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1.
Insects ; 14(3)2023 Mar 21.
Article in English | MEDLINE | ID: mdl-36975990

ABSTRACT

Invasive insects pose an increasing risk to global agriculture, environmental stability, and public health. Giant pine scale (GPS), Marchalina hellenica Gennadius (Hemiptera: Marchalinidae), is a phloem feeding scale insect endemic to the Eastern Mediterranean Basin, where it primarily feeds on Pinus halepensis and other Pinaceae. In 2014, GPS was detected in the southeast of Melbourne, Victoria, Australia, infesting the novel host Pinus radiata. An eradication program was unsuccessful, and with this insect now established within the state, containment and management efforts are underway to stop its spread; however, there remains a need to understand the insect's phenology and behaviour in Australia to better inform control efforts. We documented the annual life cycle and seasonal fluctuations in activity of GPS in Australia over a 32 month period at two contrasting field sites. Onset and duration of life stages were comparable to seasons in Mediterranean conspecifics, although the results imply the timing of GPS life stage progression is broadening or accelerating. GPS density was higher in Australia compared to Mediterranean reports, possibly due to the absence of key natural predators, such as the silver fly, Neoleucopis kartliana Tanasijtshuk (Diptera, Chamaemyiidae). Insect density and honeydew production in the Australian GPS population studied varied among locations and between generations. Although insect activity was well explained by climate, conditions recorded inside infested bark fissures often provided the weakest explanation of GPS activity. Our findings suggest that GPS activity is strongly influenced by climate, and this may in part be related to changes in host quality. An improved understanding of how our changing climate is influencing the phenology of phloem feeding insects such as GPS will help with predictions as to where these insects are likely to flourish and assist with management programs for pest species.

2.
Clin Chem ; 66(1): 77-88, 2020 01 01.
Article in English | MEDLINE | ID: mdl-31811004

ABSTRACT

BACKGROUND: The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT: The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY: The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.


Subject(s)
DNA/chemistry , High-Throughput Nucleotide Sequencing/methods , DNA/metabolism , DNA Methylation , Genome, Human , High-Throughput Nucleotide Sequencing/instrumentation , Humans , Metagenomics , Nanostructures/chemistry , Polymerase Chain Reaction , Sequence Analysis, DNA
3.
BMC Cancer ; 19(1): 352, 2019 Apr 11.
Article in English | MEDLINE | ID: mdl-30975103

ABSTRACT

BACKGROUND: High risk human papillomaviruses (HPV) plays important roles in the development of cervical cancer, a number of other anogenital cancer and they are increasingly found in oropharyngeal squamous cell carcinoma (OPSCC), however there has not been comprehensive analysis about the role how these viruses play in the development of OPSCC. METHODS: To characterize the physical status of HPV within OPSCC and to determine the effect this has throughout the host genome, we have performed 30-40X whole genome sequencing (WGS) on the BGI sequencing platform on 34 OPSCCs: 28 of which were HPV positive. We then examined the sequencing data to characterize the HPV copy number and HPV physical status to determine what effect they have on both HPV and human genome structural changes. RESULTS: WGS determined the HPV copy number across the viral genome. HPV copy number ranged from 1 copy to as high as 150 copies in each individual OPSCC. Independent of HPV copy number, most tumors had either a small or a very large deletion in the viral genome. We discovered that these deletions were the result of either HPV integration into the human genome or HPV-HPV sequence junctions. WGS revealed that ~ 70% of these tumors had HPV integrations within the human genome and HPV integration occurred independent of HPV copy number. Individual HPV integrations were found to be highly disruptive resulting in structural variations and copy number changes at or around the integration sites. CONCLUSIONS: WGS reveals that there is a great complexity in both HPV sequences present and the HPV integrations events in HPV positive OPSCCs tumors. Thus HPV may be playing different roles in the development of different OPSCCs and this further challenge the HPV-driven carcinogenesis model first proposed for cervical cancer.


