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Article ; Online: Genetic biomarkers to guide poly(ADP-ribose) polymerase inhibitor precision treatment of prostate cancer.

Varnai, Reka / Sipeky, Csilla

2020 Volume 21, Issue 15, Page(s) 1101–1115

Abstract: Precision therapy for a subgroup of genetically defined metastatic castration-resistant prostate cancer patients may become a reality in the near future. DNA damage repair gene mutated prostate cancer might be vulnerable to treatment with PARP inhibitors ...

Abstract	Precision therapy for a subgroup of genetically defined metastatic castration-resistant prostate cancer patients may become a reality in the near future. DNA damage repair gene mutated prostate cancer might be vulnerable to treatment with PARP inhibitors (PARPi). PARPi clinical trials for prostate cancer investigate both germline and somatic genomic alterations of 43 genes for the applicability as genomic biomarker of PARPi sensitivity. Clinical trials with preliminary results show that
MeSH term(s)	Biomarkers, Tumor/genetics ; Clinical Trials as Topic/methods ; Genetic Association Studies/methods ; Genetic Markers/genetics ; Humans ; Male ; Poly(ADP-ribose) Polymerase Inhibitors/adverse effects ; Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use ; Precision Medicine/methods ; Prostatic Neoplasms, Castration-Resistant/drug therapy ; Prostatic Neoplasms, Castration-Resistant/genetics
Chemical Substances	Biomarkers, Tumor ; Genetic Markers ; Poly(ADP-ribose) Polymerase Inhibitors
Language	English
Publishing date	2020-10-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2019513-8
ISSN	1744-8042 ; 1462-2416
ISSN (online)	1744-8042
ISSN	1462-2416
DOI	10.2217/pgs-2020-0019
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Article ; Online: Overview of Registered Clinical Trials on Manual Therapy: Possible Implications of Genetic Testing for Personalized Treatment.

Pozsgai, Miklos / Szabo, Istvan / Nusser, Nora / Varnai, Reka / Sipeky, Csilla

In vivo (Athens, Greece)

2022 Volume 36, Issue 1, Page(s) 294–305

Abstract: Background/aim: Manual therapy (MT) is a frequently applied intervention offering individualized treatment in the clinic. In addition to the traditional approaches of MT, measuring molecular response to MT may offer better understanding of MT outcomes ... ...

Abstract	Background/aim: Manual therapy (MT) is a frequently applied intervention offering individualized treatment in the clinic. In addition to the traditional approaches of MT, measuring molecular response to MT may offer better understanding of MT outcomes in order to provide specific personalized treatment. The aim of this study was to summarize MT-related registered clinical trials, as well as to search for any evidence on MT and genetics. Patients and methods: A comprehensive search was conducted within the Clinical Trials database with predefined keywords mining for all types of MT-related clinical trials. Results: From the 47 trials, 20 had results and 27 had no results. MT alleviated pain and improved function almost in all trials. One registered clinical trial had investigated molecular outcomes of MT. Conclusion: MT is an effective and individualized treatment offering option in the management of several conditions. Interestingly, a clinical trial was found investigating molecular genetics and MT pinpointing an already existing link between genetics and MT. Therefore, further clinical trials may focus on genetics and MT for providing specific personalized treatment in future.
MeSH term(s)	Clinical Trials as Topic ; Exercise Therapy ; Genetic Testing ; Humans ; Musculoskeletal Manipulations ; Pain Management ; Precision Medicine
Language	English
Publishing date	2022-01-01
Publishing country	Greece
Document type	Journal Article
ZDB-ID	807031-3
ISSN	1791-7549 ; 0258-851X
ISSN (online)	1791-7549
ISSN	0258-851X
DOI	10.21873/invivo.12702
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Article ; Online: Novel prostate cancer susceptibility gene SP6 predisposes patients to aggressive disease.

Sipeky, Csilla / Tammela, Teuvo L J / Auvinen, Anssi / Schleutker, Johanna

Prostate cancer and prostatic diseases

2021 Volume 24, Issue 4, Page(s) 1158–1166

Abstract: Prostate cancer (PrCa) is one of the most common cancers in men, but little is known about factors affecting its clinical outcomes. Genome-wide association studies have identified more than 170 germline susceptibility loci, but most of them are not ... ...

