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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Dynamic Changes in Circulating Methylated Markers in Response to Antitumor Therapy of Rectal Cancer. J Gastrointest Cancer 2024:10.1007/s12029-024-01066-y. [PMID: 38829580 DOI: 10.1007/s12029-024-01066-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Rectal cancer (RC) occupies a leading position in the structure of oncological morbidity and mortality. Aberrant methylation of tumor-suppressor genes and hypomethylation of retrotransposons were shown to be detectable in cell-free DNA, circulating in the blood (cfDNA) of cancer patients, indicating the possibility to use them as diagnostic and prognosis markers. PURPOSE Evaluation of the changes in the methylation level of LINE-1 elements and SEPTIN9 and IKZF1 genes in the cell-surface-bound cfDNA (csb-cfDNA) from the blood of RC patients after antitumor therapy at a long-term follow-up. METHODS Blood samples were obtained from RC patients (n = 25) before treatment, after preoperative chemotherapy (3 courses according to the XELOX scheme), 10-15 days after surgery, and every 3 months during 12 months of dynamic observation. The methylation level of LINE-1, SEPTIN9, and IKZF1 in the csb-cfDNA was evaluated by quantitative methyl-specific PCR. RESULTS The LINE-1 methylation level in the csb-cfDNA increased 1.6 times in RC patients after chemotherapy and 3 times after tumor resection versus methylation level before therapy. The SEPTIN9 gene methylation level in the csb-cfDNA decreased by 1.7 times in RC patients after chemotherapy and by 2.3 times after tumor resection compared with the values before the treatment. The IKZF1 gene methylation level decreased by 2 times in RC patients after combined therapy. Notably, all patients with relapses (n = 5) showed an increase in methylation level for the SEPTIN9 and IKZF1 genes and a decrease of methylation level for the LINE-1 elements by 2 times or more in comparison with the level 10-15 days after surgery. There were no changes in the circulating SEPTIN9, IKZF1, and LINE-1 methylation levels during the 12-month follow-up period after the combined therapy of RC patients (n = 20) without relapses. CONCLUSION The results indicate that SEPTIN9, IKZF1, and LINE-1 methylation levels in the csb-cfDNA are potential markers of the effectiveness of antitumor therapy and early detection of relapse in RC patients.
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Affiliation(s)
- Anastasia A Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia.
| | - Elena Yu Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087, Novosibirsk, Russia
| | - Anastasia I Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050, Tomsk, Russia
| | - Anna S Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Dmitry N Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Alexey Yu Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Sergey A Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Nadezhda V Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050, Tomsk, Russia
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Agudelo MC, Agudelo S, Lorincz A, Ramírez AT, Castañeda KM, Garcés-Palacio I, Zea AH, Piyathilake C, Sanchez GI. Folate deficiency modifies the risk of CIN3+ associated with DNA methylation levels: a nested case-control study from the ASCUS-COL trial. Eur J Nutr 2024; 63:563-572. [PMID: 38129362 PMCID: PMC10899296 DOI: 10.1007/s00394-023-03289-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE To our knowledge, there are very few studies evaluating if the levels of folate modify the risk of cervical intraepithelial neoplasia grade 2 and higher (CIN2+ and CIN3+) associated with the levels of HPV genome methylation, two cofactors related to single carbon metabolism and independently associated with cervical cancer in previous studies. We conducted a case-control study nested in a three-arm randomized clinical pragmatic trial (ASCUS-COL trial) to evaluate the risk of CIN3+ associated with methylation levels according to serum folate concentrations. METHODS Cases (n = 155) were women with histologically confirmed CIN2+ (113 CIN2, 38 CIN3, and 4 SCC) and controls were age and follow-up time at diagnosis-matched women with histologically confirmed ≤ CIN1 (n = 155), selected from the 1122 hrHPV + women of this trial. The concentrations of serum folate were determined by the radioimmunoassay SimulTRAC-SNB-VitaminB12/Folate-RIAKit and the methylation levels by the S5 classifier. Stepwise logistic regression models were used to estimate the association between folate or methylation levels and CIN2+ or CIN3+. The joint effect of folate levels and methylation on the risk of CIN3+ was estimated using combinations of categorical stratifications. RESULTS Folate levels were significantly lower in women with CIN3+ than in other diagnostic groups (p = 0.019). The risk of CIN3+ was eight times higher (OR 8.9, 95% CI 3.4-24.9) in women with folate deficiency and high methylation levels than in women with normal folate and high methylation levels (OR 1.4, 95% CI 0.4-4.6). CONCLUSION High methylation and deficient folate independently increased the risk of CIN3+ while deficient folate combined with high methylation was associated with a substantially elevated risk of CIN3+.
