Kazim Yalcin Arga

• Professor
• Professor at Marmara University

Objectives Acute myeloid leukemia (AML) is a severe blood cancer with less than 50 % long-term survival. Despite advancements in treatment options, relapse is still the major obstacle. The main reason of this problem is ineffective targeting of leukemic stem cells (LSCs), which play an important role in tumor development and relapse. In our previou...

Earthquakes are one of the most destructive natural hazards that cause loss of life, loss of property and destruction of infrastructure when they interact with vulnerabilities in human systems. The health impacts of these events are not only limited to immediate trauma and injuries, but also affect both physical and mental health in the short and l...

Background Clinical biomarkers, allow better classification of patients according to their disease risk, prognosis, and/or response to treatment. Although affordable omics-based approaches have paved the way for quicker identification of putative biomarkers, validation of biomarkers is necessary for translation of discoveries into clinical applicat...

Objectives Behçet disease (BD) has heterogeneous presentations, mainly mucocutaneous, vascular, and ocular manifestations. The mechanisms associated with different phenotypes have not been clarified. We aimed to investigate the expression of innate and adaptive immunity–related cytokines in these 3 main BD phenotypes in active and untreated states...

Background & Aims Hepatocellular Carcinoma (HCC) is the most prevalent types of liver cancer worldwide, with chronic infection of Hepatitis B Virus (HBV) being a major risk factor. The ubiquitin-proteasome system plays a critical role in protein degradation, cellular homeostasis, and cell cycle regulation. Dysregulation of proteasomal activity has...

Infection with SARS-CoV2, which is responsible for COVID-19, can lead to differences in disease development, severity and mortality rates depending on gender, age or the presence of certain diseases. Considering that existing studies ignore these differences, this study aims to uncover potential differences attributable to gender, age and source of...

In recent years, significant progress has been made in elucidating the pathogenic mechanisms underlying acute myeloid leukemia (AML), leading to the accelerated discovery of new therapeutics and innovative treatment strategies. There is growing interest in understanding the central role of the immune system in the development, progression, and recu...

Tumor mutation burden (TMB) has profound implications for personalized cancer therapy, particularly immunotherapy. However, the size of the panel and the cutoff values for an accurate determination of TMB are still controversial. In this study, a pan-cancer analysis was performed on 22 cancer types from The Cancer Genome Atlas. The efficiency of ge...

The genome-scale metabolic model (GEM) has emerged as one of the leading modeling approaches for systems-level metabolic studies and has been widely explored for a broad range of organisms and...

Ovarian cancer is a major cause of cancer deaths among women. Early diagnosis and precision/personalized medicine are essential to reduce mortality and morbidity of ovarian cancer, as with new molecular targets to accelerate drug discovery. We report here an integrated systems biology and machine learning (ML) approach based on the differential coe...

Pharmacomicrobiomics is a rapidly developing field that promises to make significant contributions to predictive, personalized, preventive, and participatory (P4) medicine. This is becoming evident particularly in the field of precision (P4) oncology by taking seriously the crucial role microbiome plays in health and disease. Several studies have a...

Background/aim: The complicated nature of tumor formation makes it difficult to identify discriminatory genes. Recently, transcriptome-based supervised classification methods using support vector machines (SVMs) have become popular in this field. However, the inclusion of less significant variables in the construction of classification models can l...

Acute myeloid leukemia (AML) is a heterogeneous disease and the most common form of acute leukemia with a poor prognosis. Due to its complexity, the disease requires the identification of biomarkers for reliable prognosis. To identify potential disease genes that regulate patient prognosis, we used differential co‐expression network analysis and tr...

Cancer research calls for new approaches that account for the regulatory complexities of biology. We present, in this study, the differential transcriptional regulome (DIFFREG) approach for the identification and prioritization of key transcriptional regulators and apply it to the case of renal cell carcinoma (RCC) biology. Of note, RCC has a poor...