Abstract	Prostate cancer (PrCa) is one of the most common cancers in men, but little is known about factors affecting its clinical outcomes. Genome-wide association studies have identified more than 170 germline susceptibility loci, but most of them are not associated with aggressive disease. We performed a genome-wide analysis of 185,478 SNPs in Finnish samples (2738 cases, 2400 controls) from the international Collaborative Oncological Gene-Environment Study (iCOGS) to find underlying PrCa risk variants. We identified a total of 21 common, low-penetrance susceptibility loci, including 10 novel variants independently associated with PrCa risk. Novel risk loci were located in the 8q24 (CASC8 rs16902147, OR 1.86, p
MeSH term(s)	Aged ; Finland ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Kruppel-Like Transcription Factors/genetics ; Male ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; Polymorphism, Single Nucleotide ; Prostate-Specific Antigen/blood ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/pathology
Chemical Substances	Kruppel-Like Transcription Factors ; Prostate-Specific Antigen (EC 3.4.21.77)
Language	English
Publishing date	2021-05-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1419277-9
ISSN	1476-5608 ; 1365-7852
ISSN (online)	1476-5608
ISSN	1365-7852
DOI	10.1038/s41391-021-00378-5
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Article ; Online: ShAn: An easy-to-use tool for interactive and integrated variant annotation.

Rathinakannan, Venkat Subramaniam / Schukov, Hannu-Pekka / Heron, Samuel / Schleutker, Johanna / Sipeky, Csilla

PloS one

2020 Volume 15, Issue 7, Page(s) e0235669

Abstract: Motivation: Annotation of large amounts of generated sequencing data is a demanding task. Most of the currently available robust annotation tools, like ANNOVAR, are command-line based tools which require a certain degree of programming skills. User- ... ...

Abstract	Motivation: Annotation of large amounts of generated sequencing data is a demanding task. Most of the currently available robust annotation tools, like ANNOVAR, are command-line based tools which require a certain degree of programming skills. User-friendly tools for variant annotation of sequencing data with graphical interface are under-represented. Results: We have developed an interactive application, which harnesses the easy usability of R Shiny and combines it with the versatile annotation features of ANNOVAR. This application is easy to use and gives comprehensive annotations for user supplied vcf files using multiples databases. The output table contains the list of variants and their corresponding annotation presented within the graphical interface. In addition, the annotation results are downloadable as text file.
MeSH term(s)	Databases, Genetic ; Datasets as Topic ; Humans ; Molecular Sequence Annotation/methods ; Molecular Sequence Data ; Software
Language	English
Publishing date	2020-07-07
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Validation Study
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0235669
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Article ; Online: Prostate cancer risk prediction using a polygenic risk score.

Sipeky, Csilla / Talala, Kirsi M / Tammela, Teuvo L J / Taari, Kimmo / Auvinen, Anssi / Schleutker, Johanna

Scientific reports

2020 Volume 10, Issue 1, Page(s) 17075

Abstract: Hereditary factors have a strong influence on prostate cancer (PC) risk and poorer outcomes, thus stratification by genetic factors addresses a critical need for targeted PC screening and risk-adapted follow-up. In this Finnish population-based ... ...

Abstract	Hereditary factors have a strong influence on prostate cancer (PC) risk and poorer outcomes, thus stratification by genetic factors addresses a critical need for targeted PC screening and risk-adapted follow-up. In this Finnish population-based retrospective study 2283 clinically diagnosed and 455 screen-detected patients from the Finnish Randomised Study of Screening for Prostate Cancer (FinRSPC), 2400 healthy individuals have been involved. Individual genetic risk through establishment of a polygenic risk score based on 55 PC risk SNPs identified through the Finnish subset of the Collaborative Oncological Gene-Environment Study was assessed. Men with PC had significantly higher median polygenic risk score compared to the controls (6.59 vs. 3.83, P < 0.0001). The polygenic risk score above the control median was a significant predictor of PC (OR 2.13, 95% CI 1.90-2.39). The polygenic risk score predicted the risk of PC with an AUC of 0.618 (95% CI 0.60-0.63). Men in the highest polygenic risk score quartile were 2.8-fold (95% CI 2.4-3.30) more likely to develop PC compared with men in the lowest quartile. In the FinRSPC cohort, a significantly higher percentage of men had a PSA level of ≥ 4 ng/mL in polygenic risk score quartile four compared to quartile one (18.7% vs 8.3%, P < 0.00001). Adding the PRS to a PSA-only model contributed additional information in predicting PC in the FinRSPC model. Results strongly suggest that use of the polygenic risk score would facilitate the identification of men at increased risk for PC.
MeSH term(s)	Aged ; Aged, 80 and over ; Cohort Studies ; Finland/epidemiology ; Genetic Predisposition to Disease ; Humans ; Male ; Middle Aged ; Multifactorial Inheritance ; Polymorphism, Single Nucleotide ; Prostate-Specific Antigen/blood ; Prostatic Neoplasms/blood ; Prostatic Neoplasms/epidemiology ; Prostatic Neoplasms/genetics ; Retrospective Studies ; Risk Factors
Chemical Substances	Prostate-Specific Antigen (EC 3.4.21.77)
Language	English
Publishing date	2020-10-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-74172-z
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Article ; Online: PARP Inhibitors in Prostate Cancer—The Preclinical Rationale and Current Clinical Development.