Subject(s)
Biomarkers, Tumor/genetics , Carcinoma, Squamous Cell/genetics , Oropharyngeal Neoplasms/genetics , Papillomaviridae/genetics , Papillomavirus Infections/genetics , Adult , Aged , Carcinogenesis/genetics , Carcinoma, Squamous Cell/pathology , DNA, Viral/genetics , DNA, Viral/isolation & purification , Female , Gene Dosage , Genome, Human/genetics , Genome, Viral/genetics , Humans , Male , Middle Aged , Oropharyngeal Neoplasms/pathology , Papillomaviridae/isolation & purification , Papillomavirus Infections/pathology , Virus Integration/genetics , Whole Genome Sequencing
4.
Gynecol Oncol ; 146(2): 334-339, 2017 08.
Article in English | MEDLINE | ID: mdl-28587748

ABSTRACT

INTRODUCTION: Cervical cancer is the fourth most common female cancer worldwide. The prognosis for women with advanced-stage or recurrent cervical cancer remains poor and response to treatment is variable. Standardized management protocols leave little room for individualization. We report on a novel blood-based liquid biopsy for specific PIK3CA mutations as a clinically useful biomarker in patients with invasive cervical cancer. METHODS: One hundred seventeen Hong Kong Chinese women with primary invasive cervical cancer and their pre-treatment plasma samples were investigated. Two PIK3CA mutations, p.E542K and p.E545K were measured in cell free DNA (cfDNA) extracted from plasma using droplet digital PCR. This liquid biopsy of PIK3CA in cervical cancer was correlated to clinico-pathological features to verify the potential of PIK3CA as a clinically useful molecular biomarker for predicting disease prognosis and monitoring for progression. RESULTS: PIK3CA mutations, either p.E542K or p.E545K, were detected in plasma cfDNA from 22.2% of the patients. PIK3CA mutation status was significantly correlated to median tumor size (p<0.01). PIK3CA mutations detected in the plasma were significantly associated with decreased disease-free survival and overall survival (p<0.05). CONCLUSIONS: As a liquid molecular biopsy, analysis of circulating PIK3CA mutations shows promise as a way to refine risk stratification of individual patients with cervical cancer, and provides a platform for further research to offer individualized therapy with the purpose of improving outcomes.


Subject(s)
Adenocarcinoma/blood , Biomarkers, Tumor/blood , Carcinoma, Squamous Cell/blood , DNA, Neoplasm/blood , Phosphatidylinositol 3-Kinases/genetics , Uterine Cervical Neoplasms/blood , Adenocarcinoma/genetics , Adenocarcinoma/mortality , Adenocarcinoma/pathology , Asian People , Biomarkers, Tumor/genetics , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/mortality , Carcinoma, Squamous Cell/pathology , Class I Phosphatidylinositol 3-Kinases , DNA Mutational Analysis , Disease-Free Survival , Feasibility Studies , Female , Hong Kong , Humans , Middle Aged , Polymerase Chain Reaction , Tumor Burden , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/mortality , Uterine Cervical Neoplasms/pathology
6.
Genes Chromosomes Cancer ; 56(1): 59-74, 2017 01.
Article in English | MEDLINE | ID: mdl-27636103

ABSTRACT

Common fragile sites (CFS) are chromosome regions that are prone to form gaps or breaks in response to DNA replication stress. They are often found as hotspots for sister chromatid exchanges, deletions, and amplifications in different cancers. Many of the CFS regions are found to span genes whose genomic sequence is greater than 1 Mb, some of which have been demonstrated to function as important tumor suppressors. CFS regions are also hotspots for human papillomavirus (HPV) integrations in cervical cancer. We used mate-pair sequencing to examine HPV integration events and chromosomal structural variations in 34 oropharyngeal squamous cell carcinoma (OPSCC). We used endpoint PCR and Sanger sequencing to validate each HPV integration event and found HPV integrations preferentially occurred within CFS regions similar to what is observed in cervical cancer. We also found that many of the chromosomal alterations detected also occurred at or near the cytogenetic location of CFSs. Several large genes were also found to be recurrent targets of rearrangements, independent of HPV integrations, including CSMD1 (2.1Mb), LRP1B (1.9Mb), and LARGE1 (0.7Mb). Sanger sequencing revealed that the nucleotide sequences near to identified junction sites contained repetitive and AT-rich sequences that were shown to have the potential to form stem-loop DNA secondary structures that might stall DNA replication fork progression during replication stress. This could then cause increased instability in these regions which could lead to cancer development in human cells. Our findings suggest that CFSs and some specific large genes appear to play important roles in OPSCC. © 2016 Wiley Periodicals, Inc.