Precision/personalized medicine in oncology has two key pillars: molecular profiling of the tumors and personalized reporting of the results in ways that are clinically contextualized and triangulated. Moreover, neurosurgery as a field stands to benefit from precision/personalized medicine and new tools for reporting of the molecular findings. In t...

Regeneration is a homeostatic process that involves the restoration of cells and body parts. Most of the molecular mechanisms and signalling pathways involved in wound healing, such as proliferation, have also been associated with cancer cell growth, suggesting that cancer is an over/unhealed wound. In this study, we examined differentially express...

Plectin, encoded by PLEC, is a cytoskeletal and scaffold protein with a number of unique isoforms that act on various cellular functions such as cell adhesion, signal transduction, cancer cell invasion, and migration. While plectin has been shown to display high expression and mislocalization in tumor cells, our knowledge of the biological signific...

Human papillomavirus (HPV) infection, especially HPV16, is one of the causative factors for the development of head and neck squamous cell (HNSC) carcinoma. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and clinical features, so they should be evaluated differently depending on their HPV status. Given...

New technologies and dizzying developments in the field of molecular biology and genetics have placed the molecular perspective at the center of health and life sciences. This book provides basic information about the field, as well as current approaches and application areas. Starting from the DNA molecule, which is the entry key to the world of m...

Breast cancer is the second leading cause of death for women in the United States, and early detection could offer patients the opportunity to receive early intervention. The current methods of diagnosis rely on mammograms and have relatively high rates of false positivity, causing anxiety in patients. We sought to identify protein markers in saliv...

Cancer and arachidonic acid (AA) have important linkages. For example, AA metabolites regulate several critical biological functions associated with carcinogenesis: angiogenesis, apoptosis, and cancer invasion. However, little is known about the comparative changes in metabolite expression of the arachidonic acid pathway (AAP) in carcinogenesis. In...

Introduction Integrating interaction data with biological knowledge can be a critical approach for drug development or drug repurposing. In this context, host-pathogen-protein-protein interaction (HP-PPI) networks are useful instrument to uncover the phenomena underlying therapeutic effects in infectious diseases, including cervical cancer, which i...

Aims Diabetes mellitus is a chronic disease that limits the quality and duration of life. We aimed to estimate the impact of demographic change on the burden of prediabetes and diabetes between 2010 and 2021, and the projections to 2030 and 2045 in Turkiye. Materials and methods Prediabetes and diabetes estimates were calculated by direct standard...

Acute myeloid leukemia (AML) is a heterogeneous disease defined by the proliferation of immature myeloid progenitor cells in the bone marrow that impairs normal blood cell development and leads to bone marrow failure. AML is characterized by a variety of chromosomal abnormalities and gene mutations. These abnormalities and mutations result in marke...

Cancer hallmark genes and proteins orchestrate and drive carcinogenesis to a large extent, therefore, it is important to study these features in different cancer types to understand the process of tumorigenesis and discover measurable indicators. We performed a pan-cancer analysis to map differentially interacting hallmarks of cancer proteins (DIHC...

Purpose: Non-functioning pituitary neuroendocrine tumors are challengingly diagnosed tumors in the clinic. Transsphenoidal surgery remains the first-line treatment. Despite the development of state-of-the-art techniques, no drug therapy is currently approved for the treatment. There are also no randomized controlled trials comparing therapeutic st...

Introduction: Although the idea that carcinogenesis might be caused by viruses was first voiced about 100 years ago, today's data disappointingly show that we have not made much progress in preventing and/or treating viral cancers in a century. According to recent studies, infections are responsible for approximately 13% of cancer development in t...

Amyotrophic lateral sclerosis (ALS) is a fatal disease of motor neurons that mainly affects the motor cortex, brainstem, and spinal cord. Under disease conditions, microglia could possess two distinct profiles, M1 (toxic) and M2 (protective), with the M2 profile observed at disease onset. SOD1 (superoxide dismutase 1) gene mutations account for up...

