Berna Yıldırım

Dr. Berna Yıldırım

Faculty of Medicine, Histology and Embryology Department, İstanbul Atlas University, Istanbul, İstanbul, Turkey (Türkiye)
orcid

Research Focus & Metrics

Academic Career Length

11Years (2016-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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1 October 2020 in OMICS: A Journal of Integrative Biology
Verified
Journal Article
Closed access
MSMustafa Sibai
Mustafa Sibai
EAEbru Altuntaş
Ebru Altuntaş
Berna YıldırımBerna Yıldırım
Berna Yıldırım
GÖGürkan Öztürk
Gürkan Öztürk
SYSüleyman Yıldırım
Süleyman Yıldırım
TDTuran Demircan
Turan Demircan
With a world population living longer as well as marked disparities in life expectancy, understanding the determinants of longevity is one of the priority research agendas in 21st century life sciences. To this end, the blind mole-rat ( Spalax leucodon ), a subterranean mammalian, has emerged as an exceptional model organism due to its astonishing features such as remarkable longevity, hypoxia and hypercapnia tolerance, and cancer resistance. The microbiome has been found to be a vital parameter for cellular physiology and it is safe to assume that it has an impact on life expectancy. Although the unique characteristics of Spalax make it an ideal experimental model for longevity research, there is limited knowledge of the bacterial composition of Spalax microbiome, which limits its in-depth utilization. In this study, using 16S rRNA amplicon sequencing, we report the gut and skin bacterial structure of Spalax for the first time. The diversity between fecal and skin samples was manifested in the distant clustering, as revealed by beta diversity analysis. Importantly, the longevity-linked Muribaculaceae bacterial family was found to be the dominating bacterial taxa in Spalax fecal samples. These new findings contribute toward further development of Spalax as a model for longevity research and potential linkages between microbiome composition and longevity.

1 September 2016 in Acta Histochemica
Verified
Journal Article
Closed access
TDTuran Demircan
Turan Demircan
AİAyşe Elif İlhan
Ayşe Elif İlhan
NANilüfer Aytürk
Nilüfer Aytürk
Berna YıldırımBerna Yıldırım
Berna Yıldırım
GOGurkan Ozturk
Gurkan Ozturk
IKIlknur Keskin
Ilknur Keskin

20 July 2018 in Scientific Reports
Verified
Journal Article
Open access
PDF file
TDTuran Demircan
Turan Demircan
GOGuvanch Ovezmyradov
Guvanch Ovezmyradov
Berna YıldırımBerna Yıldırım
Berna Yıldırım
IKİlknur Keskin
İlknur Keskin
AİAyşe Elif İlhan
Ayşe Elif İlhan
SYSüleyman Yıldırım
Süleyman Yıldırım
Axolotl (Ambystoma mexicanum) is a critically endangered salamander species and a model organism for regenerative and developmental biology. Despite life-long neoteny in nature and in captive-bred colonies, metamorphosis of these animals can be experimentally induced by administering Thyroid hormones (THs). However, microbiological consequences of this experimental procedure, such as host microbiota response, remain largely unknown. Here, we systematically compared host bacterial microbiota associated with skin, stomach, gut tissues and fecal samples, between neotenic and metamorphic axolotls based on 16S rRNA gene sequences. Our results show that distinct bacterial communities inhabit individual organs of axolotl and undergo substantial restructuring through metamorphosis. Skin microbiota among others, shifted sharply, as highlighted by a major transition from Firmicutes-enriched to Proteobacteria-enriched relative abundance and precipitously decreased diversity. Fecal microbiota of neotenic and metamorphic axolotl shared relatively higher similarity, suggesting that diet continues to shape microbiota despite fundamental transformations in the host digestive organs. We also reproduced the previous finding on reduction in regenerative capacity in limbs of axolotl following metamorphosis, highlighting the need to investigate whether shifts in microbiota is causally linked to regenerative capacity of axolotl. The initial results on axolotl microbiota provide novel insights into microbiological aspects of axolotl metamorphosis and will establish a baseline for future in-depth studies.