Subject(s)
Biomarkers, Tumor/genetics , Carcinoma, Squamous Cell/genetics , Chromosome Fragile Sites/genetics , Gene Rearrangement , Oropharyngeal Neoplasms/genetics , Papillomaviridae/genetics , Papillomavirus Infections/genetics , Virus Integration/genetics , Base Pairing , Base Sequence , Carcinoma, Squamous Cell/pathology , Carcinoma, Squamous Cell/virology , Chromosome Aberrations , Humans , Membrane Proteins/genetics , Oropharyngeal Neoplasms/pathology , Oropharyngeal Neoplasms/virology , Papillomavirus Infections/pathology , Papillomavirus Infections/virology , Prognosis , Receptors, LDL/genetics , Sequence Homology, Nucleic Acid , Tumor Suppressor Proteins
7.
Case Rep Otolaryngol ; 2016: 8481235, 2016.
Article in English | MEDLINE | ID: mdl-27418994

ABSTRACT

Background. Although alcohol and tobacco use are known risk factors for development of squamous cell carcinoma in the head and neck, human papillomavirus (HPV) has been increasingly associated with this group of cancers. We describe the case of a married couple who presented with HPV-positive oropharynx squamous cell carcinoma within two months of each other. Methods. Tumor biopsies were positive for p16 and high-risk HPV in both patients. Sanger sequencing showed a nearly identical HPV16 strain in both patients. Both patients received chemoradiation, and one patient also underwent transoral robotic tongue base resection with bilateral neck dissection. Results. Both patients showed no evidence of recurrent disease on follow-up PET imaging. Conclusions. New head and neck symptoms should be promptly evaluated in the partner of a patient with known HPV-positive oropharynx cancer. This case expands the limited current literature on concurrent presentation of HPV-positive oropharynx squamous cell carcinoma in couples.

8.
Cytogenet Genome Res ; 150(3-4): 185-193, 2016.
Article in English | MEDLINE | ID: mdl-28245440

ABSTRACT

Human papillomaviruses (HPV) are responsible for the development of almost all cervical cancers. HPV is also found in 85% of anal cancer and in 50% of penile, vulvar, and vaginal cancers, and they are increasingly found in a subset of head and neck cancers, i.e., oropharyngeal squamous cell carcinomas (OPSCC). The model for how HPV causes cancer is derived from several decades of study on cervical cancer, and it is just presumed that this model is not only completely valid for cervical cancer but for all other HPV-driven cancers as well. Next-generation sequencing (NGS) has now provided the necessary tools to characterize genomic alterations in cancer cells and can precisely determine the physical status of HPV in those cells as well. We discuss recent discoveries from different applications of NGS in both cervical cancer and OPSCCs, including whole-genome sequencing and mate-pair NGS. We also discuss what NGS studies have revealed about the different ways that HPV can be involved in cancer formation, specifically comparing cervical cancer and OPSCC.


Subject(s)
Alphapapillomavirus/pathogenicity , Carcinoma, Squamous Cell/virology , Oropharyngeal Neoplasms/virology , Uterine Cervical Neoplasms/virology , Carcinoma, Squamous Cell/genetics , Female , High-Throughput Nucleotide Sequencing , Humans , Oropharyngeal Neoplasms/genetics , Uterine Cervical Neoplasms/genetics
9.
Cytogenet Genome Res ; 150(3-4): 217-226, 2016.
Article in English | MEDLINE | ID: mdl-28142148

ABSTRACT

High-risk human papillomaviruses (HPVs) are known to be associated with different anogenital cancers including cervical, anal, penile, and vaginal cancers. They are also found to be responsible for the dramatic increases in oropharyngeal squamous cell carcinoma (OPSCC) observed in the United States and Europe. The model for how high-risk HPVs induce cancer formation comes from studies of cervical cancer which usually involves integration of the HPV into the human genome and subsequent changes due to induced chromosomal instability. Recent work, discussed here, however suggests that this model may not be completely correct. In addition, we summarize studies now done in OPSCC which demonstrate that the role of HPV in these cancers may be different from that in cervical cancer. Finally, we propose new models for how HPV may be involved in the formation of these 2 cancers.


