1
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Zayakin P. sRNAflow: A Tool for the Analysis of Small RNA-Seq Data. Noncoding RNA 2024; 10:6. [PMID: 38250806 PMCID: PMC10801628 DOI: 10.3390/ncrna10010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/29/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
The analysis of small RNA sequencing data across a range of biofluids is a significant research area, given the diversity of RNA types that hold potential diagnostic, prognostic, and predictive value. The intricate task of segregating the complex mixture of small RNAs from both human and other species, including bacteria, fungi, and viruses, poses one of the most formidable challenges in the analysis of small RNA sequencing data, currently lacking satisfactory solutions. This study introduces sRNAflow, a user-friendly bioinformatic tool with a web interface designed for the analysis of small RNAs obtained from biological fluids. Tailored to the unique requirements of such samples, the proposed pipeline addresses various challenges, including filtering potential RNAs from reagents and environment, classifying small RNA types, managing small RNA annotation overlap, conducting differential expression assays, analysing isomiRs, and presenting an approach to identify the sources of small RNAs within samples. sRNAflow also encompasses an alternative alignment-free analysis of RNA-seq data, featuring clustering and initial RNA source identification using BLAST. This comprehensive approach facilitates meaningful comparisons of results between different analytical methods.
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Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia;
- European Bioinformatics Institute, EMBL-EBI, Hinxton CB10 1SD, UK
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2
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Brokāne A, Bajo-Santos C, Zayakin P, Belovs A, Jansons J, Lietuvietis V, Martens-Uzunova ES, Jenster GW, Linē A. Validation of potential RNA biomarkers for prostate cancer diagnosis and monitoring in plasma and urinary extracellular vesicles. Front Mol Biosci 2023; 10:1279854. [PMID: 38099195 PMCID: PMC10720733 DOI: 10.3389/fmolb.2023.1279854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction: Prostate cancer (PCa), one of the most prevalent malignancies affecting men worldwide, presents significant challenges in terms of early detection, risk stratification, and active surveillance. In recent years, liquid biopsies have emerged as a promising non-invasive approach to complement or even replace traditional tissue biopsies. Extracellular vesicles (EVs), nanosized membranous structures released by various cells into body fluids, have gained substantial attention as a source of cancer biomarkers due to their ability to encapsulate and transport a wide range of biological molecules, including RNA. In this study, we aimed to validate 15 potential RNA biomarkers, identified in a previous EV RNA sequencing study, using droplet digital PCR. Methods: The candidate biomarkers were tested in plasma and urinary EVs collected before and after radical prostatectomy from 30 PCa patients and their diagnostic potential was evaluated in a test cohort consisting of 20 benign prostate hyperplasia (BPH) and 20 PCa patients' plasma and urinary EVs. Next, the results were validated in an independent cohort of plasma EVs from 31 PCa and 31 BPH patients. Results: We found that the levels of NKX3-1 (p = 0.0008) in plasma EVs, and tRF-Phe-GAA-3b (p < 0.0001) tRF-Lys-CTT-5c (p < 0.0327), piR-28004 (p = 0.0081) and miR-375-3p (p < 0.0001) in urinary EVs significantly decreased after radical prostatectomy suggesting that the main tissue source of these RNAs is prostate and/or PCa. Two mRNA biomarkers-GLO1 and NKX3-1 showed promising diagnostic potential in distinguishing between PCa and BPH with AUC of 0.68 and 0.82, respectively, in the test cohort and AUC of 0.73 and 0.65, respectively, in the validation cohort, when tested in plasma EVs. Combining these markers in a biomarker model yielded AUC of 0.85 and 0.71 in the test and validation cohorts, respectively. Although the PSA levels in the blood could not distinguish PCa from BPH in our cohort, adding PSA to the mRNA biomarker model increased AUC from 0.71 to 0.76. Conclusion: This study identified two novel EV-enclosed RNA biomarkers-NKX3-1 and GLO1-for the detection of PCa, and highlights the complementary nature of GLO1, NKX3-1 and PSA as combined biomarkers in liquid biopsies of PCa.
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Affiliation(s)
- Agnese Brokāne
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | - Guido W. Jenster
- Department of Urology, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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3
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Ķimsis J, Pokšāne A, Kazarina A, Vilcāne A, Petersone‐Gordina E, Zayakin P, Gerhards G, Ranka R. Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD. Environ Microbiol Rep 2023; 15:383-391. [PMID: 37057308 PMCID: PMC10472514 DOI: 10.1111/1758-2229.13157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.
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Affiliation(s)
- Jānis Ķimsis
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alise Pokšāne
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alisa Kazarina
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | | | - Pawel Zayakin
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | - Renate Ranka
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
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4
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Zayakin P, Sadovska L, Eglītis K, Romanchikova N, Radoviča-Spalviņa I, Endzeliņš E, Liepniece-Karele I, Eglītis J, Linē A. Extracellular Vesicles-A Source of RNA Biomarkers for the Detection of Breast Cancer in Liquid Biopsies. Cancers (Basel) 2023; 15:4329. [PMID: 37686605 PMCID: PMC10487078 DOI: 10.3390/cancers15174329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Over the past decade, extracellular vesicles (EVs) have emerged as a promising source of cancer-derived RNAs for liquid biopsies. However, blood contains a pool of heterogeneous EVs released by a variety of cell types, making the identification of cancer RNA biomarkers challenging. Here, we performed deep sequencing of plasma EV RNA cargo in 32 patients with locally advanced breast cancer (BC) at diagnosis and 7 days after breast surgery and in 30 cancer-free healthy controls (HCs). To identify BC-derived RNA biomarkers, we searched for RNAs that had higher levels in BC EVs at the time of diagnosis compared with HCs and decreased after surgery. Data analysis showed that the fractions of miRNAs, snRNAs, snoRNAs, and tRFs were increased, but the fraction of lncRNAs was decreased in BC EVs as compared to HCs. BC-derived biomarker candidates were identified across various RNA biotypes. Considered individually, they had very high specificity but moderate sensitivity for the detection of BC, whereas a biomarker model composed of eight RNAs: SNORD3H, SNORD1C, SNORA74D, miR-224-5p, piR-32949, lnc-IFT-122-2, lnc-C9orf50-4, and lnc-FAM122C-3 was able to distinguish BC from HC EVs with an AUC of 0.902 (95% CI = 0.872-0.931, p = 3.4 × 10-9) in leave-one-out cross-validation. Furthermore, a number of RNA biomarkers were correlated with the ER and HER2 expression and additional biomarker models were created to predict hormone receptor and HER2 status. Overall, this study demonstrated that the RNA composition of plasma EVs is altered in BC patients and that they contain cancer-derived RNA biomarkers that can be used for BC detection and monitoring using liquid biopsies.
