänninen, Johanna Kondelin, Heikki Ristolainen, Riku Katainen, Esa Pitkänen, Minna Taipale, Jussi Taipale, Claus Lindbjerg Andersen, Laura Renkonen-Sinisalo, Heikki Järvinen, Jan Böhm, Jukka-Pekka Mecklin, Pia Vahteristo, Lauri A. Aaltonen. Novel candidate oncogenes with mutation hot spots in microsatellite unstable colorectal cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5193. doi:10.1158/1538-7445.AM2014-5193

Type of Medium: Online Resource

ISSN: 0008-5472 , 1538-7445

URL: Article

DOI: 10.1158/1538-7445.AM2014-5193

RVK:

XA 36000

RVK:

XA 10000

Language: English

Publisher: American Association for Cancer Research (AACR)

Publication Date: 2014

detail.hit.zdb_id: 2036785-5

detail.hit.zdb_id: 1432-1

detail.hit.zdb_id: 410466-3

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Abstract 2401: Identification of new target genes in microsatellite unstable colorectal cancer by exome sequencing

Kondelin, Johanna ; Pitkänen, Esa ; Gylfe, Alexandra E. ; [et al.]

American Association for Cancer Research (AACR) ; 2014

In: Cancer Research Vol. 74, No. 19_Supplement ( 2014-10-01), p. 2401-2401

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In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 2401-2401

Abstract: Colorectal cancer (CRC) is the third most common cancer in Western countries. Approximately 15% of CRCs display microsatellite instability (MSI) caused by defective cellular mismatch repair. Most of the MSI CRCs are sporadic and result from biallelic inactivation of the MLH1 gene, which is most often due to hypermethylation of its promoter. Cells displaying MSI accumulate a high number of mutations throughout the genome, especially in short repeat areas called microsatellites. These mutations typically lead to a premature stop codon resulting in a truncated protein product that may inactivate the gene, a mechanism known typical of tumor suppressor genes. The aim of this study is to identify new target genes in MSI CRC. To date, several genes have been proposed as MSI target genes based on high mutation frequency in targeted searches of microsatellites. The availability of new sequencing and bioinformatic technologies has enabled genome-wide investigation of mutations in human cancers. This has led to identification of a vast amount of mutations in cancer, most of which are passenger mutations that do not confer selective growth advantage. The challenge is therefore to distinguish true driver genes from passengers. The high number of mutations in MSI tumors augments this challenge. In this study, 25 sporadic MSI CRCs and their corresponding normal samples have been exome sequenced to identify changes of somatic origin. An analysis and visualization program developed in our group, “RikuRator” (unpublished), will be utilized along with a script to estimate the accurate somatic mutation frequency of each coding mononucleotide repeat. A statistical model based on exome sequencing data will be developed that takes into account the background mutation frequency of microsatellites depending on the repeat length and nucleotide context. The most mutated repeats will be validated by Sanger sequencing in a set of additional MSI CRCs. Functional studies will be carried out to further investigate the pathogenic effect of the new target genes identified. The systematic screening of mutations in microsatellites will improve our understanding on the mutation profile typical of these tumors. With our approach that takes into account the background mutation frequency of microsatellites we aim to identify true driver genes in MSI CRC. A detailed understanding of the molecular background of this tumor type is important for the development of more efficient screening methods and personalized treatments to improve the prognosis of patients diagnosed with MSI type CRC. Citation Format: Johanna Kondelin, Esa Pitkänen, Alexandra E. Gylfe, Kimmo Palin, Heikki Ristolainen, Riku Katainen, Eevi Kaasinen, Minna Taipale, Jussi Taipale, Laura Renkonen-Sinisalo, Heikki Järvinen, Jan Böhm, Jukka-Pekka Mecklin, Pia Vahteristo, Sari Tuupanen, Lauri A. Aaltonen. Identification of new target genes in microsatellite unstable colorectal cancer by exome sequencing. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2401. doi:10.1158/1538-7445.AM2014-2401

Type of Medium: Online Resource

ISSN: 0008-5472 , 1538-7445

URL: Article

DOI: 10.1158/1538-7445.AM2014-2401

RVK:

XA 36000

RVK:

XA 10000

Language: English

Publisher: American Association for Cancer Research (AACR)

Publication Date: 2014

detail.hit.zdb_id: 2036785-5

detail.hit.zdb_id: 1432-1

detail.hit.zdb_id: 410466-3

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Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer : ARID mutations in MSI CRC

Cajuso, Tatiana ; Hänninen, Ulrika A. ; Kondelin, Johanna ; [et al.]

Wiley ; 2014

In: International Journal of Cancer Vol. 135, No. 3 ( 2014-08-01), p. 611-623

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In: International Journal of Cancer, Wiley, Vol. 135, No. 3 ( 2014-08-01), p. 611-623

Type of Medium: Online Resource

ISSN: 0020-7136

URL: Issue

URL: Article

DOI: 10.1002/ijc.v135.3

DOI: 10.1002/ijc.28705

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XA 10000

Language: English

Publisher: Wiley

Publication Date: 2014

detail.hit.zdb_id: 218257-9

detail.hit.zdb_id: 1474822-8

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Piloting a Smart Rollator: User experiences with technology-related motivation and physical activity

Orenius, Tage ; Paloniemi, Susanna ; Hurri, Heikki ; [et al.]

International Society for Gerontechnology (ISG) ; 2020

In: Gerontechnology Vol. 20, No. 1 ( 2020-8-31), p. 1-10

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In: Gerontechnology, International Society for Gerontechnology (ISG), Vol. 20, No. 1 ( 2020-8-31), p. 1-10

Type of Medium: Online Resource

ISSN: 1569-1101 , 1569-111X

URL: Issue

URL: Journal

URL: Article

DOI: 10.4017/gt.2020.20.000.00

DOI: 10.4017/gt.0000.00.00.000.00

DOI: 10.4017/gt.2021.20.420.01

Language: Unknown

Publisher: International Society for Gerontechnology (ISG)

Publication Date: 2020

detail.hit.zdb_id: 2509019-7

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