Subject(s)
Alphapapillomavirus/pathogenicity , Carcinoma, Squamous Cell/virology , Chromosome Fragile Sites , Oropharyngeal Neoplasms/virology , Uterine Cervical Neoplasms/virology , Female , Genomic Instability , Humans , Models, Biological
10.
Viruses ; 7(8): 4507-28, 2015 Aug 07.
Article in English | MEDLINE | ID: mdl-26262638

ABSTRACT

DNA viruses are known to be associated with a variety of different cancers. Human papillomaviruses (HPV) are a family of viruses and several of its sub-types are classified as high-risk HPVs as they are found to be associated with the development of a number of different cancers. Almost all cervical cancers appear to be driven by HPV infection and HPV is also found in most cancers of the anus and at least half the cancers of the vulva, penis and vagina, and increasingly found in one sub-type of head and neck cancers namely oropharyngeal squamous cell carcinoma. Our understanding of HPVs role in cancer development comes from extensive studies done on cervical cancer and it has just been assumed that HPV plays an identical role in the development of all other cancers arising in the presence of HPV sequences, although this has not been proven. Most invasive cervical cancers have the HPV genome integrated into one or more sites within the human genome. One powerful tool to examine all the sites of HPV integration in a cancer but that also provides a comprehensive view of genomic alterations in that cancer is the use of next generation sequencing of mate-pair libraries produced from the DNA isolated. We will describe how this powerful technology can provide important information about the genomic organization within an individual cancer genome, and how this has demonstrated that HPVs role in oropharyngeal squamous cell carcinoma is distinct from that in cervical cancer. We will also describe why the sequencing of mate-pair libraries could be a powerful clinical tool for the management of patients with a DNA viral etiology and how this could quickly transform the care of these patients.


Subject(s)
DNA Virus Infections/complications , Neoplasms/pathology , Pathology, Molecular/methods , Sequence Analysis, DNA/methods , Virus Integration , Cell Transformation, Viral , Gene Order , Humans
11.
Otolaryngol Head Neck Surg ; 152(4): 752-8, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25724573

ABSTRACT

OBJECTIVE: Assess human papilloma virus (HPV) transcriptional activity in inverted Schneiderian papillomas (IPs). STUDY DESIGN: Case series with chart review. SETTING: Academic tertiary care center. SUBJECTS AND METHODS: Retrospective clinicopathologic review of 19 cases of IP in patients undergoing surgical excision from 1995 to 2013 at Mayo Clinic in Rochester, Minnesota. Surgical pathology archival material was histopathologically reviewed using hematoxylin and eosin-stained slides. Formalin-fixed, paraffin-embedded material from each case was evaluated for p16 expression using immunohistochemistry as well as HPV DNA and E6/E7 messenger RNA (mRNA) transcription using polymerase chain reaction (PCR) and in situ hybridization (via RNAscope technology), respectively. RESULTS: Eight patients were female (42%), with an average age of 53 years (range, 23-82 years). Three demonstrated malignancy, and 5 subsequently recurred. Average follow-up was 49 months (range, 0-200 months), and 1 patient died from squamous cell carcinoma arising from the IP. RNAscope detected HPV mRNA transcripts exclusively within IP in 100% of cases; however, in 11 patients (58%), less than 1% of cells exhibited transcriptional activity. Only 2 of 19 cases (11%) demonstrated mRNA activity in 50% or more cells. HPV DNA was detected in only 2 specimens by PCR. CONCLUSIONS: This study reveals wide prevalence but limited transcriptional activity of HPV in IP. No correlation between HPV transcriptional activity and progression, recurrence, or malignant transformation was identified. These data suggest that transcription of HPV may contribute to the pathogenesis of IP, but prospective data are needed to definitively demonstrate this connection. These results also suggest that RNAscope may be more sensitive than PCR in detecting HPV activity in IP.