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Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Lilite Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | - Kristaps Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Nadezhda Romanchikova
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Edgars Endzeliņš
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
| | | | - Jānis Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, LV-1038 Riga, Latvia; (K.E.)
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia; (P.Z.); (L.S.); (N.R.); (E.E.)
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5
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Erenpreisa J, Vainshelbaum NM, Lazovska M, Karklins R, Salmina K, Zayakin P, Rumnieks F, Inashkina I, Pjanova D, Erenpreiss J. The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer. Int J Mol Sci 2023; 24:11660. [PMID: 37511419 PMCID: PMC10380301 DOI: 10.3390/ijms241411660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.
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Affiliation(s)
| | | | - Marija Lazovska
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Roberts Karklins
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Dace Pjanova
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Juris Erenpreiss
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
- Clinic iVF-Riga, Zala 1, LV-1010 Riga, Latvia
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6
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Kazarina A, Kuzmicka J, Bortkevica S, Zayakin P, Kimsis J, Igumnova V, Sadovska D, Freimane L, Kivrane A, Namina A, Capligina V, Poksane A, Ranka R. Oral microbiome variations related to ageing: possible implications beyond oral health. Arch Microbiol 2023; 205:116. [PMID: 36920536 PMCID: PMC10016173 DOI: 10.1007/s00203-023-03464-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
The global population is getting older due to a combination of longer life expectancy and declining birth rates. Growing evidence suggests that the oral microbiota composition and distribution may have a profound effect on how well we age. The purpose of this study was to investigate age-related oral microbiome variations of supragingival plaque and buccal mucosa samples in the general population in Latvia. Our results indicated significant difference between supragingival plaque bacterial profiles of three age groups (20-40; 40-60; 60 + years). Within supragingival plaque samples, age group 20-40 showed the highest bacterial diversity with a decline during the 40-60 age period and uprise again after the age of 60. Among other differences, the important oral commensal Neisseria had declined after the age of 40. Additionally, prevalence of two well-documented opportunistic pathogens Streptococcus anginosus and Gemella sanguinis gradually rose with age within our samples. Furthermore, supragingival plaque and buccal mucosa samples significantly differed in overall bacterial composition.
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Affiliation(s)
- Alisa Kazarina
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia.
| | | | - Santa Bortkevica
- Riga Stradins University, 16 Dzirciema Str., Riga, LV-1007, Latvia
| | - Pawel Zayakin
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Janis Kimsis
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Viktorija Igumnova
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Darja Sadovska
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Lauma Freimane
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Agnija Kivrane
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Agne Namina
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Valentina Capligina
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Alise Poksane
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Renate Ranka
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
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7
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Kidere D, Zayakin P, Livcane D, Makrecka-Kuka M, Stavusis J, Lace B, Lin TK, Liou CW, Inashkina I. Impact of the m.13513G>A Variant on the Functions of the OXPHOS System and Cell Retrograde Signaling. Curr Issues Mol Biol 2023; 45:1794-1809. [PMID: 36975485 PMCID: PMC10047405 DOI: 10.3390/cimb45030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Mitochondria are involved in many vital functions in living cells, including the synthesis of ATP by oxidative phosphorylation (OXPHOS) and regulation of nuclear gene expression through retrograde signaling. Leigh syndrome is a heterogeneous neurological disorder resulting from an isolated complex I deficiency that causes damage to mitochondrial energy production. The pathogenic mitochondrial DNA (mtDNA) variant m.13513G>A has been associated with Leigh syndrome. The present study investigated the effects of this mtDNA variant on the OXPHOS system and cell retrograde signaling. Transmitochondrial cytoplasmic hybrid (cybrid) cell lines harboring 50% and 70% of the m.13513G>A variant were generated and tested along with wild-type (WT) cells. The functionality of the OXPHOS system was evaluated by spectrophotometric assessment of enzyme activity and high-resolution respirometry. Nuclear gene expression was investigated by RNA sequencing and droplet digital PCR. Increasing levels of heteroplasmy were associated with reduced OXPHOS system complex I, IV, and I + III activities, and high-resolution respirometry also showed a complex I defect. Profound changes in transcription levels of nuclear genes were observed in the cell lines harboring the pathogenic mtDNA variant, indicating the physiological processes associated with defective mitochondria.
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Affiliation(s)
- Dita Kidere
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Diana Livcane
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | | | - Janis Stavusis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
- Children’s Clinical University Hospital, LV-1004 Riga, Latvia
| | - Tsu-Kung Lin
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83305, Taiwan
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83305, Taiwan
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
- Correspondence:
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8
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Bajo-Santos C, Brokāne A, Zayakin P, Endzeliņš E, Soboļevska K, Belovs A, Jansons J, Sperga M, Llorente A, Radoviča-Spalviņa I, Lietuvietis V, Linē A. Plasma and urinary extracellular vesicles as a source of RNA biomarkers for prostate cancer in liquid biopsies. Front Mol Biosci 2023; 10:980433. [PMID: 36818049 PMCID: PMC9935579 DOI: 10.3389/fmolb.2023.980433] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Extracellular vesicles (EVs) have emerged as a very attractive source of cancer- derived RNA biomarkers for the early detection, prognosis and monitoring of various cancers, including prostate cancer (PC). However, biofluids contain a mixture of EVs released from a variety of tissues and the fraction of total EVs that are derived from PC tissue is not known. Moreover, the optimal biofluid-plasma or urine-that is more suitable for the detection of EV- enclosed RNA biomarkers is not yet clear. Methodology: In the current study, we performed RNA sequencing analysis of plasma and urinary EVs collected before and after radical prostatectomy, and matched tumor and normal prostate tissues of 10 patients with prostate cancer. Results and Discussion: The most abundant RNA biotypes in EVs were miRNA, piRNA, tRNA, lncRNA, rRNA and mRNA. To identify putative cancer-derived RNA biomarkers, we searched for RNAs that were overexpressed in tumor as compared to normal tissues, present in the pre-operation EVs and decreased in the post-operation EVs in each RNA biotype. The levels of 63 mRNAs, 3 lncRNAs, 2 miRNAs and 1 piRNA were significantly increased in the tumors and decreased in the post-operation urinary EVs, thus suggesting that these RNAs mainly originate from PC tissue. No such RNA biomarkers were identified in plasma EVs. This suggests that the fraction of PC-derived EVs in urine is larger than in plasma and allows the detection and tracking of PC-derived RNAs.