The rise of machine learning (ML) has recently buttressed the efforts for big data-driven precision oncology. This study used ensemble ML for precision oncology in breast cancer, which is one of the most common malignancies worldwide with marked heterogeneity of the underlying molecular mechanisms. We analyzed clinical and RNA-seq data from The Can...

Acute myeloid leukemia (AML) is a common, complex, and multifactorial malignancy of the hematopoietic system. AML diagnosis and treatment outcomes display marked heterogeneity and patient-to-patient variations. To date, AML-related biomarker discovery research has employed single omics inquiries. Multiomics analyses that reconcile and integrate the...

Cervical cancer is the fourth most commonly diagnosed cancer worldwide and, in almost all cases is caused by infection with highly oncogenic Human Papillomaviruses (HPVs). On the other hand, inflammation is one of the hallmarks of cancer research. Here, we focused on inflammatory proteins that classify cervical cancer patients by considering indivi...

Cardiovascular disease (CVD) is the leading cause of death among adults in developed countries. Among CVDs, abdominal aortic aneurysm (AAA) and aortic occlusive disease (AOD) are of great public health importance because of the high mortality rate in the elderly population. Despite significant molecular insights into AAA and AOD, the molecular mech...

Human papillomavirus (HPV) infection is one of the causative factors in the development of head and neck squamous cell carcinoma (HNSC). One in four HNSC cases is positive for HPV infection, and HPV16 is the most common infection in HNSC cancer. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and clinica...

Maturity-onset diabetes of the young (MODY) is a highly heterogeneous group of monogenic and nonautoimmune diseases. Misdiagnosis of MODY is a widespread problem and about 5% of patients with type 2 diabetes mellitus and nearly 10% with type 1 diabetes mellitus may actually have MODY. Using next-generation DNA sequencing (NGS) to facilitate accurat...

Innovation roadmaps are important, because they encourage the actors in an innovation ecosystem to creatively imagine multiple possible science future(s), while anticipating the prospects and challenges on the innovation trajectory. In this overarching context, this expert review highlights the present unmet need for therapeutic innovations for pit...

Aims Diabetes is a chronic disease that limits the quality and duration of life. We aimed to estimate the trends in prediabetes and diabetes between 2010-2020, and the projections to 2023 and 2045 in Turkey. Materials and methods Prediabetes and diabetes estimates were calculated by direct standardization using age/sex-specific data from the previo...

Pituitary neuroendocrine tumors (PitNETs) constitute 9% to 12% of all primary brain tumors. However, pituitary adenomas are one of the rare types of cancer in the world that have not undergone enough research and whose mechanisms have not been elucidated yet. Therefore, there is an unmet need for reliable biological markers for the diagnosis, strat...

Genomic medicine has made important strides over the past several decades, but as new insights and technologies emerge, the applications of genomics in medicine and planetary health continue to evolve and expand. An important grand challenge is harnessing and making sense of the genomic big data in ways that best serve public and planetary health....

The identification of biomolecules associated with papillary thyroid cancer (PTC) has upmost importance for the elucidation of the disease mechanism and the development of effective diagnostic and treatment strategies. Despite particular findings in this regard, a holistic analysis encompassing molecular data from different biological levels has be...

Background: Breast cancer (BC) is one of the most life-threatening cancer types among women. Despite major developments in medical sciences and technologies, the incidence and mortality rates of BC cases are still increasing. One of the reasons for this increase is the absence of an easy to perform early-diagnostic tool. Although there are defined...

There is a critical requirement for alternative strategies to provide the better treatment in colorectal cancer (CRC). Hence, our goal was to propose novel biomarkers as well as drug candidates for its treatment through differential interactome based drug repositioning. Differentially interacting proteins and their modules were identified, and thei...

Introduction: To investigate the effect of preexisting treatment with dipeptidyl peptidase-4 inhibitors (DPP-4is) on COVID-19-related hospitalization and mortality in patients with type 2 diabetes mellitus (T2DM). Methods: A multicenter, retrospective cohort study was conducted using patient data extracted from the Turkish National Electronic Da...