11 June 2025 in Discover Oncology
Verified
Journal Article
Open access
PDF file
Berna YıldırımBerna Yıldırım
Berna Yıldırım
KKKudret Kulak
Kudret Kulak
ABAyhan Bilir
Ayhan Bilir
Midkine (MDK) is a heparin-binding growth factor implicated in the pathogenesis of various diseases, including cancer, chronic inflammation, and multidrug resistance (MDR). While its expression is minimal in adult tissues, it becomes markedly elevated during embryogenesis and in response to injury, infection, or hypoxia. MDK modulates inflammatory responses by recruiting immune cells and enhancing proinflammatory cytokine production. In oncogenesis, it promotes tumor proliferation, angiogenesis, epithelial-to-mesenchymal transition (EMT), and therapeutic resistance. Elevated MDK levels are frequently associated with aggressive tumor behavior and poor clinical outcomes. This review synthesizes current knowledge on MDK’s expression profiles, molecular mechanisms, and functional roles across pathological conditions. It also discusses MDK’s emerging value as a diagnostic and prognostic biomarker, and highlights recent advances in therapeutic strategies including small molecule inhibitors, RNA-based approaches, and receptor-blocking peptides. Overall, MDK represents a promising target for future personalized therapies, although further preclinical and clinical validation is warranted to confirm its translational potential.

1 July 2024 in European Journal of Breast Health
Verified
Journal Article
Open access
Berna YıldırımBerna Yıldırım
Berna Yıldırım
KKKudret Kulak
Kudret Kulak
ABAyhan Bilir
Ayhan Bilir
Midkine (MDK) is a protein that contributes to both physiological and pathological processes. Several studies provide insight into the different roles of MDK in development, tissue repair, neural plasticity, and health and disease processes. This research further examined how MDK contributed to conditions, including neurological diseases, inflammation, and ischaemia. Furthermore, MDK overexpression has been reported in many kinds of cancer and MDK is recognized as a malignancy marker. MDK stimulates pro-tumor activity by regulating a number of signaling pathways, which increase cancer cell proliferation, survival, metastasis, and treatment resistance. However, studies have shown that MDK also functions as a molecule that regulates drug resistance. Several cancer therapy techniques have been suggested to modify MDK function, including antibody-based therapies, oligonucleotides, oncolytic viruses, and small compounds. Further research and experimentation will be required to establish the therapeutic relevance and efficacy of these treatments. This review focuses on the role of MDK in cancer biology, as well as its multiple different roles in health and disease processes.

28 October 2025 in Scientific Reports
Verified
Journal Article
Open access
PDF file
Berna YıldırımBerna Yıldırım
Berna Yıldırım
AAAgnes Ansa Archibong-Omon
Agnes Ansa Archibong-Omon
ABAyhan Bilir
Ayhan Bilir
Lithium chloride (LiCl), a widely used mood stabilizer, has been reported to modulate selective autophagy pathways, including mitophagy. However, its ultrastructural effects in three-dimensional (3D) tumor models remain incompletely characterized. In this study, we examined the subcellular alterations induced by LiCl in 3D spheroid cultures derived from Ishikawa endometrial cancer and SH-SY5Y neuroblastoma cells. Spheroids were treated with 1, 10, or 50 mM LiCl and analyzed using transmission electron microscopy (TEM). The analysis revealed double-membrane-bound vesicles surrounding degenerating mitochondria, along with cytoplasmic vacuolization and membrane remodeling. These morphological features are suggestive of mitophagic activity, accompanied by stress-related ultrastructural remodeling. Although molecular validation (e.g., LC3B or PINK1/Parkin Western blotting) was not performed, the observed ultrastructural profiles are consistent with organelle-selective autophagy. These findings underscore the dose-dependent cellular responses to LiCl and support the value of 3D cancer spheroids as models to explore non-canonical autophagy-related stress pathways. Future studies incorporating molecular markers such as LC3B, PINK1, Parkin, and Lamin B1 will be essential to confirm these observations.