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Affiliation(s)
| | - Agnese Brokāne
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | | | - Alicia Llorente
- Department Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway,Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
| | | | | | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia,*Correspondence: Aija Linē,
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9
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Sadovska L, Zayakin P, Eglītis K, Endzeliņš E, Radoviča-Spalviņa I, Avotiņa E, Auders J, Keiša L, Liepniece-Karele I, Leja M, Eglītis J, Linē A. Comprehensive characterization of RNA cargo of extracellular vesicles in breast cancer patients undergoing neoadjuvant chemotherapy. Front Oncol 2022; 12:1005812. [PMID: 36387168 PMCID: PMC9644097 DOI: 10.3389/fonc.2022.1005812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/10/2022] [Indexed: 08/30/2023] Open
Abstract
Extracellular vesicles (EVs) are g7aining increased attention as carriers of cancer-derived molecules for liquid biopsies. Here, we studied the dynamics of EV levels in the plasma of breast cancer (BC) patients undergoing neoadjuvant chemotherapy (NAC) and explored the relevance of their RNA cargo for the prediction of patients' response to the therapy. EVs were isolated from serial blood samples collected at the time of diagnosis, at the end of NAC, and 7 days, 6, and 12 months after the surgery from 32 patients with locally advanced BC, and 30 cancer-free healthy controls (HCs) and quantified by nanoparticle tracking analysis. The pre-treatment levels of EVs in BC patients were higher than in HCs, significantly increased during the NAC and surgery, and decreased to the levels found in HCs 6 months after surgery, thus showing that a substantial fraction of plasma EVs in BC patients are produced due to the disease processes and treatment. RNA sequencing analysis revealed that the changes in the EV levels were associated with the alterations in the proportions of various RNA biotypes in EVs. To search for RNA biomarkers that predict response to the NAC, patients were dichotomized as responders and non-responders based on Miller-Payne grades and differential expression analyses were carried out between responders and non-responders, and HCs. This resulted in the identification of 6 miRNAs, 4 lncRNAs, and 1 snoRNA that had significantly higher levels in EVs from non-responders than responders at the time of diagnosis and throughout the NAC, and significantly lower levels in HCs, thus representing biomarkers for the prediction of response to NAC at the time of diagnosis. In addition, we found 14 RNAs representing piRNA, miRNA, lncRNA, snoRNA, and snRNA biotypes that were induced by NAC in non-responders and 2 snoRNAs and 1 piRNA that were induced by NAC in patients with early disease progression, thus warranting further functional studies on their role in chemoresistance and metastasis.
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Affiliation(s)
- Lilite Sadovska
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kristaps Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
| | - Edgars Endzeliņš
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Elīza Avotiņa
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Jānis Auders
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laura Keiša
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Inta Liepniece-Karele
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
- Department of Pathology, Riga Stradins University, Riga, Latvia
| | - Mārcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Jānis Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
- University of Latvia, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Aija Linē
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
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10
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Sadovska L, Zayakin P, Bajo-Santos C, Endzeliņš E, Auders J, Keiša L, Jansons J, Lietuvietis V, Linē A. Effects of urinary extracellular vesicles from prostate cancer patients on the transcriptomes of cancer-associated and normal fibroblasts. BMC Cancer 2022; 22:1055. [PMID: 36224527 PMCID: PMC9555094 DOI: 10.1186/s12885-022-10107-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 08/26/2022] [Accepted: 09/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing evidence suggests that cancer-derived extracellular vesicles (EVs) alter the phenotype and functions of fibroblasts and trigger the reprogramming of normal fibroblasts into cancer-associated fibroblasts (CAFs). Here, we for the first time studied the effects of urinary EVs from PC patients and healthy males on the transcriptional landscape of prostate CAFs and normal foreskin fibroblasts. METHODS Patient-derived prostate fibroblast primary cultures PCF-54 and PCF-55 were established from two specimens of PC tissues. EVs were isolated from urine samples of 3 patients with PC and 2 healthy males and used for the treatment of prostate fibroblast primary cultures and normal foreskin fibroblasts. The EV-treated fibroblasts were subjected to RNA sequencing analysis. RESULTS RNA sequencing analysis showed that the fibroblast cultures differed significantly in their response to urinary EVs. The transcriptional response of foreskin fibroblasts to the urinary EVs isolated from PC patients and healthy controls was very similar and mostly related to the normal functions of fibroblasts. On the contrary, PCF-54 cells responded very differently - EVs from PC patients elicited transcriptional changes related to the regulation of the cell division and chromosome segregation, whereas EVs from healthy males affected mitochondrial respiration. In PCF-55 cells, EVs from both, PC-patients and controls induced the expression of a number of chemokines such as CCL2, CCL13, CXCL1, CXCL8, whereas pathways related to regulation of apoptotic signaling and production of cell adhesion molecules were triggered specifically by EVs from PC patients. CONCLUSION This study demonstrates that urinary EVs from PC patients and healthy controls elicit distinct transcriptional responses in prostate CAFs and supports the idea that EVs contribute to the generation of functional heterogeneity of CAFs. Moreover, this study suggests that the changes in the gene expression pattern in EV recipient cells might serve as a novel type of functional cancer biomarkers.
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Affiliation(s)
- Lilite Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1, k-1, LV-1067, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1, k-1, LV-1067, Riga, Latvia
| | - Cristina Bajo-Santos
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1, k-1, LV-1067, Riga, Latvia
| | - Edgars Endzeliņš
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1, k-1, LV-1067, Riga, Latvia
| | - Jānis Auders
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1, k-1, LV-1067, Riga, Latvia.,Faculty of Medicine, University of Latvia, Raina blvd. 19, 1586, LV, Riga, Latvia
| | - Laura Keiša
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1, k-1, LV-1067, Riga, Latvia.,Faculty of Medicine, University of Latvia, Raina blvd. 19, 1586, LV, Riga, Latvia
| | - Juris Jansons
- Riga Stradiņš University, Dzirciema Str 16, LV-1007, Riga, Latvia
| | | | - Aija Linē
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1, k-1, LV-1067, Riga, Latvia.
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11
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Mroczek M, Inashkina I, Stavusis J, Zayakin P, Khrunin A, Micule I, Kenina V, Zdanovica A, Zídková J, Fajkusová L, Limborska S, van der Kooi AJ, Brusse E, Leonardis L, Maver A, Pajusalu S, Õunap K, Puusepp S, Dobosz P, Sypniewski M, Burnyte B, Lace B. CAPN3 c.1746-20C>G variant is hypomorphic for LGMD R1 calpain 3-related. Hum Mutat 2022; 43:1347-1353. [PMID: 35731190 DOI: 10.1002/humu.24421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 11/08/2022]
Abstract
The investigated intronic CAPN3 variant NM_000070.3:c.1746-20C>G occurs in the Central and Eastern Europe with a frequency of >1% and there are conflicting interpretations on its pathogenicity. We collected data on 14 patients carrying the CAPN3 c.1746-20C>G variant in trans position with another CAPN3 pathogenic/likely pathogenic variant. The patients compound heterozygous for the CAPN3 c.1746-20C>G variant presented a phenotype consistent with calpainopathy of mild/medium severity. This variant is most frequent in the North/West regions of Russia and may originate from that area. Molecular studies revealed that different splicing isoforms are produced in the muscle. We hypothesize that c.1746-20C>G is a hypomorphic variant with a reduction of RNA and protein expression and only individuals having a higher ratio of abnormal isoforms are affected. Reclassification of the CAPN3 variant c.1746-20C>G from variant with a conflicting interpretation of pathogenicity to hypomorphic variant explains many unidentified cases of limb girdle muscular dystrophy R1 calpain 3-related in Eastern and Central Europe.