Virtanen, Verneri / Paunu, Kreetta / Ahlskog, Johanna K / Varnai, Reka / Sipeky, Csilla / Sundvall, Maria

Genes

2019 Volume 10, Issue 8

Abstract: Prostate cancer is globally the second most commonly diagnosed cancer type in men. Recent studies suggest that mutations in DNA repair genes are associated with aggressive forms of prostate cancer and castration resistance. Prostate cancer with DNA ... ...

Abstract	Prostate cancer is globally the second most commonly diagnosed cancer type in men. Recent studies suggest that mutations in DNA repair genes are associated with aggressive forms of prostate cancer and castration resistance. Prostate cancer with DNA repair defects may be vulnerable to therapeutic targeting by Poly(ADP-ribose) polymerase (PARP) inhibitors. PARP enzymes modify target proteins with ADP-ribose in a process called PARylation and are in particular involved in single strand break repair. The rationale behind the clinical trials that led to the current use of PARP inhibitors to treat cancer was to target the dependence of BRCA-mutant cancer cells on the PARP-associated repair pathway due to deficiency in homologous recombination. However, recent studies have proposed therapeutic potential for PARP inhibitors in tumors with a variety of vulnerabilities generating dependence on PARP beyond the synthetic lethal targeting of BRCA1/BRCA2 mutated tumors, suggesting a wider potential than initially thought. Importantly, PARP-associated DNA repair pathways are also closely connected to androgen receptor (AR) signaling, which is a key regulator of tumor growth and a central therapeutic target in prostate cancer. In this review, we provide an extensive overview of published and ongoing trials exploring PARP inhibitors in treatment of prostate cancer and discuss the underlying biology. Several clinical trials are currently studying PARP inhibitor mono- and combination therapies in the treatment of prostate cancer. Integration of drugs targeting DNA repair pathways in prostate cancer treatment modalities allows developing of more personalized care taking also into account the genetic makeup of individual tumors.
MeSH term(s)	Animals ; Antineoplastic Agents/therapeutic use ; Clinical Trials as Topic ; Drug Evaluation, Preclinical ; Humans ; Male ; Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use ; Poly(ADP-ribose) Polymerases/genetics ; Poly(ADP-ribose) Polymerases/metabolism ; Prostatic Neoplasms/drug therapy ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism
Chemical Substances	Antineoplastic Agents ; Poly(ADP-ribose) Polymerase Inhibitors ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30)
Language	English
Publishing date	2019-07-26
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10080565
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Article ; Online: CYP2C9 and VKORC1 in therapeutic dosing and safety of acenocoumarol treatment: implication for clinical practice in Hungary.

Varnai, Reka / Sipeky, Csilla / Nagy, Lajos / Balogh, Sandor / Melegh, Bela

Environmental toxicology and pharmacology

2017 Volume 56, Page(s) 282–289

Abstract: The purpose of this work was to investigate the contribution of CYP2C9 and VKORC1 to acenocoumarol (AC) dose variability, bleeding events in Hungary. The study recruited 117 patients on long-term AC therapy (INR 2-3), and 510 healthy individuals to model ...

