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Banerjee A, Bardhan A, Sarkar P, Datta C, Pal DK, Saha A, Ghosh A. Dysregulation of DNA epigenetic modulators during prostate carcinogenesis in an eastern Indian patient population: Prognostic implications. Pathol Res Pract 2024; 253:154970. [PMID: 38056136 DOI: 10.1016/j.prp.2023.154970] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
The role of epigenetic alteration in prostate cancer pathogenesis was reported. We aimed to analyze dysregulation of DNA methylase (DNA methyl transferase/DNMT) and demethylase (ten eleven translocase/TET) and the associated interplay between them during prostate tumorigenesis. Promoter methylation and RNA/protein expression of selected DNMT and TETs were analysed in normal prostate, benign prostatic hyperplasia (BPH), and prostate cancer (PCa). Genomic 5-hydroxymethylcytosine (5hmC) level was detected and correlated with DNMT and TET proteins. Clinicopathological association of molecular data was done. Our data revealed a very low frequency of promoter methylation for DNMT1 (5-3% and high frequency for TET1 (22-38%), TET2 (68-90 %), and TET3 (43-32 %) in BPH and PCa. The promoter methylation of DNMT1 (p = 0.019) showed a significantly decreasing trend, while that of TET1 (p = 0.0005) and TET2 (p < 0.0001) showed an increasing trend from normal prostate to BPH to PCa, indicating their epigenetic dysregulation during prostate tumorigenesis. RNA/protein overexpression of DNMT1 and reduced expression of TET1 and TET2 in PCa compared to BPH were associated with the promoter methylation status of genes. The 5hmC level was significantly lower in PCa than in BPH and correlated negatively with DNMT1 but positively with TET1 and TET2 proteins, suggesting dysregulation of DNA methylase and de-methylase activities during prostate tumorigenesis. Lastly, tumors having methylated TET1 and TET2 promoters showed advanced clinicopathological features (a higher PSA level/Gleason score) and increased risk of bone metastasis. In conclusion, DNMT1 upregulation and epigenetic silencing of TET1 and TET2 was seen during PCa development. TET1 and TET2 promoter methylation has prognostic importance.
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Affiliation(s)
- Anwesha Banerjee
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Abhishek Bardhan
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Purandar Sarkar
- Institute of Health Sciences, Presidency University, New Town, Kolkata, West Bengal, India
| | - Chhanda Datta
- Department of Pathology, IPGME&R, Kolkata, West Bengal, India
| | | | - Abhik Saha
- Institute of Health Sciences, Presidency University, New Town, Kolkata, West Bengal, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.
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Bardhan A, Banerjee A, Pal DK, Ghosh A. HAGLR, A Long Non-coding RNA of Potential Tumor Suppressive Function in Clear Cell Renal Cell Carcinoma: Diagnostic and Prognostic Implications. Mol Biotechnol 2023:10.1007/s12033-023-00948-z. [PMID: 37955777 DOI: 10.1007/s12033-023-00948-z] [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: 05/08/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023]
Abstract
Research works suggested the role of long non-coding RNAs (lncRNAs) in pathogenesis of clear cell renal cell carcinoma (ccRCC). lncRNA HAGLR is studied in several malignancies, but not in ccRCC. From The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) dataset, we analyzed molecular alterations of HAGLR and constructed a competitive endogenous RNA (ceRNA) network with related miRNAs and mRNAs. Gene Ontology analysis was done to identify important pathways enriched with HAGLR recovered mRNAs. Clinical importance of HAGLR and related mRNAs was assessed and, the impact of selected mRNA-encoding genes on tumor immune infiltration was studied using TIMER. HAGLR expression was reduced in ccRCC than in normal kidneys, and correlated significantly with gene promoter methylation. Low HAGLR level in tumors showed diagnostic potency, and was associated with clinicopathological parameters (stage/grade/metastasis) and poor patient survival. The HAGLR-associated ceRNA network constituted 13 miRNAs and 23 mRNAs differentially expressed in the TCGA-KIRC dataset. From HAGLR recovered mRNA-encoding genes, we developed a 5-gene (PAQR5, ARHGAP24, HABP4, PDLIM5, and RPS6KA2) prognostic signature in the training dataset and validated it in testing as well as entire datasets. The expression level of signature genes showed negative correlation with tumor infiltration of immune cells having adverse impact on ccRCC prognosis and also with tumor derived chemokines facilitating the infiltration. In conclusion, HAGLR seemed to play a tumor suppressive role in ccRCC. HAGLR and associated gene signature may have implementation in improving existing prognostic measure and developing effective immunotherapeutic strategies for ccRCC.
