Impact of Genetic Polymorphisms in NF-ĸB2 and TRAF3 Genes on Response to Bortezomib-Based Therapy in Multiple Myeloma Patients.

BACKGROUND: Multiple myeloma (MM), being the second most common hematological malignancy, has garnered significant attention. The ubiquitin proteasomal pathway (UPP), crucial for normal cell function, plays a pivotal role in myeloma pathophysiology, especially with the advent of bortezomib (BTZ). Dysregulation of the UPP has implications ranging from developmental abnormalities to cancer. OBJECTIVES: This study aimed to delineate the clinical characteristics of newly diagnosed multiple myeloma patients and investigate the influence of single nucleotide polymorphisms (SNPs) in NF-ĸB2 and TRAF3 genes on the risk and treatment response to bortezomib-based chemotherapy. MATERIALS AND METHODS: Conducted at JIPMER, Pondicherry, this prospective study enrolled 184 participants, comprising cases and controls. DNA extraction from peripheral blood samples was followed by SNP analysis through Real-time Polymerase Chain Reaction. Patients were categorized into Good and Poor responders, and SNP associations with treatment response, response rates, and survival outcomes were assessed using chi-square and Kaplan-Meier analyses. RESULTS: The median age of participants was 55 years, with backache being the most prevalent symptom (66.3%). Hypercalcemia (22%), renal failure (8.7%), and bone fractures (45.7%) were also observed, alongside high prevalence of anemia. Notably, the frequency of the TRAF3 rs12147254 A allele was lower in cases compared to controls (31% vs. 49%, P-value=0.002). Poor responders exhibited higher frequencies of the GA+AA genotypes in TRAF3 rs12147254 (OR-3.882(1.629-9.251), P-value-0.002) and NFKB2 rs1056890 (OR-3.308(1.366-8.012), P-value-0.008) when compared to good responders. The GA+AA genotype in TRAF3 rs11160707 SNP correlated with improved progression-free survival. CONCLUSION: The study findings underscore a significant association between genetic polymorphisms and treatment response outcomes, suggesting their utility in prognostic determinations and clinical outcomes prediction in multiple myeloma patients.

Absence of the frequently reported PIK3CA, CASP8, and NOTCH1 mutations in South Indian oral cancers.

OBJECTIVES: Somatic mutations of the PIK3CA, CASP8, and NOTCH1 have been frequently detected in various human cancers. Our study aimed to analyze the mutational status of these genes in South Indian oral cancers. SUBJECTS AND METHODS: We performed mutational analysis of the PIK3CA (exons 9 and 20), CASP8 (exon 9), and NOTCH1 (exons 5, 6, 7, 8, and 9) genes in 96, 48, and 44 oral cancer samples, respectively. All the specified exons were PCR (polymerase chain reaction)-amplified and directly sequenced by Sanger sequencing. RESULTS: PIK3CA gene mutations were not found; however, a synonymous single nucleotide polymorphism (SNP) [rs17849079] was observed frequently [35/96 (36.4%)] in oral cancer samples. Further, no mutations were detected in the CASP8 gene, but observed a frequent [32/48 (66.6%)] SNP [rs1045487] in the oral cancer samples. We did not detect any mutation in the NOTCH1 gene (exons 5, 6, 7, 8, and 9) in all the [0/44] analyzed oral cancer samples. CONCLUSIONS: This is the first study that reports the status of the PIK3CA, CASP8, and NOTCH1 mutations in South Indian oral cancer samples. Our study suggests that either mutations in these genes are uncommon in South Indian oral cancer samples or likely other genes in this pathway might be mutated.

Promoter hypermethylation analysis in myelodysplastic syndromes: diagnostic & prognostic implication.