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Affiliation(s)
- Magdalena Mroczek
- Department of Neurology and Neurophysiology, Balgrist University Hospital, University of Zurich, Zürich, Switzerland
| | | | | | | | - Andrey Khrunin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ieva Micule
- Biomedical Research and Study Center, Riga, Latvia
| | - Victorija Kenina
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia.,Rare Disease Center, Riga East Clinical University Hospital, Riga, Latvia
| | | | - Jana Zídková
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Svetlana Limborska
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Anneke J van der Kooi
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Esther Brusse
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Lea Leonardis
- Department of Neurology, University Medical Centre Ljubljana, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sanna Puusepp
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Paula Dobosz
- MNM Diagnostics Sp. z o.o., Poznań, Poland.,Department of Hematology, Transplantation and Internal Medicine, University Clinical Center of the Medical University of Warsaw, Warsaw, Poland.,Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | | | - Birute Burnyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Baiba Lace
- Biomedical Research and Study Center, Riga, Latvia.,Medical Genetics Clinic, Children's Clinical University Hospital, Riga, Latvia
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12
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Plūme J, Galvanovskis A, Šmite S, Romanchikova N, Zayakin P, Linē A. Early and strong antibody responses to SARS-CoV-2 predict disease severity in COVID-19 patients. J Transl Med 2022; 20:176. [PMID: 35428263 PMCID: PMC9012069 DOI: 10.1186/s12967-022-03382-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Background Antibody response to SARS-CoV-2 is a valuable biomarker for the assessment of the spread of the virus in a population and evaluation of the vaccine candidates. Recent data suggest that antibody levels also may have a prognostic significance in COVID-19. Most of the serological studies so far rely on testing antibodies against spike (S) or nucleocapsid (N) protein, however antibodies can be directed against other structural and nonstructural proteins of the virus, whereas their frequency, biological and clinical significance is unknown. Methods A novel antigen array comprising 30 SARS-CoV-2 antigens or their fragments was developed and used to examine IgG, IgA, IgE and IgM responses to SARS-CoV-2 in sera from 103 patients with COVID-19 including 34 patients for whom sequential samples were available, and 20 pre-pandemic healthy controls. Results Antibody responses to various antigens are highly correlated and the frequencies and peak levels of antibodies are higher in patients with severe/moderate disease than in those with mild disease. This finding supports the idea that antibodies against SARS-CoV-2 may exacerbate the severity of the disease via antibody-dependent enhancement. Moreover, early IgG and IgA responses to full length S protein may be used as an additional biomarker for the identification of patients who are at risk of developing severe disease. Importantly, this is the first study reporting that SARS-CoV-2 elicits IgE responses and their serum levels positively correlate with the severity of the disease thus suggesting a link between high levels of antibodies and mast cell activation. Conclusions This is the first study assessing the prevalence and dynamics IgG, IgA, IgE and IgM responses to multiple SARS-CoV-2 antigens simultaneously. Results provide important insights into the pathogenesis of COVID-19 and have implications in planning and interpreting antibody-based epidemiological studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03382-y.
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13
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Sadovska L, Auders J, Keiša L, Romanchikova N, Silamiķele L, Kreišmane M, Zayakin P, Takahashi S, Kalniņa Z, Linē A. Exercise-Induced Extracellular Vesicles Delay the Progression of Prostate Cancer. Front Mol Biosci 2022; 8:784080. [PMID: 35087866 PMCID: PMC8787363 DOI: 10.3389/fmolb.2021.784080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Increasing evidence suggests that regular physical exercise not only reduces the risk of cancer but also improves functional capacity, treatment efficacy and disease outcome in cancer patients. At least partially, these effects are mediated by the secretome of the tissues responding to exercise. The secreted molecules can be released in a carrier-free form or enclosed into extracellular vesicles (EVs). Several recent studies have shown that EVs are actively released into circulation during physical exercise. Here, we for the first time investigated the effects of exercise-induced EVs on the progression of cancer in an F344 rat model of metastatic prostate cancer. Although we did not observe a consistent increase in the circulating EV levels, RNA sequencing analysis demonstrated substantial changes in the RNA content of EVs collected before and immediately after forced wheel running exercise as well as differences between EVs from runners at resting state and sedentary rats. The major RNA biotype in EVs was mRNA, followed by miRNA and rRNA. Molecular functions of differentially expressed RNAs reflected various physiological processes including protein folding, metabolism and regulation of immune responses triggered by the exercise in the parental cells. Intravenous administration of exercise-induced EVs into F344 rats with orthotopically injected syngeneic prostate cancer cells PLS10, demonstrated reduction of the primary tumor volume by 35% and possibly—attenuation of lung metastases. Hence, our data provide the first evidence that exercise-induced EVs may modulate tumor physiology and delay the progression of cancer.
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Affiliation(s)
- Lilite Sadovska
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Jānis Auders
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Laura Keiša
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | | | - Laila Silamiķele
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Madara Kreišmane
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Zane Kalniņa
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Aija Linē
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Biology, University of Latvia, Riga, Latvia
- *Correspondence: Aija Linē,
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14
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Erenpreisa J, Krigerts J, Salmina K, Gerashchenko BI, Freivalds T, Kurg R, Winter R, Krufczik M, Zayakin P, Hausmann M, Giuliani A. Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis). Cells 2021; 10:1582. [PMID: 34201566 PMCID: PMC8304199 DOI: 10.3390/cells10071582] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.
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Affiliation(s)
- Jekaterina Erenpreisa
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Bogdan I. Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine;
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia;
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia;
| | - Ruth Winter
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
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15
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Kazarina A, Petersone-Gordina E, Kimsis J, Kuzmicka J, Zayakin P, Griškjans Ž, Gerhards G, Ranka R. The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles. Genes (Basel) 2021; 12:genes12020309. [PMID: 33671794 PMCID: PMC7927102 DOI: 10.3390/genes12020309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.