Abstract	The purpose of this work was to investigate the contribution of CYP2C9 and VKORC1 to acenocoumarol (AC) dose variability, bleeding events in Hungary. The study recruited 117 patients on long-term AC therapy (INR 2-3), and 510 healthy individuals to model the findings. Patients were genotyped for alleles proved to affect lower AC overdose CYP2C92, CYP2C93, VKORC12. Additionally, we tested VKORC13, VKORC14 to examine their effect in patients with higher AC requirements. Most impact on dose reduction is accountable for CYP2C92/3 (59%) and for VKORC12/2 (45.5%), and on dose increase for newly evaluated VKORC13/4 (22.5%) diplotypes. VKORC13 and 4 alleles seem to balance the dose-reducing effect of VKORC12 allele. Being a carrier of combination of VKORC12 and CYP2C92,*3 polymorphisms, rather than of one of these SNPs, is associated with higher risk of over-anticoagulation (up to 34.3%) in long-term AC treatment. The pharmacogenetic dosing algorithm involving VKORC1, CYP2C9 diplotypes and age explains 30.4% of AC dosing variability (p<6.10×10
MeSH term(s)	Acenocoumarol/administration & dosage ; Acenocoumarol/pharmacokinetics ; Adult ; Aged ; Aged, 80 and over ; Algorithms ; Anticoagulants/administration & dosage ; Anticoagulants/pharmacokinetics ; Case-Control Studies ; Cytochrome P-450 CYP2C9/genetics ; Dose-Response Relationship, Drug ; Female ; Genotype ; Humans ; Hungary ; Male ; Middle Aged ; Pharmacogenomic Variants ; Polymorphism, Single Nucleotide ; Vitamin K Epoxide Reductases/genetics ; Young Adult
Chemical Substances	Anticoagulants ; CYP2C9 protein, human (EC 1.14.13.-) ; Cytochrome P-450 CYP2C9 (EC 1.14.13.-) ; VKORC1 protein, human (EC 1.17.4.4) ; Vitamin K Epoxide Reductases (EC 1.17.4.4) ; Acenocoumarol (I6WP63U32H)
Language	English
Publishing date	2017-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2015938-9
ISSN	1872-7077 ; 1382-6689
ISSN (online)	1872-7077
ISSN	1382-6689
DOI	10.1016/j.etap.2017.10.003
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Article ; Online: Pharmacogenomic Biomarkers in Docetaxel Treatment of Prostate Cancer: From Discovery to Implementation.

Varnai, Reka / Koskinen, Leena M / Mäntylä, Laura E / Szabo, Istvan / FitzGerald, Liesel M / Sipeky, Csilla

Genes

2019 Volume 10, Issue 8

Abstract: Prostate cancer is the fifth leading cause of male cancer death worldwide. Although docetaxel chemotherapy has been used for more than fifteen years to treat metastatic castration resistant prostate cancer, the high inter-individual variability of ... ...

Abstract	Prostate cancer is the fifth leading cause of male cancer death worldwide. Although docetaxel chemotherapy has been used for more than fifteen years to treat metastatic castration resistant prostate cancer, the high inter-individual variability of treatment efficacy and toxicity is still not well understood. Since prostate cancer has a high heritability, inherited biomarkers of the genomic signature may be appropriate tools to guide treatment. In this review, we provide an extensive overview and discuss the current state of the art of pharmacogenomic biomarkers modulating docetaxel treatment of prostate cancer. This includes (1) research studies with a focus on germline genomic biomarkers, (2) clinical trials including a range of genetic signatures, and (3) their implementation in treatment guidelines. Based on this work, we suggest that one of the most promising approaches to improve clinical predictive capacity of pharmacogenomic biomarkers in docetaxel treatment of prostate cancer is the use of compound, multigene pharmacogenomic panels defined by specific clinical outcome measures. In conclusion, we discuss the challenges of integrating prostate cancer pharmacogenomic biomarkers into the clinic and the strategies that can be employed to allow a more comprehensive, evidence-based approach to facilitate their clinical integration. Expanding the integration of pharmacogenetic markers in prostate cancer treatment procedures will enhance precision medicine and ultimately improve patient outcomes.
MeSH term(s)	Animals ; Antineoplastic Agents/therapeutic use ; Biomarkers, Tumor/genetics ; Docetaxel/therapeutic use ; Humans ; Male ; Pharmacogenomic Variants ; Prostatic Neoplasms, Castration-Resistant/drug therapy ; Prostatic Neoplasms, Castration-Resistant/genetics
Chemical Substances	Antineoplastic Agents ; Biomarkers, Tumor ; Docetaxel (15H5577CQD)
Language	English
Publishing date	2019-08-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10080599
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Article: A Rare Variant in

