Chromosome 9 instability and alterations of p16 gene in squamous cell carcinoma of the lung and in adjacent normal bronchi: FISH and immunohistochemical study

Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation

INTRODUCTION

Chronic graft-versus-host disease (cGVHD) is a debilitating side effect of allogeneic hematopoietic cell transplantation (HCT), affecting the quality of life of patients. We used whole exome sequencing to identify candidate SNPs and complete a multi-marker gene-level analysis using a cohort of cGVHD( +) (N = 16) and cGVHD( -) (N = 66) HCT patients.

METHODS

Saliva samples were collected from HCT patients (N = 82) pre-conditioning in a multi-center study from March 2011 to May 2018. Exome sequencing was performed and FASTQ files were processed for sequence alignments. Significant SNPs were identified by logistic regression using PLINK2v3.7 and Fisher's exact test. One cGVHD( -) patient sample was excluded from further analysis since no SNP was present in at least 10% of the sample population. The FUMA platform's SNP2GENE was utilized to annotate SNPs and generate a MAGMA output. Chromatin state visualization of lead SNPs was completed using Epilogos tool. FUMA's GENE2FUNC was used to obtain gene function and tissue expression from lead genomic loci.

RESULTS

Logistic regression classified 986 SNPs associated with cGVHD( +). SNP2GENE returned three genomic risk loci, four lead SNPs, 48 candidate SNPs, seven candidate GWAS tagged SNPs, and four mapped genes. Fisher's exact test identified significant homozygous genotypes of four lead SNPs (p < 0.05). GENE2FUNC analysis of multi-marker SNP sets identified one positional gene set including lead SNPs for KANK1 and KDM4C and two curated gene sets including lead SNPs for PTPRD, KDM4C, and/or KANK1.

CONCLUSIONS

Our data suggest that SNPs in three genes located on chromosome 9 confer genetic susceptibility to cGVHD in HCT patients. These genes modulate STAT3 expression and phosphorylation in cancer pathogenesis. The findings may have implications in the modulation of pathways currently targeted by JAK inhibitors in cGVHD clinical trials.

Homozygous Co-Deletion of Type I Interferons and CDKN2A Genes in Thoracic Cancers: Potential Consequences for Therapy

Homozygous deletion (HD) of the tumor suppressor gene CDKN2A is the most frequent genetic alteration in malignant pleural mesothelioma and is also frequent in non-small cell lung cancers. This HD is often accompanied by the HD of the type I interferons (IFN I) genes that are located closed to the CDKN2A gene on the p21.3 region of chromosome 9. IFN I genes encode sixteen cytokines (IFN-α, IFN-β…) that are implicated in cellular antiviral and antitumor defense and in the induction of the immune response. In this review, we discuss the potential influence of IFN I genes HD on thoracic cancers therapy and speak in favor of better taking these HD into account in patients monitoring.

Loss of P16 Protein Expression and Its Association with Epstein-Barr Virus LMP-1 Expression in Hodgkin's Lymphoma

Background

Expression of Epstein-Barr virus Latent Member Protein-1 (EBV LMP-1) and loss of P16 protein expression are documented in lymphoma, indicating a relationship between them, but this relationship is not clear and sometimes contradictory. Thus, this study was conducted to examine the relationship between the loss of P16 and EBV LMP-1 expression in Jordanian patients diagnosed with lymphoma.

Methods

Sections were made from archival formalin-fixed and paraffin-embedded blocks from 55 patients diagnosed with lymphoma. P16 expression and LMP-1 expression were detected by immunohistochemistry using monoclonal antibodies.

Results

In Hodgkin's Lymphoma (HL), the loss of P16 was higher in LMP-1 positive cases (61%) than LMP-1 negative cases (25%; P = 0.072). Conversely, in Non-Hodgkin's Lymphoma (NHL), none of LMP-1 positive samples showed loss of P16. Furthermore, among LMP-1 HL positive cases, the loss of P16 was more frequent in male (75%) than female (33%). Also, there was a significantly higher proportion of LMP-1 positive cases showing loss of P16 in HL (11:18), compared to those in NHL (0:8, P < 0.001), confirming a difference between HL and NHL, concerning the LMP-1/P16 relationship.