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Affiliation(s)
- María C Agudelo
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Samuel Agudelo
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Attila Lorincz
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Arianis Tatiana Ramírez
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
- Postdoctoral Fellow at the Prevention and Implementation Group, International Agency for Research On Cancer/World Health Organization, Lyon, France
| | - Kelly Melisa Castañeda
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Isabel Garcés-Palacio
- Epidemiology Group, School of Public Health, Universidad de Antioquia, Medellín, Colombia
| | - Arnold H Zea
- Stanley S. Scott Cancer Center, Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, USA
| | - Chandrika Piyathilake
- Department of Nutrition Sciences, The University of Alabama at Birmingham, Birmingham, USA
| | - Gloria Ines Sanchez
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia.
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Inciuraite R, Steponaitiene R, Raudze O, Kulokiene U, Kiudelis V, Lukosevicius R, Ugenskiene R, Adamonis K, Kiudelis G, Jonaitis LV, Kupcinskas J, Skieceviciene J. Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level. Sci Rep 2024; 14:4456. [PMID: 38396014 PMCID: PMC10891043 DOI: 10.1038/s41598-024-55076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.
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Affiliation(s)
- Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ruta Steponaitiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Odeta Raudze
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ugne Kulokiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Vytautas Kiudelis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Kestutis Adamonis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Laimas Virginijus Jonaitis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania.
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Tisato V, Silva JA, Scarpellini F, Capucci R, Marci R, Gallo I, Salvatori F, D'Aversa E, Secchiero P, Serino ML, Zauli G, Singh AV, Gemmati D. Epigenetic role of LINE-1 methylation and key genes in pregnancy maintenance. Sci Rep 2024; 14:3275. [PMID: 38332006 PMCID: PMC10853191 DOI: 10.1038/s41598-024-53737-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/04/2024] [Indexed: 02/10/2024] Open
Abstract
Spontaneous abortion is a pregnancy complication characterized by complex and multifactorial etiology. About 5% of childbearing women are globally affected by early pregnancy loss (EPL) and most of them experience recurrence (RPL). Epigenetic mechanisms and controlled inflammation are crucial for pregnancy maintenance and genetic predispositions may increase the risk affecting the maternal-fetal crosstalk. Combined analyses of global methylation, inflammation and inherited predispositions may contribute to define pregnancy loss etiopathogenesis. LINE-1 epigenetic regulation plays crucial roles during embryo implantation, and its hypomethylation has been associated with senescence and several complex diseases. By analysing a group of 230 women who have gone through pregnancy interruption and comparing those experiencing spontaneous EPL (n = 123; RPL, 54.5%) with a group of normal pregnant who underwent to voluntary interruption (VPI, n = 107), the single statistical analysis revealed significant lower (P < 0.00001) LINE-1 methylation and higher (P < 0.0001) mean cytokine levels (CKs: IL6, IL10, IL17A, IL23) in EPL. Genotyping of the following SNPs accounted for different EPL/RPL risk odds ratio: F13A1 rs5985 (OR = 0.24; 0.06-0.90); F13B rs6003 (OR = 0.23; 0.047-1.1); FGA rs6050 (OR = 0.58; 0.33-1.0); CRP rs2808635/rs876538 (OR = 0.15; 0.014-0.81); ABO rs657152 (OR = 0.48; 0.22-1.08); TP53 rs1042522 (OR = 0.54; 0.32-0.92); MTHFR rs1801133/rs1801131 (OR = 2.03; 1.2-3.47) and FGB rs1800790 (OR = 1.97; 1.01-3.87), although Bonferroni correction did not reach significant outputs. Principal Component Analysis (PCA) and logistic regression disclosed further SNPs positive/negative associations (e.g. APOE rs7412/rs429358; FGB rs1800790; CFH rs1061170) differently arranged and sorted in four significant PCs: PC1 (F13A, methylation, CKs); PC3 (CRP, MTHFR, age, methylation); PC4 (F13B, FGA, FGB, APOE, TP53, age, methylation); PC6 (F13A, CFH, ABO, MTHFR, TP53, age), yielding further statistical power to the association models. In detail, positive EPL risk association was with PC1 (OR = 1.81; 1.33-2.45; P < 0.0001) and negative associations with PC3 (OR = 0.489; 0.37-0.66; P < 0.0001); PC4 (OR = 0.72; 0.55-0.94; P = 0.018) and PC6 (OR = 0.61; 0.46-0.81; P = 0.001). Moreover, significant inverse associations were detected between methylation and CKs levels in the whole group (rIL10 = - 0.22; rIL17A = - 0.25; rIL23 = - 0.19; rIL6 = - 0.22), and methylation with age in the whole group, EPL and RPL subgroups (r2TOT = 0.147; r2EPL = 0.136; r2 RPL = 0.248), while VPI controls lost significance (r2VPI = 0.011). This study provides a valuable multilayer approach for investigating epigenetic abnormalities in pregnancy loss suggesting genetic-driven dysregulations and anomalous epigenetic mechanisms potentially mediated by LINE-1 hypomethylation. Women with unexplained EPL might benefit of such investigations, providing new insights for predicting the pregnancy outcome and for treating at risk women with novel targeted epidrugs.
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Affiliation(s)
- Veronica Tisato
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy.
- University Strategic Centre for Studies On Gender Medicine, University of Ferrara, 44121, Ferrara, Italy.
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121, Ferrara, Italy.
- LTTA Centre, University of Ferrara, 44121, Ferrara, Italy.
| | - Juliana A Silva
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | | | - Roberta Capucci
- Department of Medical Sciences, University of Ferrara, 44121, Ferrara, Italy
| | - Roberto Marci
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Ines Gallo
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Francesca Salvatori
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Elisabetta D'Aversa
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Paola Secchiero
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Maria L Serino
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121, Ferrara, Italy
| | - Giorgio Zauli
- Department of Environmental Sciences and Prevention, University of Ferrara, 44121, Ferrara, Italy
| | - Ajay V Singh
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Donato Gemmati
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy.
- University Strategic Centre for Studies On Gender Medicine, University of Ferrara, 44121, Ferrara, Italy.
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121, Ferrara, Italy.
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Bergin CJ, Mendes da Silva A, Benoit YD. Where to Draw the LINE-Are Retrotransposable Elements Here to Stay? Cancers (Basel) 2023; 15:4119. [PMID: 37627147 PMCID: PMC10452504 DOI: 10.3390/cancers15164119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The frequency of somatic retrotranspositions of Long Interspersed Nuclear Elements 1 (LINE1) over a lifetime in healthy colonic epithelium and colorectal tumors has recently been reported. Indicative of a cell type-specific effect, LINE1 sequences in colonic epithelium showed lower levels of DNA methylation compared to other cell types examined in the study. Consistent with a role for DNA methylation in transposon silencing, the decreases in DNA methylation observed at LINE1 elements in colonic epithelium were accompanied by increases in LINE1 mRNA levels. In human primary colorectal tumors, LINE1 retrotransposition frequency was tenfold higher than in normal colonic tissues, with insertions potentially altering genomic stability and cellular functions. Here, we discuss the discoveries made by Nam and colleagues, emphasizing the intestinal-specific methylation signature regulating the LINE1 lifecycle and how this new information could shape future drug discovery endeavors against colorectal cancer.
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Affiliation(s)
- Christopher J. Bergin
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (C.J.B.); (A.M.d.S.)
| | - Amanda Mendes da Silva
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (C.J.B.); (A.M.d.S.)
| | - Yannick D. Benoit
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (C.J.B.); (A.M.d.S.)