BACKGROUND & OBJECTIVE: Myelodysplastic syndromes (MDS) are a heterogenous group of haematopoietic stem cell disorders that are multifactorial in their aetiology. Unique genetic alterations in combinations or in isolation account for a small fraction of MDS suggesting the epigenetic hypermethylation as a possible leading cause for MDS and its transformation to acute myelocytic leukaemia (AML). Therefore, in this study, promoter hypermethylation status of key cell cycle regulators was assessed as markers in MDS patients and association of hypermethylation with clinical progression of disease was also studied. METHODS: Promoter hypermethylation analysis of five tumour associated genes namely p16, p15, MGMT, hMLH1 and E-cadherin were done for 41 MDS patient samples with its various subtype. The hypermethylation analysis was done by using semi-nested multiplex PCR. RESULTS: Eighty per cent of (33/41) of the MDS samples were found to be methylated in any one of the four genes (p16, p15, MGMT and E-cadherin). The p15 methylation was found to be the most frequent 61 per cent (25/41), E-cadherin was methylated in 39 per cent (16/41) and p16 in 37 per cent (15/41) of the cases. MGMT gene showed a low 5 per cent (2/41) methylation whereas hMLH1 gene was not methylated in any one of the samples analysed. INTERPRETATION & CONCLUSION: Differential rate of methylation of the four genes (p16, p15, MGMT and E-cadherin) was observed in MDS samples. All the samples analysed showed the absence of a methylator phenotype in MDS. The methylation frequency of all these genes increased with the clinical severity of the MDS subtypes. Therefore, hypermethylation may be used as a diagnostic and prognostic tool in ascertaining the clinical severity of MDS.

FHIT gene mutations and single nucleotide polymorphism in Indian oral and cervical squamous cell carcinomas.

Genetic alterations at the FHIT (fragile histidine triad) tumor suppressor gene have been found in various human cancers. We have made an attempt to find point mutations of this gene in two different cancers from India, with entirely different etiologic factors: oral cancer (55 samples) caused by chewing tobacco and cervical cancer (43 samples) caused mainly by HPV (human papilloma virus) infection. Analysis of tumor DNA by the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was performed on each of FHIT exons 5-9 individually, using exon-flanking primers. Two different mutations were identified in both oral and cervical tumors: one at the second nucleotide 3' to the termination codon (TGA) in exon 9 and the other at the ninth nucleotide upstream to the beginning of exon 9. These results indicate that mutations in the FHIT gene are rare events in these tumors in India (approximately 4%). In addition, we found a single nucleotide FHIT gene polymorphism which is due to T/A replacement at 17 nucleotides upstream to exon 9 where the A allele is 0.6 of the population.

The p16INK4alpha/p19ARF gene mutations are infrequent and are mutually exclusive to p53 mutations in Indian oral squamous cell carcinomas.

Eighty-seven untreated primary oral squamous cell carcinomas (SCCs) associated with betel quid and tobacco chewing from Indian patients were analysed for the presence of mutations in the commonly shared exon 2 of p16INK4alpha/p19ARF genes. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing analysis were used to detect mutations. SSCP analysis indicated that only 9% (8/87) of the tumours had mutation in p16INK4alpha/p19ARF genes. Seventy-two tumours studied here were previously analysed for p53 mutations and 21% (15/72) of them were found to have mutations in p53 gene. Only one tumour was found to have mutation at both p53 and p16INK4alpha/p19ARF genes. Thus, the mutation rates observed were 21% for p53, 9% for p16INK4alpha/p19ARF, and 1% for both. Sequencing analysis revealed two types of mutations; i) G to C (GCAG to CCAG) transversion type mutation at intron 1-exon 2 splice junction and ii) another C to T transition type mutation resulting in CGA to TGA changing arginine to a termination codon at p16INK4alpha gene codon 80 and the same mutation will alter codon 94 of p19ARF gene from CCG to CTG (proline to leucine). These results suggest that p16INK4alpha/p19ARF mutations are less frequent than p53 mutations in Indian oral SCCs. The p53 and p16INK4alpha/p19ARF mutational events are independent and are mutually exclusive suggesting that mutational inactivation of either p53 or p16INK4alpha/p19ARF may alleviate the need for the inactivation of the other gene.

Low incidence of p53 mutations in betel quid and tobacco chewing-associated oral squamous carcinoma from India.

Mutations of the p53 tumor suppressor gene have been found to be the single most frequent event in human cancers. In India and other southeast Asian countries tobacco chewing with betel quid was attributed to be the major factor in oral carcinogenesis. We have analyzed 72 untreated primary oral squamous cell carcinomas (SCCs) for mutations in the tumor suppressor gene p53 exons 4-9 by PCR-SSCP and DNA sequencing. Sequencing analysis revealed 16 missense mutations, one silent mutation in codon 307 and four A to G substitution polymorphism in codon 213. The incidence of p53 mutation was 21% (15 of 72) excluding the polymorphism and the silent mutation. Eight mutations were clustered in codons 266-282 of exon 8. Of the total mutation events 37.5% were G to A transitions and 31.3% were G to T transversions. These results indicate the possible involvement of tobacco derived nitrosamines and their adducts in the genesis of oral cancer among Indians.