Conclusion

A trend for an association between loss of P16 and LMP-1 expression was observed in HL but not NHL patients. These findings suggest that there are molecular and clinical differences in the pathogenesis and development of different subtypes of lymphoma.

Altered p16(INK4) and RB1 Expressions Are Associated with Poor Prognosis in Patients with Nonsmall Cell Lung Cancer

p16(INK4) and RB1 are two potent cell cycle regulators to control the G1/S transition by interacting with CDK4/6, E2F, and D-type cyclins, respectively. Depending on the tumour type, genetic alterations resulting in the functional inactivation have frequently been reported in both genes. By contrast, much less is known regarding the overexpression of these proteins in the tumor cells. In this study, expressions of p16(INK4) RB1, and CDKN2A copy number variances (CNV) in the tumor cells were assessed by immunohistochemistry and fluorescence in situ hybridization (FISH), respectively, in 73 nonsmall cell lung cancer (NSCLC) with known 5-year survivals. The histologic type (P = 0.01), p16(INK4) (P = 0.004), and RB1 (P < 0.001) were predictive of survivals. The CDKN2A CNV (P < 0.05) was also significant when compared to those cases without CNV. Therefore, among the molecular genetic prognostic factors, expressions of RB1 and p16(INK4) in the tumor cells were the most strongly predictive of adverse outcomes in stage I and II nonsquamous NSCLC.

Usefulness of p16 for differentiating primary pulmonary squamous cell carcinoma from cervical squamous cell carcinoma metastatic to the lung

To date, there is no reliable immunohistochemical marker that discriminates between primary pulmonary squamous cell carcinoma (SCC) and cervical SCC metastatic to the lung. In this study, immunohistochemical staining of p16 was performed on 33 primary pulmonary SCCs, 48 primary cervical SCCs, and 17 cases of cervical SCC with pulmonary metastasis. Expression of p16 was noted in 47 cases of cervical SCC (47/48 [98%]), and all were strongly stained. Of the 7 cases of primary pulmonary SCC (7/33 [21%]) in which p16 expression was detected, 3 were weakly positive, 1 was moderately positive, and 3 were strongly positive. Among these p16+ pulmonary SCCs, only 1 showed detectable human papillomavirus DNA. Of the 17 cases of cervical SCC with pulmonary metastasis, all of the pulmonary and cervical tumors were positive for p16. p16 is a useful marker for the discrimination between cervical and pulmonary SCCs. The performance of p16 staining at different cutoff values was also compared.

Increased gamma-tubulin expression and P16INK4A promoter methylation occur together in preinvasive lesions and carcinomas of the breast

BACKGROUND

Loss of p16(INK4A) due to promoter hypermethylation is correlated with the ability to acquire centrosomal abnormalities in variant human mammary epithelial cells. gamma-Tubulin is a highly conserved component of centrosome in most animal cells and gamma-tubulin protein overexpression could lead to centrosome aberration.

MATERIALS AND METHODS

A large series of breast premalignant lesions and carcinoma was analyzed. Real-time quantitative PCR and immunohistochemistry were carried out to measure gamma-tubulin copy numbers and protein expression. MethyLight and immunohistochemistry were carried out to determine p16(INK4A) methylation and protein expression.

RESULTS

gamma-Tubulin protein expression was concordant with gene amplification; both of them were found to increase with atypical ductal hyperplasia-carcinoma sequence. The median value and positive rate of p16(INK4a) methylation increased while protein expression displayed a decreasing trend. P16(INK4a) methylation showed a firm association with gamma-tubulin gene amplification.

CONCLUSION

gamma-Tubulin gene amplification and the concomitant protein overexpression present not only in invasive carcinoma but also in a significant fraction of atypical hyperplasia and in situ carcinomas. P16(INK4a) methylation and gamma-tubulin gene amplification had a synergistic effect on tumor progression. The synergism might arise as a result of the combined influence that p16(INK4a) and gamma-tubulin have on the G1-S cell cycle checkpoints and centrosome.