Subject(s)
Nose Neoplasms/virology , Oncogene Proteins, Viral/genetics , Papilloma, Inverted/virology , Papillomaviridae/genetics , RNA, Messenger/metabolism , Transcriptional Activation , Adult , Aged , Aged, 80 and over , Cyclin-Dependent Kinase Inhibitor p16 , DNA Probes, HPV , DNA, Viral/analysis , DNA, Viral/genetics , Female , Humans , In Situ Hybridization , Male , Middle Aged , Nasal Mucosa/pathology , Nasal Mucosa/virology , Neoplasm Proteins/metabolism , Papillomaviridae/isolation & purification , Papillomavirus Infections/genetics , Retrospective Studies , Young Adult
12.
Exp Biol Med (Maywood) ; 240(3): 285-95, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25595185

ABSTRACT

WWOX is a gene that spans an extremely large chromosomal region. It is derived from within chromosomal band 16q23.2 which is a region with frequent deletions and other alterations in a variety of different cancers. This chromosomal band also contains the FRA16D common fragile site (CFS). CFSs are chromosomal regions found in all individuals which are highly unstable. WWOX has also been demonstrated to function as a tumor suppressor that is involved in the development of many cancers. Two other highly unstable CFSs, FRA3B (3p14.2) and FRA6E (6q26), also span extremely large genes, FHIT and PARK2, respectively, and these two genes are also found to be important tumor suppressors. There are a number of interesting similarities between these three large CFS genes. In spite of the fact that they are derived from some of the most unstable chromosomal regions in the genome, they are found to be highly evolutionarily conserved and the chromosomal region spanning the mouse homologs of both WWOX and FHIT are also CFSs in mice. Many of the other CFSs also span extremely large genes and many of these are very attractive tumor suppressor candidates. WWOX is therefore a member of a very interesting family of very large CFS genes.


Subject(s)
Carcinogenesis/genetics , Chromosome Fragile Sites/genetics , Neoplasms/genetics , Oxidoreductases/genetics , Tumor Suppressor Proteins/genetics , Animals , Chromosome Fragile Sites/physiology , Disease Models, Animal , Genomic Instability/genetics , Genomic Instability/physiology , Humans , Mice , Neoplasms/physiopathology , Oxidoreductases/physiology , Signal Transduction/genetics , Signal Transduction/physiology , Tumor Suppressor Proteins/physiology , WW Domain-Containing Oxidoreductase
13.
Int J Cancer ; 137(4): 776-83, 2015 Aug 15.
Article in English | MEDLINE | ID: mdl-25626421

ABSTRACT

Although the rates of cervical squamous cell carcinoma have been declining, the rates of cervical adenocarcinoma are increasing in some countries. Outcomes for advanced cervical adenocarcinoma remain poor. Precision mapping of genetic alterations in cervical adenocarcinoma may enable better selection of therapies and deliver improved outcomes when combined with new sequencing diagnostics. We present whole-exome sequencing results from 15 cervical adenocarcinomas and paired normal samples from Hong Kong Chinese women. These data revealed a heterogeneous mutation spectrum and identified several frequently altered genes including FAT1, ARID1A, ERBB2 and PIK3CA. Exome sequencing identified human papillomavirus (HPV) sequences in 13 tumors in which the HPV genome might have integrated into and hence disrupted the functions of certain exons, raising the possibility that HPV integration can alter pathways other than p53 and pRb. Together, these provisionary data suggest the potential for individualized therapies for cervical adenocarcinoma based on genomic information.