Esophageal squamous cell carcinoma (ESCC) is among the most dangerous cancers with high mortality and lack of robust diagnostics and personalized/precision therapeutics. To achieve a systems-level understanding of tumorigenesis, unraveling of variations in the protein interactome and determination of key proteins exhibiting significant alterations...

Colorectal cancer (CRC) is the most commonly diagnosed fatal cancer in both women and men worldwide. CRC ranked second in mortality and third in incidence in 2020. It is difficult to diagnose CRC at an early stage as there are no clinical symptoms. Despite advances in molecular biology, only a limited number of biomarkers have been translated into...

In a digital society, shall we be the authors of our own experience, not only during our lifetime but also after we die? We ask this question because dying and bereavement have become even harder, and much less private, in the digital age. New big data-driven digital industries and technologies are on the rise, with promises of interactive 3D avata...

Pituitary neuroendocrine tumors (PitNETs) are the second most common type of intracranial neoplasia. Since their manifestation usually causes hormone hypersecretion, effective management of PitNETs is indisputably necessary. Most of the non-functioning PitNETs pose a real challenge in diagnosis as they grow without giving any signs. Despite the goo...

Diabetes is a common disorder with a heterogeneous clinical presentation and an enormous burden on health care worldwide. About 1-6% of patients with diabetes suffer from maturity-onset diabetes of the young (MODY), the most common form of monogenic diabetes with autosomal dominant inheritance. MODY is genetically and clinically heterogeneous and c...

Amaç: Sağlık Meslek Yüksekokulu öğrencilerinin tütün ve tütün ürünleri kullanma davranışlarını incelemek ve bu davranış üzerinde belirleyici faktörleri ortaya koymaktır. Yöntem: Bu araştırma, Medipol Üniversitesi Sağlık Hizmetleri Meslek Yüksekokulu'nda gerçekleştirilmiştir. Toplam 26 soruluk olarak hazırlanan, yapılandırılmış bir anket, 307 öğrenc...

Aim: To examine tobacco and tobacco use behaviors of the students of Health Vocational School and to reveal the determining factors on this behavior. Methods: This research was carried out in Medipol University Health Services Vocational School. A structured questionnaire with a total of 26 questions was applied to 307 students face to face. The da...

Cancer stem-like cells (CSCs) possess the ability to self-renew and differentiate, and they are among the major factors driving tumorigenesis, metastasis, and resistance to chemotherapy. Therefore, it is critical to understand the molecular substrates of CSC biology so as to discover novel molecular biosignatures that distinguish CSCs and tumor cel...

Özet: Bu derlemenin amacı, Türkiye'deki üniversite öğrencilerinin tütün ve tütün ürünleri kullanımına yönelik tutum ve davranışları ve bunları etkileyen faktörleri belirlemek için yapılan çalışmaları kapsamlı bir şekilde incelemek ve bu çalışmalardan elde edilen sonuçları sistematik olarak değerlendirmektir. Bu sistematik derlemede Google Akademik,...

Editorial

Introduction: Prolactinomas, also called lactotroph adenomas, are the most encountered type of hormone-secreting pituitary neuroendocrine tumors (PitNET) in the clinic. The preferred first-line therapy is a medical treatment with dopamine agonists (DA), mainly cabergoline, to reduce serum prolactin levels, tumor volume, and mass effect. However, i...

Aims Type 2 diabetes mellitus (T2DM) is a risk factor for severe COVID-19. Our aim was to compare the clinical outcomes of patients with and without T2DM during the first hit of COVID-19 in Istanbul Methods A retrospective population-based study was conducted including all consecutive adult symptomatic COVID-19 cases. Patients were confirmed with...

Although many studies have been conducted on single gene therapies in cancer patients, the reality is that tumor arises from different coordinating protein groups. Unveiling perturbations in protein interactome related to the tumor formation may contribute to the development of effective diagnosis, treatment strategies, and prognosis. In this study...