Cannon-Albright, Lisa Anne / Teerlink, Craig Carl / Stevens, Jeff / Huang, Franklin W / Sipeky, Csilla / Schleutker, Johanna / Hernandez, Rolando / Facelli, Julio / Agarwal, Neeraj / Trump, Donald L

Cancers

2021 Volume 13, Issue 10

Abstract: Pairs of related bladder cancer cases who belong to pedigrees with an excess of bladder cancer were sequenced to identify rare, shared variants as candidate predisposition variants. Candidate variants were tested for association with bladder cancer risk. ...

Abstract	Pairs of related bladder cancer cases who belong to pedigrees with an excess of bladder cancer were sequenced to identify rare, shared variants as candidate predisposition variants. Candidate variants were tested for association with bladder cancer risk. A validated variant was assayed for segregation to other related cancer cases, and the predicted protein structure of this variant was analyzed. This study of affected bladder cancer relative pairs from high-risk pedigrees identified 152 bladder cancer predisposition candidate variants. One variant in
Language	English
Publishing date	2021-05-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13102399
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Article ; Online: Pharmacogenomic biomarker information differences between drug labels in the United States and Hungary: implementation from medical practitioner view.

Varnai, Reka / Szabo, Istvan / Tarlos, Greta / Szentpeteri, Laszlo Jozsef / Sik, Attila / Balogh, Sandor / Sipeky, Csilla

The pharmacogenomics journal

2019 Volume 20, Issue 3, Page(s) 380–387

Abstract: Pharmacogenomic biomarker availability of Hungarian Summaries of Product Characteristics (SmPC) was assembled and compared with the information in US Food and Drug Administration (FDA) drug labels of the same active substance (July 2019). The level of ... ...

Abstract	Pharmacogenomic biomarker availability of Hungarian Summaries of Product Characteristics (SmPC) was assembled and compared with the information in US Food and Drug Administration (FDA) drug labels of the same active substance (July 2019). The level of action of these biomarkers was assessed from The Pharmacogenomics Knowledgebase database. From the identified 264 FDA approved drugs with pharmacogenomic biomarkers in drug label, 195 are available in Hungary. From them, 165 drugs include pharmacogenomic data disposing 222 biomarkers. Most of them are metabolizing enzymes (46%) and pharmacological targets (41%). The most frequent therapeutic area is oncology (37%), followed by infectious diseases (12%) and psychiatry (9%) (p < 0.00001). Most common biomarkers in Hungarian SmPCs are CYP2D6, CYP2C19, estrogen and progesterone hormone receptor (ESR, PGS). Importantly, US labels present more specific pharmacogenomic subheadings, the level of action has a different prominence, and offer more applicable dose modifications than Hungarians (5% vs 3%). However, Hungarian SmPCs are at 9 oncology drugs stricter than FDA, testing is obligatory before treatment. Out of the biomarkers available in US drug labels, 62 are missing completely from Hungarian SmPCs (p < 0.00001). Most of these belong to oncology (42%) and in case of 11% of missing biomarkers testing is required before treatment. In conclusion, more factual, clear, clinically relevant pharmacogenomic information in Hungarian SmPCs would reinforce implementation of pharmacogenetics. Underpinning future perspective is to support regulatory stakeholders to enhance inclusion of pharmacogenomic biomarkers into Hungarian drug labels and consequently enhance personalized medicine in Hungary.
MeSH term(s)	Biomarkers/metabolism ; Databases, Factual/standards ; Databases, Factual/trends ; Drug Labeling/standards ; Drug Labeling/trends ; General Practitioners/standards ; General Practitioners/trends ; Humans ; Hungary ; Pharmacogenetics/standards ; Pharmacogenetics/trends ; United States ; United States Food and Drug Administration/standards ; United States Food and Drug Administration/trends
Chemical Substances	Biomarkers
Language	English
Publishing date	2019-12-02
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2106831-8
ISSN	1473-1150 ; 1470-269X
ISSN (online)	1473-1150
ISSN	1470-269X
DOI	10.1038/s41397-019-0123-z
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