Infrequent genetic alterations of p53, p16 genes and polymorphism in fhit gene in Indian myelodysplastic syndrome.

Alterations in the tumor suppressor genes p53, p16, and fhit were studied in myelodysplastic syndrome (MDS) samples of Indian patients. PCR-SSCP analysis showed evidence for the presence of polymorphism in fhit gene in 7 of 15 samples. We failed to get any evidence for mutation in the p53, p16, and fhit genes. These results indicate that mutational inactivation of these genes may not play a major role in the development of myelodysplastic syndrome.

Detection of a rare point mutation at codon 59 and relatively high incidence of H-ras mutation in Indian oral cancer.

Analysis of H-, K- and N-ras genes for point mutations by PCR-SSCP and direct sequencing of 46 oral SCCs that were previously analyzed for p53 mutations revealed that 9 (20%) had point mutations in either the H-ras or the N-ras. A novel mutation at codon 59 (GCC-ACC) of H-ras thus far reported only in v-H-ras of Harvey murine sarcoma virus was observed in a tumor of the cheek. Majority (8/9) of these mutations were observed in H-ras, one in N-ras and none in K-ras. This study indicated that the ras gene mutation was relatively high in oral cancers associated with tobacco chewing and the ras and p53 mutational events seem to be independent and mutually exclusive.

The status of human papillomavirus and tumor suppressor genes p53 and p16 in carcinomas of uterine cervix from India.

OBJECTIVES: Infection with the high-risk strain of human papillomaviruses (HPVs) and the inactivation of the tumor suppressor gene p53 through mutation are important factors in cervical carcinogenesis. To know whether such events would occur in cervical carcinomas of Indians, 43 tumors (consisting of 36 of stage III B and 6 of stage II B) were screened for p53 and p16 gene mutations. METHODS: PCR followed by single-strand conformation polymorphism (SSCP) analysis were used to detect mutations in p53 and p16 genes and PCR for the presence of human papillomavirus genome. HPV status was ascertained by PCR amplification of parts of E6 and E7 genes using primers pU-1M and pU-2R and typing was carried out by restriction analysis. RESULTS: Of the 43 samples analyzed, 4 samples (9%) showed mobility shifts for p53 mutations; PCR products of the p16 gene did not show band shifts in SSCP analysis. HPV DNA was detected in 70% of the 43 samples analyzed: HPV 16 in 23 cases (53%), HPV 18 in 4 cases (13.3%), and HPV 33 in 1 case (3.3%). Two amplified HPV DNAs that were difficult to type with various restriction enzymes were cloned and the amplified regions were sequenced. One of these was 93% close to HPV 35 and the other was 80% close to HPV 58. Three samples had both p53 mutations and HPV genome. CONCLUSIONS: Our results indicate that HPV 16 infection was more common than HPV 18, the p53 mutations and HPV infection were not mutually exclusive events in the genesis of carcinoma of uterine cervix among Indian women, and p16 gene may not play a role in Indian cervical carcinomas.

p53 gene mutations in oral carcinomas from India.

In this study, we analyzed 53 oral squamous-cell carcinomas among Indians for the presence of alterations in the tumor-suppressor gene p53 by PCR-SSCP and sequencing methods. Our results showed that 21% (11/53) of oral carcinomas analyzed carried mutations within the exons 5-8 of the p53 gene. We have identified 11 single-base pair substitutions consisting of 10 mis-sense mutations and one at the splice acceptor site, and one deletion mutation involving 4 consecutive bases. The majority of the base substitutions were transitions (5 TA to CG and 5 GC to AT), while only one transversion (TA to GC) was observed. Probable hot-spots for the mutation induction were identified at codons 149 and 274, which have not been observed before in head-and-neck cancers. The mutational spectrum might have originated from base alkylations at guanine and thymine residues, caused by some alkylating agents. The present results are thus consistent with the involvement of tobacco-related nitrosoamines in the etiology of oral squamous-cell carcinoma.