Comprehensive Transcriptome Analysis Expands lncRNA Functional Profiles in Breast Cancer DOI Open Access
Wenyong Zhu, Hao Huang,

Zixi Hu

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(15), С. 8456 - 8456

Опубликована: Авг. 2, 2024

Breast cancer is a heterogeneous disease that arises as multi-stage process involving multiple cell types. Patients diagnosed with the same clinical stage and pathological classification may have different prognoses therapeutic responses due to alterations in molecular genetics. As an essential marker for subtyping of breast cancer, long non-coding RNAs (lncRNAs) play crucial role gene expression regulation, differentiation, maintenance genomic stability. Here, we developed modular framework lncRNA identification applied it cohort identify novel lncRNAs not previously annotated. To investigate potential biological function, regulatory mechanisms, relevance lncRNAs, elucidated chromatin features these along associated protein-coding genes putative enhancers involved networks. Furthermore, uncovered patterns annotated identified were related hormone response PAM50 criterion, well immune progression states across cells checkpoint genes. Collectively, comprehensive functional analysis revealed by altering participating networks, contributing better insight into heterogeneity avenues intervention.

Язык: Английский

Quantitative Changes in the Proteome of Chronically Inflamed Lacrimal Glands From a Sjögren's Disease Animal Model DOI Creative Commons

Danny Toribio,

Junji Morokuma,

Dante Pellino

и другие.

Investigative Ophthalmology & Visual Science, Год журнала: 2025, Номер 66(4), С. 44 - 44

Опубликована: Апрель 17, 2025

The lacrimal gland (LG) is the major source of aqueous tears, and insufficient LG secretion leads to aqueous-deficient dry eye (ADDE) disease. To provide a foundational description LG's protein expression patterns, we prepared extracts LGs from wild-type an ADDE mouse model analyzed proteome by quantitative mass spectrometry. were isolated model, male non-obese diabetic (NOD) mice control BALB/c (n = 6 each). Protein samples in urea-based lysis buffer concentrations determined BCA method. equivalent 200 µg tryptically digested nanoflow liquid chromatography tandem spectrometry (LC-MS/MS). Proteins identified quantified using PEAKS X bioinformatics suite. Downstream differential analysis was performed MS-DAP R package. Selected significantly differentially expressed detected proteins subjected spatial immunohistochemistry. Cumulatively, LC-MS/MS-based proteomics analyses murine total 31,932 peptide sequences resulting 2617 identifications at 1% false discovery rate level. Principal component (PCA) hierarchical cluster revealed separation NOD samples. Overall, diversity consistently higher After applying global filter criteria peptide-to-protein rollup, 1750 remaining MSqRob algorithm, which 580 with statistically significant differences. Data are available via ProteomeXchange identifier PXD060937. At cellular level, up- downregulation select confirmed Our data suggest that chronic inflammation alterations proteome. Ongoing studies aim identify potentially unique, inflammation-induced could be amenable pharmacological modulation.

Язык: Английский

Процитировано

0
Comprehensive Transcriptome Analysis Expands lncRNA Functional Profiles in Breast Cancer DOI Open Access
Wenyong Zhu, Hao Huang,

Zixi Hu

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(15), С. 8456 - 8456

Опубликована: Авг. 2, 2024

Breast cancer is a heterogeneous disease that arises as multi-stage process involving multiple cell types. Patients diagnosed with the same clinical stage and pathological classification may have different prognoses therapeutic responses due to alterations in molecular genetics. As an essential marker for subtyping of breast cancer, long non-coding RNAs (lncRNAs) play crucial role gene expression regulation, differentiation, maintenance genomic stability. Here, we developed modular framework lncRNA identification applied it cohort identify novel lncRNAs not previously annotated. To investigate potential biological function, regulatory mechanisms, relevance lncRNAs, elucidated chromatin features these along associated protein-coding genes putative enhancers involved networks. Furthermore, uncovered patterns annotated identified were related hormone response PAM50 criterion, well immune progression states across cells checkpoint genes. Collectively, comprehensive functional analysis revealed by altering participating networks, contributing better insight into heterogeneity avenues intervention.

Язык: Английский

Процитировано

1