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Huang CY, Chen WJ, Lee HL, Lin YC, Huang YL, Shiue HS, Pu YS, Hsueh YM. Possible Combined Effects of Plasma Folate Levels, Global DNA Methylation, and Blood Cadmium Concentrations on Renal Cell Carcinoma. Nutrients 2023; 15:nu15040937. [PMID: 36839294 PMCID: PMC9959822 DOI: 10.3390/nu15040937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Epigenetic effects of environmental pollutants may be related to carcinogenesis. This study aimed to explore the association between the global DNA methylation marker: 5-methyl-2-deoxycytidine (5mdC) and renal cell carcinoma (RCC), and further investigated whether plasma folate and vitamin B12 levels and 5mdC modified the association between blood cadmium concentrations and RCC. We recruited 174 RCC patients and 673 non-RCC controls. Blood cadmium concentrations, plasma folate and vitamin B12 levels were measured. The amount of 5mdC in the DNA sample was expressed as percentages of the total cytosine content. An increase of 5mdC (%) and plasma folate and vitamin B12 levels were associated with decreasing odds ratio (OR) of RCC. Although plasma folate levels were not directly associated with 5mdC (%), a combined effect was observed with the odds of low plasma folate levels and low 5mdC (%) were greater among RCC patients compared to controls (OR (95% confidence interval, CI) = 11.86 (5.27-26.65)). Additionally, we observed that the odds of low plasma folate and high blood cadmium levels were greater among RCC patients than in controls (OR (95% CI): 8.15 (1.39-7.13)). This study provides suggestive evidence that plasma folate levels may modify the associations between 5mdC (%) or blood cadmium concentrations and RCC.
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Affiliation(s)
- Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, College of Medicine National Taiwan University, Taipei City 110, Taiwan
| | - Wei-Jen Chen
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hui-Ling Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Ying-Chin Lin
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City 110, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 110, Taiwan
- Department of Occupational Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City 110, Taiwan
| | - Ya-Li Huang
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 110, Taiwan
| | - Horng-Sheng Shiue
- Department of Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan
| | - Yeong-Shiau Pu
- Department of Urology, National Taiwan University Hospital, College of Medicine National Taiwan University, Taipei City 110, Taiwan
| | - Yu-Mei Hsueh
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City 110, Taiwan
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 110, Taiwan
- Correspondence: ; Tel.: +886-2736-1661 (ext. 6513)
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Folate in maternal rheumatoid arthritis-filial autism spectrum disorder continuum. Reprod Toxicol 2023; 115:29-35. [PMID: 36402436 DOI: 10.1016/j.reprotox.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Rheumatoid Arthritis (RA) is an inflammatory autoimmune disease that affects women three times more than men. Epidemiological studies found that the incidence of Autism Spectrum Disorder (ASD), a neurological and developmental disorder, in children born to mothers suffering from RA is higher compared with the control population. Considering that the pathogenesis of ASD could be traced back to pregnancy and in uterine conditions, and the evidence of reduced folate levels in the brain of ASD-affected children, we aimed to study the role of folate, as an important nutritional factor during pregnancy, in associating maternal RA to ASD development in the offspring. Folate balance during RA could be influenced twice, initially during the immune activation associated with disease onset, and later during the treatment with anti-folate drugs, with a potential consequence of folate deficiency. Maternal folate deficiency during pregnancy could increase homocysteine levels, oxidative stress, and global DNA hypomethylation, all known risk factors in ASD pathogenesis. These effects could be intensified by genetic polymorphisms in the folate system, which were also found as genetic risk factors for both RA and ASD. The available evidence suggests that folate level as an important factor during RA, pregnancy and ASD could have pathological and therapeutical significance and should be carefully monitored and investigated in the RA-pregnancy-ASD axis.
