Ümit Karakaş

Dr. Ümit Karakaş

orcid

Research Focus & Metrics

Academic Career Length

10Years (2017-Present)

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

Representative Publications

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1 June 2017 in OMICS: A Journal of Integrative Biology
Verified
Journal Article
Closed access
ÜKÜmit Karakaş
Ümit Karakaş
OAOzlem Izci Ay
Ozlem Izci Ay
MAMustafa Ertan Ay
Mustafa Ertan Ay
Wei WangWei Wang
Wei Wang
MSMehmet Ali Sungur
Mehmet Ali Sungur
Mehmet Emin ErdalMehmet Emin Erdal
Mehmet Emin Erdal
Attention-deficit/hyperactivity disorder (ADHD) is one of the most prevalent complex psychiatric disorders in children as well as adults. ADHD impacts not only the affected individuals but also their families and social and professional networks. The clinical and diagnostic criteria for ADHD remain imprecise, in part, due to lack of robust biomarkers. ADHD comprises multiple subsets of diseases that present a shared set of downstream clinical findings, while displaying extensive molecular heterogeneity. This calls for innovation in diagnostic strategies that can help establish an ADHD diagnosis unequivocally as well as guiding precision medicine in this common mental health disorder. No study has examined, to the best of our knowledge, the upstream regulation of miRNAs that impact the downstream final ADHD phenotype. The latter focus on putative genetic biomarkers that regulate the regulators and can be tested empirically, for example, through genetic association analyses of the biogenesis pathways for miRNAs that impact the ADHD phenotype. Hence, we report here polymorphic variation in 10 miRNA biogenesis pathway candidate genes, including RNASEN , DGCR8 , XPO5 , RAN , DICER1 , TARBP2 , AGO1 , AGO2 , GEMIN3 , and GEMIN4 , in a large sample from the Eastern Mediterranean region ( N = 355; 191 cases and 164 controls). We found that AGO1 rs595961 was significantly associated with ADHD susceptibility ( p < 0.05). While polymorphic variation in other miRNA biogenesis pathway genes did not display a significant association in the present sample, the observations reported herein on miRNA biogenesis variation offer a new avenue of research for innovation in biomarker discovery concerning ADHD and other complex psychiatric diseases with major global health burden.

1 March 2017 in OMICS: A Journal of Integrative Biology
Verified
Journal Article
Closed access
ŞYŞenay Görücü Yılmaz
Şenay Görücü Yılmaz
Adrián LLerenaAdrián LLerena
Adrián LLerena
FAFernando De Andrés
Fernando De Andrés
ÜKÜmit Karakaş
Ümit Karakaş
HGHasan Gündoğar
Hasan Gündoğar
VÖVural Özdemir
Vural Özdemir
Public policies to stop or reduce cigarette smoking and exposure to secondhand smoke and associated diseases have yielded successful results over the past decade. Yet, the growing worldwide popularity of another form of tobacco consumption, water pipe smoking, has received relatively less attention. To the best of our knowledge, no study to date has evaluated the effects of water pipe smoking on cytochrome P450 (CYP450) activities and drug interaction potential in humans, whereas only limited information is available on the impact of secondhand smoke on drug metabolism. In a sample of 99 healthy volunteers (28 water pipe smokers, 30 secondhand tobacco smoke exposed persons, and 41 controls), we systematically compared CYP1A2 and CYP2A6 enzyme activities in vivo using caffeine urine test. The median self-reported duration of water pipe smoking was 7.5 h/week and 3 years of exposure in total. The secondhand smoke group had a median of 14 h of self-reported weekly exposure to tobacco smoke indoor where a minimum of five cigarettes were smoked/hour for a total of 3.5 years (median). Analysis of variance did not find a significant difference in CYP1A2 and CYP2A6 activities among the three study groups ( p > 0.05). Nor was there a significant association between the extent of water pipe or secondhand smoke exposure and the CYP1A2 and CYP2A6 activities ( p > 0.05). Further analysis in a subsample with smoke exposure more than the median values also did not reveal a significant difference from the controls. Although we do not rule out an appreciable possible impact of water pipe smoke and secondhand smoke on in vivo activities of these two drug metabolism pathways, variability in smoke constituents from different tobacco consumption methods (e.g., water pipe) might affect drug metabolism in ways that might differ from that of cigarette smoke. Further studies in larger prospective samples are recommended to evaluate water pipe and secondhand tobacco smoke effects on CYP450 function, particularly at higher smoke exposure conditions.

