| 1. |
|
|
| 2. |
- Campbell, Brittany B., et al.
(author)
-
Comprehensive Analysis of Hypermutation in Human Cancer
- 2017
-
In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 171:5
-
Journal article (peer-reviewed)abstract
- © 2017 Elsevier Inc. We present an extensive assessment of mutation burden through sequencing analysis of > 81,000 tumors from pediatric and adult patients, including tumors with hypermutation caused by chemotherapy, carcinogens, or germline alterations. Hypermutation was detected in tumor types not previously associated with high mutation burden. Replication repair deficiency was a major contributing factor. We uncovered new driver mutations in the replication-repair-associated DNA polymerases and a distinct impact of microsatellite instability and replication repair deficiency on the scale of mutation load. Unbiased clustering, based on mutational context, revealed clinically relevant subgroups regardless of the tumors' tissue of origin, highlighting similarities in evolutionary dynamics leading to hypermutation. Mutagens, such as UV light, were implicated in unexpected cancers, including sarcomas and lung tumors. The order of mutational signatures identified previous treatment and germline replication repair deficiency, which improved management of patients and families. These data will inform tumor classification, genetic testing, and clinical trial design. A large-scale analysis of hypermutation in human cancers provides insights into tumor evolution dynamics and identifies clinically actionable mutation signatures.
|
|
| 3. |
- D’Orazi, Valentina, et al.
(author)
-
The GALAH survey : tracing the Milky Way’s formation and evolution through RR Lyrae stars
- 2024
-
In: Monthly Notices of the Royal Astronomical Society. - 0035-8711. ; 531:1, s. 137-162
-
Journal article (peer-reviewed)abstract
- Stellar mergers and accretion events have been crucial in shaping the evolution of the Milky Way (MW). These events have been dynamically identified and chemically characterized using red giants and main-sequence stars. RR Lyrae (RRL) variables can play a crucial role in tracing the early formation of the MW since they are ubiquitous, old (t ≥ 10 Gyr) low-mass stars and accurate distance indicators. We exploited Data Release 3 of the GALAH survey to identify 78 field RRLs suitable for chemical analysis. Using synthetic spectra calculations, we determined atmospheric parameters and abundances of Fe, Mg, Ca, Y, and Ba. Most of our stars exhibit halo-like chemical compositions, with an iron peak around [Fe/H] ≈ −1.40, and enhanced Ca and Mg content. Notably, we discovered a metal-rich tail, with [Fe/H] values ranging from −1 to approximately solar metallicity. This sub-group includes almost 1/4 of the sample, it is characterized by thin disc kinematics and displays sub-solar α-element abundances, marginally consistent with the majority of the MW stars. Surprisingly, they differ distinctly from typical MW disc stars in terms of the s-process elements Y and Ba. We took advantage of similar data available in the literature and built a total sample of 535 field RRLs for which we estimated kinematical and dynamical properties. We found that metal-rich RRLs (1/3 of the sample) likely represent an old component of the MW thin disc. We also detected RRLs with retrograde orbits and provided preliminary associations with the Gaia–Sausage–Enceladus, Helmi, Sequoia, Sagittarius, and Thamnos stellar streams.
|
|
| 4. |
- Gaulton, Kyle J, et al.
(author)
-
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
- 2015
-
In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
-
Journal article (peer-reviewed)abstract
- We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
|
|
| 5. |
- Sharoyko, Vladimir, et al.
(author)
-
Loss of TFB1M results in mitochondrial dysfunction that leads to impaired insulin secretion and diabetes.
- 2014
-
In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:21, s. 5733-5749
-
Journal article (peer-reviewed)abstract
- We have previously identified Transcription Factor B1 Mitochondrial (TFB1M) as a Type 2 Diabetes (T2D) risk gene, using human and mouse genetics. To further understand the function of TFB1M and how it is associated with T2D we created a β-cell specific knockout of Tfb1 m, which gradually developed diabetes. Prior to the onset of diabetes, β-Tfb1 m(-/-) mice exhibited retarded glucose clearance due to impaired insulin secretion. β-Tfb1 m(-/-) islets released less insulin in response to fuels, contained less insulin and secretory granules, and displayed reduced β-cell mass. Moreover, mitochondria in Tfb1 m-deficient β-cells were more abundant with disrupted architecture. TFB1M is known to control mitochondrial protein translation by adenine-dimethylation of 12S ribosomal RNA (rRNA). Here, we found that levels of TFB1M and mitochondrial encoded proteins, mitochondrial 12S rRNA methylation, ATP production and oxygen consumption were reduced in β-Tfb1 m(-/-) islets. Furthermore, levels of reactive oxygen species in response to cellular stress were increased while induction of defense mechanisms was attenuated. We also show increased apoptosis and necrosis as well as infiltration of macrophages and CD4(+)-cells in the islets. Taken together, our findings demonstrate that Tfb1 m-deficiency in β-cells caused mitochondrial dysfunction and subsequently diabetes due to combined loss of β-cell function and mass. These observations reflect pathogenetic processes in human islets: using RNA sequencing, we found that the TFB1M risk variant exhibited a negative gene-dosage effect on islet TFB1M mRNA levels, as well as insulin secretion. Our findings highlight the role of mitochondrial dysfunction in impairments of β-cell function and mass, the hallmarks of T2D.
|
|