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Affiliation(s)
- Abhishek Bardhan
- Genetics of Non-communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Anwesha Banerjee
- Genetics of Non-communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | | | - Amlan Ghosh
- Genetics of Non-communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
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Balacco D, Bardhan A, Grant M, Kuehne S, Hirschfeld J, Heagerty A, Chapple I. LB978 High relative abundance of bacillales is associated with epidermolysis bullosa (EB) at different stages of wound healing. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.1001] [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: 10/17/2022]
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Hunjan M, Devecchi V, Bardhan A, Harper N, Falla D, Hegearty A. 488 Ground reaction forces(GRF) in patients with epidermolysis bullosa simplex(EBS) during walking. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.497] [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: 11/30/2022]
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Wen D, Balacco DL, Bardhan A, Harper N, Walsh D, Ryan G, Liu L, Guy A, McGrath JA, Ogboli M, Heagerty AHM. Localized autosomal recessive epidermolysis bullosa simplex arising from a novel homozygous frameshift mutation in DST (BPAG1). Clin Exp Dermatol 2021; 47:497-502. [PMID: 34806203 DOI: 10.1111/ced.14917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 11/26/2022]
Affiliation(s)
- D Wen
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Adult Epidermolysis Bullosa Unit, Department of Dermatology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - D L Balacco
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - A Bardhan
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Adult Epidermolysis Bullosa Unit, Department of Dermatology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - N Harper
- Adult Epidermolysis Bullosa Unit, Department of Dermatology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - D Walsh
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - G Ryan
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - L Liu
- National Diagnostic EB Laboratory, Viapath, St Thomas' Hospital, London, UK
| | - A Guy
- National Diagnostic EB Laboratory, Viapath, St Thomas' Hospital, London, UK
| | - J A McGrath
- National Diagnostic EB Laboratory, Viapath, St Thomas' Hospital, London, UK
| | - M Ogboli
- Paediatric Epidermolysis Bullosa Unit, Department of Paediatric Dermatology, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - A H M Heagerty
- Adult Epidermolysis Bullosa Unit, Department of Dermatology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.,Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Bardhan A, Banerjee A, Basu K, Pal DK, Ghosh A. PRNCR1: a long non-coding RNA with a pivotal oncogenic role in cancer. Hum Genet 2021; 141:15-29. [PMID: 34727260 PMCID: PMC8561087 DOI: 10.1007/s00439-021-02396-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/21/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been gaining importance in the field of cancer research in recent years. PRNCR1 (prostate cancer-associated non-coding RNA1) is a 12.7 kb, intron-less lncRNA found to play an oncogenic role in malignancy of diverse organs including prostate, breast, lung, oral cavity, colon and rectum. Single-nucleotide polymorphisms (SNPs) of PRNCR1 locus have been found to be associated with cancer susceptibility in different populations. In this review, an attempt has been made for the first time to summarize all sorts of available data on PRNCR1 to date from relevant databases (GeneCard, LncExpDB, Ensembl genome browser, and PubMed). As functional roles of PRNCR1, miRNA (microRNA) sponging was mostly highlighted in the pathogenesis of different cancer; in addition, an association of the lncRNA with chromatin-modifying complex to enhance androgen receptor-mediated gene transcription was reported in prostate cancer. Diagnostic and prognostic importance of PRNCR1 was found in some malignancies suggesting potency of the lncRNA to serve as a clinical biomarker. For PRNCR1 SNPs, although cancer susceptibility of the risk alleles/genotypes was reported in different populations, majorities of the findings were not replicated and underlying molecular mechanisms remained unexplored. Therapeutic implication of PRNCR1 was not studied well and future research may come up in this direction for intervening novel strategies to fight against cancer.