19 December 2025 in Diagnostics
Verified
Journal Article
Open access
PDF file
CACemile Ardıç
Cemile Ardıç
MAMustafa Ertan Ay
Mustafa Ertan Ay
KÇKenan Çevik
Kenan Çevik
ATANIL TOMBAK
ANIL TOMBAK
ÖAÖzlem IZCI İzci Ay
Özlem IZCI İzci Ay
Mehmet Emin ErdalMehmet Emin Erdal
Mehmet Emin Erdal
Background: Myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML) are clonal hematological disorders that share molecular origins but present with distinct clinical features. MicroRNAs (miRNAs) are key post-transcriptional regulators, and their altered expression may reflect biological shifts contributing to disease progression. Methods: Expression levels of miR-155, miR-181, miR-221, miR-222, and miR-223 were analyzed by RT-qPCR in bone marrow samples from 37 MDS patients, 20 AML patients, and 7 controls. Group comparisons were performed using ANOVA (with Benjamini–Hochberg correction) and Tukey post hoc testing. Diagnostic performance and network behavior were evaluated using ROC analysis, Pearson correlation matrices, and principal component analysis (PCA). Results: miR-155, miR-181, and miR-223 were upregulated in AML, whereas miR-221 and miR-222 were downregulated. miR-222 showed the highest diagnostic accuracy (AUC ~0.87 for both AML vs. control and MDS vs. control). Its expression was significantly higher in high IPSS-R MDS cases (p = 0.046), with a similar upward tendency for miR-221 (p = 0.054). Progressive loss of coordinated miRNA expression was observed from controls to MDS and AML. PCA supported these findings by showing separation mainly driven by miR-222 and miR-155. Conclusions: Combined miRNA profiling highlights miR-222 and, to a lesser extent miR-155, as consistent indicators of myeloid disease transformation. While further validation in larger and genetically stratified cohorts is warranted, these findings support the potential contribution of miRNA signatures to diagnostic evaluation and risk stratification in MDS and AML, in line with precision hematology approaches.

31 January 2025 in Mersin Üniversitesi Tıp Fakültesi Lokman Hekim Tıp Tarihi ve Folklorik Tıp Dergisi
Verified
Journal Article
Open access
PDF file
ÜKÜmit Karakaş
Ümit Karakaş
Amaç: Lavanta yağı, Lamiaceae ailesinin önemli bir üyesi olan lavanta bitkisinden elde edilen ve çeşitli terapötik etkilerle öne çıkan bir uçucu yağdır. Tarihsel olarak, antik medeniyetlerden günümüze kadar antibakteriyel, antienflamatuar, anksiyolitik, antifungal ve yara iyileştirici özellikleri nedeniyle geniş bir kullanım alanı bulmuştur. Lavanta yağının temel bileşenleri olan linalool ve linalil asetat, sinir sistemi üzerinde yatıştırıcı etkiler gösterirken, inflamasyonu ve oksidatif stresi azaltarak çeşitli kronik hastalıkların tedavisine yardımcı olabilmektedir. Yapılan araştırmalar, lavanta yağının nörolojik bozukluklardan kansere kadar uzanan geniş bir etki spektrumu olduğunu ortaya koymuş, ancak bu etkilerin moleküler düzeyde nasıl gerçekleştiği henüz tam olarak anlaşılmamıştır. Çalışmanın amacı güncel literatürü mikroRNA’lar çerçevesinde derlemektir. Yöntem: Çalışmanın içeriği “Lavanta yağı”, “miRNA”, “epigenetik”, “gen ifadesi” anahtar kelimelerinin kombinasyonları ile PubMed, Google akademik, Web of science ve Science direct veri tabanlarından yapılan taramalarla oluşturulmuştur. Bulgular: Son yıllarda, esansiyel yağların genetik ve epigenetik düzeydeki etkileri üzerinde durulmakta ve miRNA'lar ile olası etkileşimleri incelenmektedir. miRNA'ların gen ekspresyonunun düzenlenmesindeki kritik rolü göz önüne alındığında, lavanta yağının özellikle stres, depresyon ve inflamasyonla ilişkili miRNA'ları etkileyerek genetik mekanizmaları modüle etme potansiyeli büyük bir araştırma alanı olarak karşımıza çıkmaktadır. Ancak, bu alandaki literatür eksikliği dikkat çekmektedir. Lavanta yağının terapötik etkilerinin daha iyi anlaşılması, özellikle miRNA'lar üzerindeki etkilerine odaklanan moleküler çalışmaların artmasıyla mümkün olacaktır. Sonuç: Gelecekteki çalışmalar, lavanta yağının moleküler biyolojideki yerini sağlamlaştırabilir ve klinik kullanımı genişletebilir. Bu doğrultuda, lavanta yağının biyolojik mekanizmalarını aydınlatmak, onu hastalıkların tedavisinde daha etkili bir araç haline getirebilir.