Subject(s)
Adenocarcinoma/genetics , High-Throughput Nucleotide Sequencing , Uterine Cervical Neoplasms/genetics , Adenocarcinoma/pathology , Adenocarcinoma/virology , Adult , Aged , Exome , Female , Hong Kong , Humans , Middle Aged , Mutation , Neoplasm Staging , Papillomaviridae/genetics , Papillomaviridae/pathogenicity , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/virology
14.
Aust N Z J Psychiatry ; 49(5): 471-80, 2015 May.
Article in English | MEDLINE | ID: mdl-25526944

ABSTRACT

OBJECTIVE: The over-representation of mental illness among homeless people across the globe is well documented. However, there is a dearth of Australian literature on the mental health needs of homeless individuals. Furthermore, longitudinal research examining the factors that contribute to better housing outcomes among this population is sparse. The aim of this research is to describe the mental illness profile of a sample of homeless men in an Australian urban centre (in Sydney) and examine the factors associated with better housing outcomes at 12-month follow-up. METHODS: A longitudinal survey was administered to 253 homeless men who were involved in the Michael Project: a 3-year initiative which combined existing accommodation support services with assertive case management and access to coordinated additional specialist allied health and support services. A total of 107 participants were followed up 12 months later. The survey examined the demographics of the sample and lifetime mental disorder diagnoses, and also included psychological screeners for current substance use and dependence, psychological distress, psychosis, and post-traumatic stress. RESULTS: Consistent with existing literature, the prevalence of mental illness was significantly greater amongst this sample than the general Australian population. However, mental illness presentation was not associated with housing situation at 12-month follow-up. Instead, type of support service at baseline was the best predictor of housing outcome, wherein participants who received short to medium-term accommodation and support were significantly more likely to be housed in stable, long-term housing at the 12-month follow-up than participants who received outreach or emergency accommodation support. CONCLUSIONS: This study provides evidence to support an innovative support model for homeless people in Australia and contributes to the limited Australian research on mental illness in this population.


Subject(s)
Housing , Ill-Housed Persons/psychology , Ill-Housed Persons/statistics & numerical data , Mental Disorders/diagnosis , Adult , Australia/epidemiology , Case Management , Female , Follow-Up Studies , Health Services Needs and Demand , Humans , Longitudinal Studies , Male , Middle Aged , Multivariate Analysis , Regression Analysis , Self Report
15.
Transl Oncol ; 7(6): 726-31, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25500082

ABSTRACT

Common fragile sites (CFSs) are large regions with profound genomic instability that often span extremely large genes a number of which have been found to be important tumor suppressors. RNA sequencing previously revealed that there was a group of six large CFS genes which frequently had decreased expression in oropharyngeal squamous cell carcinomas (OPSCCs) and real-time reverse transcriptase polymerase chain reaction experiments validated that these six large CFS genes (PARK2, DLG2, NBEA, CTNNA3, DMD, and FHIT) had decreased expression in most of the tumor samples. In this study, we investigated whether the decreased expression of these genes has any clinical significance in OPSCCs. We analyzed the six CFS large genes in 45 OPSCC patients and found that 27 (60%) of the OPSCC tumors had decreased expression of these six genes. When we correlated the expression of these six genes to each patient's clinical records, for 11 patients who had tumor recurrence, 10 of them had decreased expression of almost all 6 genes. When we divided the patients into two groups, one group with decreased expression of the six genes and the other group with either slight changes or increased expression of the six genes, we found that there is significant difference in the incidence of tumor recurrence between these two groups by Kaplan-Meier plot analysis (P < .05). Our results demonstrated that those OPSCC tumors with decreased expression of this select group of six large CFS genes were much more likely to be associated with tumor recurrence and these genes are potential prognostic markers for predicting tumor recurrence in OPSCC.

16.
Cell Mol Life Sci ; 71(23): 4601-15, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25300511

ABSTRACT

Common fragile sites (CFSs) are large chromosomal regions that are hot-spots for alterations especially within cancer cells. The three most frequently expressed CFS regions (FRA3B, FRA16D and FRA6E) contain genes that span extremely large genomic regions (FHIT, WWOX and PARK2, respectively), and these genes were found to function as important tumor suppressors. Many other CFS regions contain extremely large genes that are also targets of alterations in multiple cancers, but none have yet been demonstrated to function as tumor suppressors. The loss of expression of just FHIT or WWOX has been found to be associated with a worse overall clinical outcome. Studies in different cancers have revealed that some cancers have decreased expression of multiple large CFS genes. This loss of expression could have a profound phenotypic effect on these cells. In this review, we will summarize the known large common fragile site genes and discuss their potential relationship to cancer development.