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Affiliation(s)
- Alisa Kazarina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Elina Petersone-Gordina
- Institute of Latvian History, University of Latvia, Kalpaka Bulvaris 4, LV-1050 Riga, Latvia
| | - Janis Kimsis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Jevgenija Kuzmicka
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Žans Griškjans
- Institute of Stomatology, Riga Stradins University, Dzirciema Str. 20, LV-1007 Riga, Latvia
| | - Guntis Gerhards
- Institute of Latvian History, University of Latvia, Kalpaka Bulvaris 4, LV-1050 Riga, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
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16
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Krigerts J, Salmina K, Freivalds T, Zayakin P, Rumnieks F, Inashkina I, Giuliani A, Hausmann M, Erenpreisa J. Differentiating cancer cells reveal early large-scale genome regulation by pericentric domains. Biophys J 2021; 120:711-724. [PMID: 33453273 PMCID: PMC7896032 DOI: 10.1016/j.bpj.2021.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Finding out how cells prepare for fate change during differentiation commitment was our task. To address whether the constitutive pericentromere-associated domains (PADs) may be involved, we used a model system with known transcriptome data, MCF-7 breast cancer cells treated with the ErbB3 ligand heregulin (HRG), which induces differentiation and is used in the therapy of cancer. PAD-repressive heterochromatin (H3K9me3), centromere-associated-protein-specific, and active euchromatin (H3K4me3) antibodies, real-time PCR, acridine orange DNA structural test (AOT), and microscopic image analysis were applied. We found a two-step DNA unfolding after 15–20 and 60 min of HRG treatment, respectively. This behavior was consistent with biphasic activation of the early response genes (c-fos - fosL1/myc) and the timing of two transcriptome avalanches reported in the literature. In control, the average number of PADs negatively correlated with their size by scale-free distribution, and centromere clustering in turn correlated with PAD size, both indicating that PADs may create and modulate a suprachromosomal network by fusing and splitting a constant proportion of the constitutive heterochromatin. By 15 min of HRG treatment, the bursting unraveling of PADs from the nucleolus boundary occurred, coinciding with the first step of H3K4me3 chromatin unfolding, confirmed by AOT. The second step after 60 min of HRG treatment was associated with transcription of long noncoding RNA from PADs and peaking of fosL1/c-myc response. We hypothesize that the bursting of PAD clusters under a critical silencing threshold pushes the first transcription avalanche, whereas the destruction of the PAD network enables genome rewiring needed for differentiation repatterning, mediated by early response bivalent genes.
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Affiliation(s)
- Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, Riga, Latvia; University of Latvia, Riga, Latvia
| | | | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedicine Research and Study Centre, Riga, Latvia; University of Latvia, Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedicine Research and Study Centre, Riga, Latvia
| | - Alessandro Giuliani
- Environment and Health Department, Italian National Institute of Health, Rome, Italy
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, Heidelberg, Germany.
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17
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Salmina K, Gerashchenko BI, Hausmann M, Vainshelbaum NM, Zayakin P, Erenpreiss J, Freivalds T, Cragg MS, Erenpreisa J. When Three Isn't a Crowd: A Digyny Concept for Treatment-Resistant, Near-Triploid Human Cancers. Genes (Basel) 2019; 10:E551. [PMID: 31331093 PMCID: PMC6678365 DOI: 10.3390/genes10070551] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/10/2019] [Accepted: 06/19/2019] [Indexed: 12/19/2022] Open
Abstract
Near-triploid human tumors are frequently resistant to radio/chemotherapy through mechanisms that are unclear. We recently reported a tight association of male tumor triploidy with XXY karyotypes based on a meta-analysis of 15 tumor cohorts extracted from the Mitelman database. Here we provide a conceptual framework of the digyny-like origin of this karyotype based on the germline features of malignant tumors and adaptive capacity of digyny, which supports survival in adverse conditions. Studying how the recombinatorial reproduction via diploidy can be executed in primary cancer samples and HeLa cells after DNA damage, we report the first evidence that diploid and triploid cell sub-populations constitutively coexist and inter-change genomes via endoreduplicated polyploid cells generated through genotoxic challenge. We show that irradiated triploid HeLa cells can enter tripolar mitosis producing three diploid sub-subnuclei by segregation and pairwise fusions of whole genomes. Considering the upregulation of meiotic genes in tumors, we propose that the reconstructed diploid sub-cells can initiate pseudo-meiosis producing two "gametes" (diploid "maternal" and haploid "paternal") followed by digynic-like reconstitution of a triploid stemline that returns to mitotic cycling. This process ensures tumor survival and growth by (1) DNA repair and genetic variation, (2) protection against recessive lethal mutations using the third genome.
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Affiliation(s)
- Kristine Salmina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Bogdan I Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, D-69120 Heidelberg, Germany
| | - Ninel M Vainshelbaum
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Juris Erenpreiss
- Riga Stradins University, LV-1007 Riga, Latvia
- Clinic IVF-Riga, LV-1010 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia
| | - Mark S Cragg
- Centre for Cancer Immunology, University of Southampton, Southampton SO16 6YD, UK
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18
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Garaud S, Zayakin P, Buisseret L, Rulle U, Silina K, de Wind A, Van den Eyden G, Larsimont D, Willard-Gallo K, Linē A. Antigen Specificity and Clinical Significance of IgG and IgA Autoantibodies Produced in situ by Tumor-Infiltrating B Cells in Breast Cancer. Front Immunol 2018; 9:2660. [PMID: 30515157 PMCID: PMC6255822 DOI: 10.3389/fimmu.2018.02660] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022] Open
Abstract
An important role for tumor infiltrating B lymphocytes (TIL-B) in the immune response to cancer is emerging; however, very little is known about the antigen specificity of antibodies produced in situ. The presence of IgA antibodies in the tumor microenvironment has been noted although their biological functions and clinical significance are unknown. This study used a 91-antigen microarray to examine the IgG and IgA autoantibody repertoires in breast cancer (BC). Tumor and adjacent breast tissue supernatants and plasma from BC patients together with normal breast tissue supernatants and plasma from healthy controls (patients undergoing mammary reduction and healthy blood donors) were analyzed to investigate relationships between autoantibodies and the clinical, histological and immunological features of tumors. Our data show that >84% of the BC samples tested contain autoantibodies to one or more antigens on the array, with ANKRD30BL, COPS4, and CTAG1B being most frequently reactive. Ex vivo TIL-B responses were uncoupled from systemic humoral responses in the majority of cases. A comparison of autoantibody frequencies in supernatants and plasma from patients and controls identified eight antigens that elicit BC-associated autoantibody responses. The overall prevalence of IgG and IgA autoantibodies was similar and while IgG and IgA responses were not linked they did correlate with distinct clinical, pathological and immunological features. Higher levels of ex vivo IgG responses to BC-associated antigens were associated with shorter recurrence-free survival (RFS), HER2 overexpression and lower tumor-infiltrating CD8+ T cell counts. Higher IgA levels were associated with estrogen and progesterone receptor-negative cancers but were not significantly associated with RFS. Furthermore, ex vivo IgA but not IgG autoantibodies reactive to BC-associated antigens were linked with germinal center and early memory B cell maturation and the presence of tertiary lymphoid structures suggesting that these TIL-B are activated in the tumor microenvironment. Overall, our results extend the current understanding of the antigen specificity, the biological and the clinical significance of IgG and IgA autoantibodies produced by BC TIL-B in situ.