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Urh K, Zidar N, Boštjančič E. Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis. Int J Mol Sci 2022; 23:ijms232113252. [PMID: 36362041 PMCID: PMC9654446 DOI: 10.3390/ijms232113252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Cancer stem cells (CSC) play one of the crucial roles in the pathogenesis of various cancers, including colorectal cancer (CRC). Although great efforts have been made regarding our understanding of the cancerogenesis of CRC, CSC involvement in CRC development is still poorly understood. Using bioinformatics and RNA-seq data of normal mucosa, colorectal adenoma, and carcinoma (n = 106) from GEO and TCGA, we identified candidate CSC genes and analyzed pathway enrichment analysis (PEI) and protein–protein interaction analysis (PPI). Identified CSC-related genes were validated using qPCR and tissue samples from 47 patients with adenoma, adenoma with early carcinoma, and carcinoma without and with lymph node metastasis and were compared to normal mucosa. Six CSC-related genes were identified: ANLN, CDK1, ECT2, PDGFD, TNC, and TNXB. ANLN, CDK1, ECT2, and TNC were differentially expressed between adenoma and adenoma with early carcinoma. TNC was differentially expressed in CRC without lymph node metastases whereas ANLN, CDK1, and PDGFD were differentially expressed in CRC with lymph node metastases compared to normal mucosa. ANLN and PDGFD were differentially expressed between carcinoma without and with lymph node metastasis. Our study identified and validated CSC-related genes that might be involved in early stages of CRC development (ANLN, CDK1, ECT2, TNC) and in development of metastasis (ANLN, PDGFD).
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Liu H, Yuan M, Mitra R, Zhou X, Long M, Lei W, Zhou S, Huang YE, Hou F, Eischen CM, Jiang W. CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research. Genome Med 2022; 14:118. [PMID: 36229842 PMCID: PMC9563764 DOI: 10.1186/s13073-022-01119-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
Abstract
Background Pathway enrichment analysis (PEA) is a common method for exploring functions of hundreds of genes and identifying disease-risk pathways. Moreover, different pathways exert their functions through crosstalk. However, existing PEA methods do not sufficiently integrate essential pathway features, including pathway crosstalk, molecular interactions, and network topologies, resulting in many risk pathways that remain uninvestigated. Methods To overcome these limitations, we develop a new crosstalk-based PEA method, CTpathway, based on a global pathway crosstalk map (GPCM) with >440,000 edges by combing pathways from eight resources, transcription factor-gene regulations, and large-scale protein-protein interactions. Integrating gene differential expression and crosstalk effects in GPCM, we assign a risk score to genes in the GPCM and identify risk pathways enriched with the risk genes. Results Analysis of >8300 expression profiles covering ten cancer tissues and blood samples indicates that CTpathway outperforms the current state-of-the-art methods in identifying risk pathways with higher accuracy, reproducibility, and speed. CTpathway recapitulates known risk pathways and exclusively identifies several previously unreported critical pathways for individual cancer types. CTpathway also outperforms other methods in identifying risk pathways across all cancer stages, including early-stage cancer with a small number of differentially expressed genes. Moreover, the robust design of CTpathway enables researchers to analyze both bulk and single-cell RNA-seq profiles to predict both cancer tissue and cell type-specific risk pathways with higher accuracy. Conclusions Collectively, CTpathway is a fast, accurate, and stable pathway enrichment analysis method for cancer research that can be used to identify cancer risk pathways. The CTpathway interactive web server can be accessed here http://www.jianglab.cn/CTpathway/. The stand-alone program can be accessed here https://github.com/Bioccjw/CTpathway. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01119-6.
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Affiliation(s)
- Haizhou Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Mengqin Yuan
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Ramkrishna Mitra
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th St., Philadelphia, PA, 19107, USA
| | - Xu Zhou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Min Long
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Wanyue Lei
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Shunheng Zhou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Yu-E Huang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Fei Hou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China
| | - Christine M Eischen
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th St., Philadelphia, PA, 19107, USA.
| | - Wei Jiang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29, Jiangjun Avenue, Nanjing, 211106, Jiangsu Province, China.
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10
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Szigeti KA, Barták BK, Nagy ZB, Zsigrai S, Papp M, Márkus E, Igaz P, Takács I, Molnár B, Kalmár A. Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples. Int J Mol Sci 2022; 23:ijms231911608. [PMID: 36232908 PMCID: PMC9569782 DOI: 10.3390/ijms231911608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.
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Affiliation(s)
- Krisztina A Szigeti
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-459-1500
| | - Barbara K Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Zsófia B Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Eszter Márkus
- Department of Anaesthesia and Intensive Care, Pest County Flor Ferenc Hospital, 2143 Kistarcsa, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
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