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Affiliation(s)
- Abhishek Bardhan
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Anwesha Banerjee
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Keya Basu
- Department of Pathology, IPGME&R, Kolkata, West Bengal, India
| | | | - Amlan Ghosh
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
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Hunjan MK, Zuzarte L, Bardhan A, Karim S, Heagerty AHM. Toxic erythema as the first sign of COVID-19 infection. Clin Exp Dermatol 2021; 46:756-758. [PMID: 33484596 PMCID: PMC8013887 DOI: 10.1111/ced.14571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/03/2022]
Affiliation(s)
- M K Hunjan
- Department of Dermatology, Solihull Hospital, University Hospitals Birmingham NHS Trust, Birmingham, UK
| | - L Zuzarte
- Department of Dermatology, Solihull Hospital, University Hospitals Birmingham NHS Trust, Birmingham, UK
| | - A Bardhan
- Department of Dermatology, Solihull Hospital, University Hospitals Birmingham NHS Trust, Birmingham, UK.,University of Birmingham, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - S Karim
- Department of Histopathology, University Hospitals Birmingham NHS Trust, Birmingham, UK
| | - A H M Heagerty
- Department of Dermatology, Solihull Hospital, University Hospitals Birmingham NHS Trust, Birmingham, UK.,University of Birmingham, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Sharma T, Bardhan A, Bahadur M. Increases and decreases of whole-arm heterochromatin in specific chromosomes: an extraordinary situation in hybrids of the Mus terricolor complex. Cytogenet Genome Res 2003; 96:244-9. [PMID: 12438806 DOI: 10.1159/000063035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The three chromosomal species of Mus terricolor display fixed variations in the short-arm heterochromatin of autosomes 1, 3, and 6. Some laboratory-generated hybrids among the chromosomal species show an unusual increase or decrease in the extent of whole-arm heterochromatin, instead of the expected heterozygosity for the heterochromatic short arms. The whole-arm increase/decrease tends to favor homozygosity for the presence or absence of the heterochromatic short arms. Interestingly, this increase/decrease conforms with the karyotypes of the parental chromosomal species. Although rapid karyotypic changes have been reported in other plant and animal hybrids, the situation observed in the M. terricolor hybrids is unique. The changes are stable and could be a product of the unusual chromosomal organization of recombinogenic telomeric sequences in this species complex. The altered karyological constitution is constant in both somatic and germ cells of each hybrid, suggesting that the changes occurred early in their development. The high frequency and nonrandom recurrence of similar changes in different hybrids seem to reflect a mechanism that might have been instrumental in the fixation of these chromosomal variations in a stable homozygous condition in natural populations.
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Affiliation(s)
- T Sharma
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India.
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Abstract
Ag-NOR staining and fluorescence in situ hybridization with rDNA probes showed an unusually high number of NORs in the Indian pygmy field mice, Mus booduga and the M. terricolor complex. The chromosomal location of the NORs was also altered in terricolor, they were shifted from the proximal regions of the long arms to the tips of the perceptible heterochromatic short arms of the acrocentric autosomes. The results suggested dispersion of the NORs in the booduga-terricolor lineage probably by transposition, and relocalization of the NORs in the terricolor complex by centric reorganization during the process of replacement of the Mus musculus-related AT-rich heterochromatin with the terricolor-specific heterochromatin.
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Affiliation(s)
- A Bardhan
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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Bardhan A, Sharma T. Sequential meiotic prophase development in the pubertal Indian pygmy field mouse: synaptic progression of the XY chromosomes, autosomal heterochromatin, and pericentric inversions. Genome 2000; 43:172-80. [PMID: 10701127 DOI: 10.1139/g99-080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequential meiotic prophase development has been followed in the pubertal male pygmy mouse Mus terricolor, with the objective to identify early meiotic prophase stages. The pygmy mouse differs from the common mouse by having large heterochromatic blocks in the X and Y chromosomes. These mice also show various chromosomal mutations; for example, fixed variations of autosomal short arms heterochromatin among different chromosomal species and pericentric inversion polymorphism. Identification of prophase stages was crucial to analyzing effects of heterozygosity for these chromosomal changes on the process of homologous synapsis. Here we describe identification of the prophase stages in M. terricolor, especially the pachytene substages, on the basis of morphology of the XY bivalent. Based on this substaging, we show delayed pairing of the heterochromatic short arms, which may be the reason for their lack of chiasmata. The identification of precise pachytene substages also reveals an early occurrence of "synaptic adjustment" in the pericentric inversion heterobivalents, a mechanism that would prevent chiasma formation in the inverted segment and thereby would abate adverse effects of such heterozygosity. The identification of pachytene substages would serve as the basis to analyze the nature of synaptic anomalies met in M. terricolor hybrids (which will be the basis of a subsequent paper).
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Affiliation(s)
- A Bardhan
- Department of Zoology, Banaras Hindu University, Varanasi, India
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Bardhan A. Change of cephalic index during the first ten months of life. Indian Pediatr 1967; 4:221-5. [PMID: 5589479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Bardhan A. A short note on the birth order, parental age and the incidence of oral clefts. Acta Genet Med Gemellol (Roma) 1967; 16:101-5. [PMID: 6063935 DOI: 10.1017/s1120962300013317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SummaryA study of 6375 births from the records of two hospitals of Delhi reveals that the incidence of oral clefts is more or less constant in both males and females. Evidence indicates that plural births are more associated with the harelip, cleft palate and cleft lip, than single births. In the same way, there is a positive association between oral clefts and higher age groups of parents. For this fact it can be mentioned that the incidence of oral clefts is lower in lower birth ranks and higher in higher birth ranks, which is again indirectly influenced by the higher age group of parents.
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