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Affiliation(s)
- Soizic Garaud
- Molecular Immunology Unit, Institut Jules Bordet, Universite Libre de Bruxelles, Brussels, Belgium
| | - Pawel Zayakin
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laurence Buisseret
- Molecular Immunology Unit, Institut Jules Bordet, Universite Libre de Bruxelles, Brussels, Belgium
| | - Undine Rulle
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Karina Silina
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Alexandre de Wind
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Gert Van den Eyden
- Translational Cancer Research Unit Antwerp, Oncology Centre, General Hospital Sint Augustinus, Wilrijk, Belgium
| | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Karen Willard-Gallo
- Molecular Immunology Unit, Institut Jules Bordet, Universite Libre de Bruxelles, Brussels, Belgium
| | - Aija Linē
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia.,Faculty of Biology, University of Latvia, Riga, Latvia
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Bajo-Santos C, Melne V, Soboļevska K, Zayakin P, Ābols A, Lietuvietis V, Llorente A, Linē A. PO-482 Analysis of small RNA cargo in urinary and plasma EVs and matching prostate cancer and normal prostate tissues. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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20
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Erenpreiss J, Punab M, Zilaitiene B, Hlevicka S, Zayakin P, Matulevicius V, Tomas Preiksa R, Jørgensen N. Semen quality of young men from the general population in Baltic countries. Hum Reprod 2018; 32:1334-1340. [PMID: 28383690 DOI: 10.1093/humrep/dex062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/14/2017] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION What are the parameters of semen quality in Baltic men? SUMMARY ANSWER Combined parameters of sperm concentration, motility and morphology revealed that 11-15% of men had low semen quality, 37-50% intermediate and 38-52% high semen quality. WHAT IS KNOWN ALREADY Previous studies have revealed regional differences in semen parameters, and semen quality of Baltic men has been suggested to be better than that of other European men. STUDY DESIGN, SIZE, DURATION This was a cross-sectional study of 1165 men aged 16-29 years from Estonia (N = 573), Latvia (N = 278) and Lithuania (N = 314) conducted in 2003-2004. PARTICIPANTS/MATERIALS SETTING METHODS Men from the general population, median age 19.8 years, provided one semen sample each, had blood samples taken, had testis size determined, and provided information on lifestyle. Based on combined data of sperm concentration, sperm motility and morphology the cohort was classified into three categories: low, intermediate or high semen quality. Comparisons between groups (including subgroups of Estonian men of Russian versus Estonian ethnicity) were tested, adjusting for ejaculation abstinence and age. MAIN RESULTS AND THE ROLE OF CHANCE The median sperm concentration of the Estonian, Latvian and Lithuanian populations of Baltic men was 63 mill/ml. Low semen quality was detected in 11-15% of the men, intermediate in 37-50% and high in 38-52%. No crucial differences between national subgroups were detected, except that a higher percentage (9.6%) of the subgroup of Russian Estonians reported having had cryptorchidism compared to the other men (2.5-3.6%, P < 0.001). Smoking had an adverse impact on both sperm concentration and total sperm counts (P < 0.001). LIMITATIONS REASONS FOR CAUTION The semen quality data were collected >10 years ago. Thus, a recent change in semen quality cannot be excluded. Owing to the study design, it is assumed, but unproven, that the men were representative of the general populations. Some men were very young (16 years), however, this was also the case for other European studies of similar populations. Assessment of sperm motility is associated with inter-observer variation, and no quality control was undertaken for sperm motility assessment to account for that. Thus, estimates of sperm motility should be interpreted with caution. WIDER IMPLICATIONS OF THE FINDINGS Analysis of the semen variables separately did not identify that a considerable percentage of Baltic men had low semen quality. The combined analysis, however, showed that more than one out of nine men had semen quality at a level indicating reduced fertility chances. We suggest that future studies of semen quality should be carried out reporting both results of single semen parameters and estimates that combine the most frequently assessed variables. STUDY FUNDING/COMPETING INTEREST(S) The study was funded by the EU fifth framework project Number QLK4-1999-01422 'Envir.Repro.Health' extension to Baltic countries Number QLRT-2001-02911; Estonian Science Foundation, grant numbers 2991 and PUT181. There are no competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Juris Erenpreiss
- Latvian Biomedical Research and Study Center, Riga LV-1067, Latvia
| | - Margus Punab
- Andrology Center, Tartu University Hospital, 50406 Tartu, Estonia
| | - Birute Zilaitiene
- Institute of Endocrinology, Lithuanian University of Health Sciences, Kaunas LT-50009, Lithuania
| | | | - Pawel Zayakin
- Latvian Biomedical Research and Study Center, Riga LV-1067, Latvia
| | - Valentinas Matulevicius
- Institute of Endocrinology, Lithuanian University of Health Sciences, Kaunas LT-50009, Lithuania
| | - Romualdas Tomas Preiksa
- Institute of Endocrinology, Lithuanian University of Health Sciences, Kaunas LT-50009, Lithuania
| | - Niels Jørgensen
- Department of Growth and Reproduction, GR-5064, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
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21
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Meistere I, Werner S, Zayakin P, Siliņa K, Rulle U, Pismennaja A, Šantare D, Kikuste I, Isajevs S, Leja M, Kupčinskas L, Kupčinskas J, Jonaitis L, Wu CY, Brenner H, Linē A, Kalniņa Z. The Prevalence of Cancer-Associated Autoantibodies in Patients with Gastric Cancer and Progressive Grades of Premalignant Lesions. Cancer Epidemiol Biomarkers Prev 2017; 26:1564-1574. [PMID: 28768706 DOI: 10.1158/1055-9965.epi-17-0238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/17/2017] [Accepted: 07/21/2017] [Indexed: 01/14/2023] Open
Abstract
Background: Serum autoantibodies against tumor-associated antigens (TAAs) are detectable in early-stage gastric cancer patients; however, the time point during cancerogenesis when they appear in circulation is still obscure.Methods: In this study, we developed a recombinant antigen microarray and analyzed the prevalence of autoantibodies against 102 TAAs in 829 gastric cancer patients and 929 healthy controls from Caucasian and Asian populations, as well as 100 patients with chronic atrophic gastritis and 775 individuals staged according to different grades of intestinal metaplasia.Results: Six antigens, including CTAG1B/CTAG2, DDX53, IGF2BP2, TP53, and MAGEA3, were predominantly reacting with sera from gastric cancer patients when compared with healthy controls, and the seroreactivity was associated with intestinal-type gastric cancer, but not with patients' Helicobacter pylori status, grade, age, gender, or stage of gastric cancer. We detected gastric cancer-associated seroreactivity in 13% of patients with advanced/severe intestinal metaplasia, which was increased in comparison with mild/moderate intestinal metaplasia (5.3%) and was comparable with that seen in early-stage gastric cancer patients (12%). Moreover, by testing serum samples taken 1 to 9 years before the clinical diagnosis of 18 incident gastric cancer cases, we detected autoantibody responses against several TAAs-SOX2, MYC, BIRC5, IGF2BP1, and MUC1.Conclusions: Our results suggest that humoral immune response against TAAs is generated already during premalignant stages.Impact: Based on the obtained results, cancer-associated autoantibodies might make a valuable contribution to the stratification of high-risk patients with premalignant lesions in the stomach through enhancing the positive predictive power of existing risk models. Cancer Epidemiol Biomarkers Prev; 26(10); 1564-74. ©2017 AACR.