Elk-1, a member of the ternary complex factors (TCFs) within the ETS (E26 transformation-specific) domain superfamily, is a transcription factor implicated in neuroprotection, neurodegeneration, and brain tumor proliferation. Except for known targets, c-fos and egr-1, few targets of Elk-1 have been identified. Interestingly, SMN, SOD1, and PSEN1 pr...

Pancreatic cancer is one of the most fatal malignancies and the seventh leading cause of cancer-related deaths related to late diagnosis, poor survival rates, and high incidence of metastasis. Unfortunately, pancreatic cancer is predicted to become the third leading cause of cancer deaths in the future. Therefore, diagnosis at the early stages of p...

Drug repositioning is a powerful method that can assists the conventional drug discovery process by using existing drugs for treatment of a disease rather than its original indication. The first examples of repurposed drugs were discovered serendipitously, however data accumulated by high-throughput screenings and advancements in computational biol...

Cancer as the leading cause of death worldwide has many issues that still need to be addressed. Since the alterations on the glycan compositions or/and structures (i.e., glycosylation, sialylation, and fucosylation) are common features of tumorigenesis, glycomics becomes an emerging field examining the structure and function of glycans. In the past...

Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with deficits in social communication ability and repetitive behavior. The pathophysiological events involved in the brain of this complex disease are still unclear. Methods: In this study, we aimed to profile the gene expression signatures of brain cortex of ASD patients,...

PEA3 transcription factor subfamily is present in a variety of tissues with branching morphogenesis, and play a particularly significant role in neural circuit formation and specificity. Many target genes in axon guidance and cell–cell adhesion pathways have been identified for Pea3 transcription factor (but not for Erm or Er81); however it was not...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease, more commonly COVID-19 has emerged as a world health pandemic. There are couples of treatment methods for COVID-19, however, well-established drugs and vaccines are urgently needed to treat the COVID-19. The new drug discovery is a tremendous challenge; repurposing of existing dr...

Advances in omics technologies have made it possible to unravel biomarkers from different biological levels. Intensive studies have been carried out to uncover the dysregulations in psoriasis and to identify molecular signatures associated with the pathogenesis of psoriasis. In this review, we presented an overview of the current status of the omic...

Colorectal cancer (CRC) is one of the most fatal types of cancers that is seen in both men and women. CRC is the third most common type of cancer worldwide. Over the years, several drugs are developed for the treatment of CRC; however, patients with advanced CRC can be resistant to some drugs. P-glycoprotein (P-gp) (also known as Multidrug Resistan...

Invitation for your contribution in a Special Issue in Journal of Personalized Medicine

Artificial intelligence, machine learning, health care robots, and algorithms for clinical decision-making are currently being sought after in diverse fields of clinical medicine and bioengineering. The field of personalized medicine stands to benefit from new technologies so as to harness the omics big data, for example, to individualize and accel...

Proteasome inhibitors have great success for their therapeutic potential against hematologic malignancies. First generation proteasome inhibitor bortezomib induced peripheral neuropathy is considered as a limiting factor in chemotherapy and its second-generation counterpart carfilzomib is associated with lower rates of neurotoxicity. The mitochondr...

Here, we review basic concepts and developments of network biology with the aid of omics technologies, discussing different types of interactome networks and the comprehensions/lessons that can be taken from analyzing them. We also discuss why interactome networks are essential in biology, how these can be reconstructed and integrated with each oth...

Until the advent of the traditional reductionist technologies, the systems biology uses a holistic and integrative approach and provides assessment to the system as a whole. Omics technologies represent the milestone of systems biology. Adding a term omics (x-omics) to any molecular term refers to a global and comprehensive evaluation of a set of b...

Deciphering the variations in the protein interactome is required to reach a systems-level understanding of tumorigenesis. To accomplish this task, we have considered the clinical and transcriptome data on >6000 samples from The Cancer Genome Atlas for 12 different cancers. Utilizing the gene expression levels as a proxy, we have identified the dif...