31 December 2019 in Mersin Üniversitesi Sağlık Bilimleri Dergisi
Verified
Journal Article
Open access
PDF file
MAMustafa Ertan Ay
Mustafa Ertan Ay
EÇEzgi Çokakli
Ezgi Çokakli
MÇMurat Çokakli
Murat Çokakli
ÜKÜmit Karakaş
Ümit Karakaş
ÖAÖzlem IZCI İzci Ay
Özlem IZCI İzci Ay
Mehmet Emin ErdalMehmet Emin Erdal
Mehmet Emin Erdal
Amaç: Amniyotik sıvı farklı seviyelerde kendini yenileyebilen hücre gruplarından oluşmaktadır ve bu hücrelerin kök hücre özellikleri henüz tam olarak karakterize edilmemiştir. Son yıllarda amniyotik sıvı hücreleri (AFC) rejenaratif tıp için umut veren kök hücre kaynağı olarak görülmektedir. AFC’ler transfeksiyonel ve kimyasal stratejiler ile indüklenmiş pluripotent kök hücre (iPSC)’ler oluşturmak için terminal olarak farklılaşmış hücrelerden daha kolay ve etkili bir şekilde yeniden programlanabilirler. Fakat AFC’lerin kök hücre potansiyelleri ve farklı hücre soylarına farklılaşma kapasitesi tam olarak anlaşılamamıştır. Bu çalışmada amniyotik sıvı hücrelerinde kök hücre pluripotensi belirteçlerinin ifadelerinin ve kök hücre karakterlerinin belirlenmesi amaçlanmıştır. Yöntem: Bu çalışmada, 17 amniyon sıvısından elde edilen AFC’lerde pluripotensi belirteçlerinin ifade edilip edilmediği geleneksel RT-PCR ile kalitatif olarak araştırılmıştır. Bulgular: Elde edilen sonuçlar, farklı hastalardan alınan AFC örneklerinde incelenen pluripotensi belirteçlerinden OCT3/OCT4, SOX2, KLF4, MYC, KIT, NANOG, DPPA3, DPPA5, FUT4, SALL4’ün ifade edildiğini, UTF1 için ise non-spesifik ifade olduğunu göstermektedir. Sonuç: Elde edilen bulgular doğrultusunda AFC’nin kendine özgü bir kök hücre profiline sahip olduğu ve pluripotensi belirteçlerinin yeniden programlama ve rejeneratif tıp uygulamaları için hücre seçiminde etkili şekilde kullanılabileceği düşünülmektedir.

14 December 2025 in Biomedicines
Verified
Journal Article
Open access
PDF file
KÇKenan Çevik
Kenan Çevik
MAMustafa Ertan Ay
Mustafa Ertan Ay
ATANIL TOMBAK
ANIL TOMBAK
ÖAÖzlem IZCI İzci Ay
Özlem IZCI İzci Ay
ÜKÜmit Karakaş
Ümit Karakaş
Mehmet Emin ErdalMehmet Emin Erdal
Mehmet Emin Erdal
Background: Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are clonal stem cell disorders in which disrupted post-transcriptional regulation contributes to aberrant hematopoiesis and leukemic transformation. The miRNA biogenesis machinery, which comprises Drosha, DGCR8, Dicer, TARBP2, and AGO1, ensures the precise maturation of miRNAs that control lineage commitment and proliferation. However, the extent to which alterations in this pathway reshape hematopoietic gene networks during myeloid disease evolution remains largely unexplored. Methods: Bone marrow samples from newly diagnosed, untreated MDS and AML patients and matched healthy controls were analyzed for the expression of five key miRNA biogenesis genes using quantitative real-time PCR. Statistical comparisons, correlation matrices, and ROC analyses were performed to characterize gene-expression differences. These results were integrated with multigene logistic modeling, decision-curve analysis, and exploratory random forest/SHAP approaches to evaluate molecular interactions and diagnostic relevance. Results: DROSHA, DICER1, and TARBP2 were significantly downregulated in both MDS and AML, suggesting impaired miRNA maturation and a loss of global post-transcriptional control. DGCR8 expression increased across higher-risk MDS groups, suggesting compensatory activation of the Microprocessor complex, whereas AGO1 levels remained relatively stable, consistent with partial maintenance of RISC function. Correlation analyses revealed a co-regulated DROSHA–TARBP2–AGO1 module. ROC, logistic, and machine learning models identified DGCR8 and DICER1 as the strongest diagnostic discriminators. The integrated five-gene signature achieved high discriminative performance (AUC ≈ 0.98) and showed promise but remains preliminary potential for clinical application. Conclusions: Our findings suggest that defects in miRNA biogenesis disrupt hematopoietic homeostasis, reflecting common mechanisms in MDS and AML. The dysregulation of DICER1, DGCR8, and TARBP2 offers insights into miRNA-driven leukemogenesis and may pave the way for miRNA-based diagnostic and therapeutic strategies, pending validation in larger cohorts. Although transcript-level data are provided, future studies should include functional validation to determine the impact on downstream miRNA processing and hematopoietic pathways.