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Affiliation(s)
- Irēna Meistere
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Simone Werner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pawel Zayakin
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Karīna Siliņa
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Undīne Rulle
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Angelina Pismennaja
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Daiga Šantare
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, Riga, Latvia.,Riga East University Hospital, Riga, Latvia
| | - Ilze Kikuste
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, Riga, Latvia.,Digestive Diseases Centre GASTRO, Riga, Latvia
| | - Sergejs Isajevs
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, Riga, Latvia.,Riga East University Hospital, Riga, Latvia
| | - Mārcis Leja
- Institute of Clinical and Preventive Medicine and Faculty of Medicine, University of Latvia, Riga, Latvia.,Riga East University Hospital, Riga, Latvia.,Digestive Diseases Centre GASTRO, Riga, Latvia
| | - Limas Kupčinskas
- Institute for Digestive Research and Department of Gastroenterology Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupčinskas
- Institute for Digestive Research and Department of Gastroenterology Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Laimas Jonaitis
- Institute for Digestive Research and Department of Gastroenterology Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Chun-Ying Wu
- Division of Gastroenterology and Hepatology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aija Linē
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Zane Kalniņa
- Cancer Biomarker and Immunotherapy Group, Latvian Biomedical Research and Study Centre, Riga, Latvia.
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22
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Zandberga E, Zayakin P, Ābols A, Pūpola D, Trapencieris P, Linē A. Depletion of carbonic anhydrase IX abrogates hypoxia-induced overexpression of stanniocalcin-1 in triple negative breast cancer cells. Cancer Biol Ther 2017; 18:596-605. [PMID: 28665755 DOI: 10.1080/15384047.2017.1345390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Carbonic anhydrase IX (CAIX) is a pH-regulating enzyme that plays a key role in maintaining an alkaline intracellular pH under hypoxic conditions. It is overexpressed in a variety of solid cancers, including breast cancer (BC), and has been implicated in the migration, invasion and stemness of breast cancer cells. Therefore, CAIX recently emerged as a novel therapeutic target for the treatment of BC. To gain an insight into the mechanism of action of CAIX inhibitors, we investigated the impact of CAIX knock-down on the transcriptional response to hypoxia in 2 BC cell lines - MCF7 and MDA-MB-231, by performing a global gene expression analysis. This showed that CAIX knock-down had a relatively minor effect on the global transcriptional response to hypoxia, however it blocked hypoxia-induced upregulation of stanniocalcin-1 (STC1), a secreted glycoprotein that has been shown to promote tumor progression and metastasis in BC. Kaplan-Meier survival analysis showed that high STC1 expression is significantly associated with poor survival in patients with basal-type breast cancer but not luminal A and HER2+ subtypes. Moreover, the association was particularly high in a subgroup of basal-type BC patients with TP53 mutations thus revealing a putative cooperation of STC1 with mutated TP53 in generating highly aggressive BC subgroup. Taken together, these findings show that CAIX inhibitors at least partially act through blocking STC1 induction in BC cells and reveal a subgroup of BC patients, who potentially would benefit most from the treatment with CAIX inhibitors.
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Affiliation(s)
- Elīna Zandberga
- a Latvian Biomedical Research and Study Centre , Riga , Latvia
| | - Pawel Zayakin
- a Latvian Biomedical Research and Study Centre , Riga , Latvia
| | - Artūrs Ābols
- a Latvian Biomedical Research and Study Centre , Riga , Latvia
| | - Dārta Pūpola
- a Latvian Biomedical Research and Study Centre , Riga , Latvia
| | | | - Aija Linē
- a Latvian Biomedical Research and Study Centre , Riga , Latvia.,c Faculty of Biology, University of Latvia , Riga , Latvia
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23
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Linē A, Zandberga E, Abols A, Santos CB, Toleikiene R, Zayakin P, Pūpola D, Shvirksts K, Grube M, Riekstina U. Hypoxic conditions regulate the molecular content, release and uptake rates of extracellular vesicles produced by colorectal cancer cells. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61338-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kalniņa Z, Meistere I, Kikuste I, Tolmanis I, Zayakin P, Linē A. Emerging blood-based biomarkers for detection of gastric cancer. World J Gastroenterol 2015; 21:11636-11653. [PMID: 26556992 PMCID: PMC4631966 DOI: 10.3748/wjg.v21.i41.11636] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/08/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
Early detection and efficient monitoring of tumor dynamics are prerequisites for reducing disease burden and mortality, and for improving the management of patients with gastric cancer (GC). Blood-based biomarker assays for the detection of early-stage GC could be of great relevance both for population-wide or risk group-based screening programs, while circulating biomarkers that reflect the genetic make-up and dynamics of the tumor would allow monitoring of treatment efficacy, predict recurrences and assess the genetic heterogeneity of the tumor. Recent research to identify blood-based biomarkers of GC has resulted in the identification of a wide variety of cancer-associated molecules, including various proteins, autoantibodies against tumor associated antigens, cell-free DNA fragments, mRNAs and various non-coding RNAs, circulating tumor cells and cancer-derived extracellular vesicles. Each type of these biomarkers provides different information on the disease status, has different advantages and disadvantages, and distinct clinical usefulness. In the current review, we summarize the recent developments in blood-based GC biomarker discovery, discuss the origin of various types of biomarkers and their clinical usefulness and the technological challenges in the development of biomarker assays for clinical use.