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). In a subgroup of patients with PTC, the disease progresses to an invasive stage or in some cases to distant organ metastasis. At present, there is an unmet clinical and diagnostic need for early identification of patients with PTC who are at risk of disease progressio...

Precision/personalized medicine is a hot topic in health care. Often presented with the motto ''the right drug, for the right patient, at the right dose, and the right time,'' precision medicine is a theory for rational therapeutics as well as practice to individualize health interventions (e.g., drugs, food, vaccines, medical devices, and exercise...

Chromophobe renal cell carcinoma (KICH) is one of renal cell carcinoma types and effective drugs are not available for treatment of this disease. With the development of technology, computer-based drug development studies have started to gain importance in order to shed light on experimental studies. The aim of this study is to discover new drug ca...

Precision/personalized medicine is a hot topic in health care. Often presented with the motto ''the right drug, for the right patient, at the right dose, and the right time,'' precision medicine is a theory for rational therapeutics as well as practice to individualize health interventions (e.g., drugs, food, vaccines, medical devices, and exercise...

Human Renal Cell Carcinoma (RCC) has the highest mortality rate of the genitourinary cancers in adults [1]. Understanding biological mechanism of RCC may improve the current diagnosis, treatment and prognosis of RCC. Renal clear cell carcinoma (KIRC), papillary renal cell carcinoma (KIRP) and chromophobe renal cell carcinoma (KICH) significantly di...

The current September issue of OMICS is featuring this exciting interview article with Professor K. Yalc¸ın Arga, PhD, a multi-omics pioneer and senior expert on statistical modeling, analysis, and translation of Big Data to health care innovation. He is at Marmara University and the Health Institutes of Turkey (TUSEB), in Istanbul, Turkey. For man...

Urodele amphibians such as the axolotl (Ambystoma mexicanum) display a large capacity for tissue regeneration and remarkable resistance to cancer. As a model organism, axolotl thus offers a unique opportunity for cancer research and anticancer drug discovery, not to mention the discerning mechanisms that underpin controlled cellular growth and rege...

Non-functioning pituitary adenomas (NFPAs) are tumors with clinically challenging features since they have insidious progression. A complex network of gene interactions is thought to have roles in tumor formation and progression. Therefore, revealing the genetic network behind NFPA tumorigenesis is not only essential to attain further knowledge of...

Triple-negative breast cancer (TNBC), which is largely synonymous with the basal-like molecular subtype, is the 5th leading cause of cancer deaths for women in the United States. The overall prognosis for TNBC patients remains poor given that few treatment options exist; including targeted therapies (not FDA approved), and multi-agent chemotherapy...

Cervical cancer is the second most common malignancy and the third reason for mortality among women in developing countries. Although infection by the oncogenic human papilloma viruses is a major cause, genomic contributors are still largely unknown. Network analyses, compared with candidate gene studies, offer greater promise to map the interactio...

Target of rapamycin (TOR) is a major signaling pathway and regulator of cell growth. TOR serves as a hub of many signaling routes and is implicated in the pathophysiology of numerous human diseases, including cancer, diabetes, and neurodegeneration. Therefore, elucidation of unknown components of TOR signaling that could serve as potential biomarke...

Background: Genome-scale metabolic models (GEMs) offer insights into cancer metabolism and have been used to identify potential biomarkers and drug targets. Drug repositioning is a time- and cost-effective method of drug discovery that can be applied together with GEMs for effective cancer treatment. Methods: In this study, we reconstruct a prostat...

Background and objectives: Colorectal cancer (CRC) is the second most common cause of cancer-related death in the world, but early diagnosis ameliorates the survival of CRC. This report aimed to identify molecular biomarker signatures in CRC. Materials and Methods: We analyzed two microarray datasets (GSE35279 and GSE21815) from the Gene Expression...