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Abols A, Ducena K, Zayakin P, Silina K, Kalnina Z, Sadovska L, Tars J, Vilmanis J, Narbuts Z, Eglitis J, Pirags V, Line A. Survey of autoantibody responses against tumor-associated antigens in thyroid cancer. Cancer Biomark 2014; 14:361-9. [DOI: 10.3233/cbm-140413] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- A. Abols
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- University of Latvia, Riga, Latvia
| | | | - P. Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - K. Silina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Z. Kalnina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - J. Tars
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
| | - J. Vilmanis
- Pauls Stradins University Hospital, Riga, Latvia
| | - Z. Narbuts
- Pauls Stradins University Hospital, Riga, Latvia
| | - J. Eglitis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
| | - V. Pirags
- University of Latvia, Riga, Latvia
- Pauls Stradins University Hospital, Riga, Latvia
| | - A. Line
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Kalnina Z, Meistere I, Zayakin P, Silina K, Pismennaja A, Leja M, Line A. 963: Potential of tumour-associated autoantibodies as biomarkers for gastric cancer detection. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50855-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zayakin P, Ancāns G, Siliņa K, Meistere I, Kalniņa Z, Andrejeva D, Endzeliņš E, Ivanova L, Pismennaja A, Ruskule A, Doniņa S, Wex T, Malfertheiner P, Leja M, Linē A. Tumor-associated autoantibody signature for the early detection of gastric cancer. Int J Cancer 2012; 132:137-47. [PMID: 22684876 DOI: 10.1002/ijc.27667] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/10/2012] [Indexed: 12/12/2022]
Abstract
Autoantibodies against tumor-associated antigens are very attractive biomarkers for the development of noninvasive serological tests for the early detection of cancer because of their specificity and stability in the sera. In our study, we applied T7 phage display-based serological analysis of recombinant cDNA expression libraries technique to identify a representative set of antigens eliciting humoral responses in patients with gastric cancer (GC), produced phage-antigen microarrays and exploited them for the survey of autoantibody repertoire in patients with GC and inflammatory diseases. We developed procedures for data normalization and cutoff determination to define sero-positive signals and ranked them by the signal intensity and frequency of reactivity. To identify autoantibodies with the highest diagnostic value, a 1,150-feature microarray was tested with sera from 100 patients with GC and 100 cancer-free controls, and then the top-ranked 86 antigens were used for the production of focused array that was tested with an independent validation set comprising serum samples from 235 patients with GC, 154 patients with peptic ulcer and gastritis and 213 healthy controls. The receiver operating characteristic curve analysis showed that 45-autoantibody signature could discriminate GC and healthy controls with area under the curve (AUC) of 0.79 (59% sensitivity and 90% specificity), GC and peptic ulcer with AUC of 0.76 and GC and gastritis with AUC of 0.64. Moreover, it could detect early GC with equal sensitivity than advanced GC. Interestingly, the autoantibody production did not correlate with histological type, H. pylori status, grade, localization and size of the primary tumor, whereas it appeared to be associated with the metastatic disease.
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Affiliation(s)
- Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Abstract
This paper presents some essential findings and results on using ranking-based kernels for the analysis and utilization of high dimensional and noisy biomedical data in applied clinical diagnostics. We claim that presented kernels combined with a state-of-the-art classification technique - a Support Vector Machine (SVM) - could significantly improve the classification rate and predictive power of the wrapper method, e.g. SVM. Moreover, the advantage of such kernels could be potentially exploited for other kernel methods and essential computer-aided tasks such as novelty detection and clustering. Our experimental results and theoretical generalization bounds imply that ranking-based kernels outperform other traditionally employed SVM kernels on high dimensional biomedical and microarray data.
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Affiliation(s)
- Vilen Jumutc
- Riga Technical University, Meža 1/4 Riga, LV-1658, Latvia.
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Kalnina Z, Zayakin P, Silina K, Meistere I, Ivanova L, Stengrevics A, Leja M, Wex T, Malfertheiner P, Line A. 146 Identification of novel tumour-associated autoantibody signatures in gastric cancer. EJC Suppl 2010. [DOI: 10.1016/s1359-6349(10)70954-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Line A, Silina K, Ivanova L, Kalnina Z, Zayakin P, Meistere I, Endzelins E, Stengrevics A. 306 Identification of novel cancer-testis antigens by studying humoral response against cancer. EJC Suppl 2010. [DOI: 10.1016/s1359-6349(10)71110-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Silina K, Kalnina Z, Meistere I, Zayakin P, Abols A, Rivosh A, Line A. Analyses of novel tumour antigens as targets for cancer immunotherapy. European Journal of Cancer Supplements 2008. [DOI: 10.1016/s1359-6349(08)71822-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kalniņa Z, Siliņa K, Meistere I, Zayakin P, Rivosh A, Ābols A, Leja M, Minenkova O, Schadendorf D, Linē A. Evaluation of T7 and lambda phage display systems for survey of autoantibody profiles in cancer patients. J Immunol Methods 2008; 334:37-50. [DOI: 10.1016/j.jim.2008.01.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 01/28/2008] [Accepted: 01/29/2008] [Indexed: 10/22/2022]
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Kalnina Z, Meistere I, Silina K, Zayakin P, Rivosh A, Abols A, Line A. 7007 POSTER Development of antigen microarray for systematic analyses of humoral responses in melanoma patients. EJC Suppl 2007. [DOI: 10.1016/s1359-6349(07)71461-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Abstract
Recent genomewide analyses of alternative splicing (AS) indicate that up to 70% of human genes may have alternative splice forms, suggesting that AS together with various posttranslational modifications plays a major role in the production of proteome complexity. Splice-site selection under normal physiological conditions is regulated in the developmental stage in a tissue type-specific manner by changing the concentrations and the activity of splicing regulatory proteins. Whereas spliceosomal errors resulting in the production of aberrant transcripts rarely occur in normal cells, they seem to be an intrinsic property of cancer cells. Changes in splice-site selection have been observed in various types of cancer and may affect genes implicated in tumor progression (for example, CD44, MDM2, and FHIT) and in susceptibility to cancer (for example, BRCA1 and APC). Splicing defects can arise from inherited or somatic mutations in cis-acting regulatory elements (splice donor, acceptor and branch sites, and exonic and intronic splicing enhancers and silencers) or variations in the composition, concentration, localization, and activity of regulatory proteins. This may lead to altered efficiency of splice-site recognition, resulting in overexpression or down-regulation of certain splice variants, a switch in splice-site usage, or failure to recognize splice sites correctly, resulting in cancer-specific splice forms. At least in some cases, changes in splicing have been shown to play a functionally significant role in tumorigenesis, either by inactivating tumor suppressors or by gain of function of proteins promoting tumor development. Moreover, cancer-specific splicing events may generate novel epitopes that can be recognized by the host's immune system as cancer specific and may serve as targets for immunotherapy. Thus, the identification of cancer-specific splice forms provides a novel source for the discovery of diagnostic or prognostic biomarkers and tumor antigens suitable as targets for therapeutic intervention.
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Affiliation(s)
- Zane Kalnina
- Biomedical Research and Study Centre, University of Latvia, Ratsupites St 1, LV-1067 Riga, Latvia
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