Subject(s)
Chromosome Fragile Sites , Genomic Instability , Neoplasms/genetics , Animals , Genes, Tumor Suppressor , Humans , Neoplasms/pathology
17.
J Neurol Neurosurg Psychiatry ; 85(11): 1265-72, 2014 Nov.
Article in English | MEDLINE | ID: mdl-24604904

ABSTRACT

BACKGROUND: Inherited polyneuropathies often go undiagnosed. We investigated whole exome sequencing (WES) in utility to identify the genetic causes of diverse forms of inherited polyneuropathies without genetic diagnosis. METHODS: WES was applied to 24 cases from 15 kindreds. These kindreds had earlier unsuccessful candidate gene testing and five probands were initially thought to have acquired neuropathy. We assessed the efficacy of WES in screening 74 known neuropathy genes and 5195 reported pathogenic mutations for hereditary motor and sensory neuropathy, distal hereditary motor neuropathy, hereditary sensory and autonomic neuropathy, complicated hereditary spastic paraplegia, and select hereditary metabolic neuropathies. RESULTS: Pathogenic mutations were identified in five kindreds: (1) ATL1-p.Val253Ile; (2) LITAF-p.Gly112Ser; (3) MFN2-p.Arg94Gln; (4) GARS-p.Ile334Phe; and (5) BSCL2-p.Ser 90Leu. Complexities in establishing inheritance, difficulties in selecting candidate genes and high cost of gene testing all hindered earlier gene discoveries. WES expanded the phenotypic spectrum of the identified known mutations. Possible causal mutations in known genes (SPTLC1, DCTN1, REEP1) were identified in three kindreds. In the remaining seven kindreds, multiple rare or novel variants were identified in novel genes not previously linked with neuropathy. Our results demonstrate an average sequencing depth of 140×, >98% coverage and >10× sequencing depth for 93% (range 89%-96%) of the diverse neuropathy genes and their known mutations. CONCLUSIONS: Diverse inherited neuropathy patients without genetic discovery by candidate gene testing have a favourable probability of receiving a genetic diagnosis by WES. Frequently, atypical phenotypes account for earlier failed candidate approaches, and WES is demonstrated to expand the clinical spectrum of known pathogenic mutations.


Subject(s)
Exome/genetics , Polyneuropathies/genetics , Adolescent , Adult , Algorithms , Child , Child, Preschool , Female , Genes/genetics , Genetic Predisposition to Disease/genetics , Humans , Infant , Male , Middle Aged , Mutation/genetics , Pedigree , Polyneuropathies/diagnosis , Sequence Analysis, DNA/methods , Young Adult
18.
Genes Chromosomes Cancer ; 53(5): 392-401, 2014 May.
Article in English | MEDLINE | ID: mdl-24481768

ABSTRACT

The common fragile sites (CFSs) are large regions of profound genomic instability found in all individuals. The frequent deletions and other alterations in these regions in multiple cancers has led to the discovery of a number of extremely large genes contained within these regions and several of the large CFS genes have already been demonstrated to function as tumor suppressors involved in the formation of many different cancers. To study the large CFS genes in oropharyngeal squamous cell carcinoma (OPSCC), we did RNA seq analysis from 11 head and neck cancer patients. This revealed that there are six large CFS genes which consistently had decreased expression in the tumor samples compared to their matched normal tissues. These six genes are PARK2, DLG2, NBEA, CTNNA3, DMD, and FHIT. PARK2 and FHIT are located within the two most frequently expressed CFSs and both have been demonstrated to function as tumor suppressors, while the other large genes are found to have frequent alterations in multiple cancers. Validation experiments using real time PCR indicated that over 60% of OPSCC tumors showed decreased expression for all six genes. Both HPV-positive and HPV-negative OPSCCs had similar proportions with loss of expression of these genes. Our results suggest that this selected group of large genes might serve as potential tumor suppressors involved in the development of OPSCCs. Further studies are needed to investigate whether the decreased expression observed is due to genomic instability within the CFS regions or the selection for alterations of specific large CFS genes.


Subject(s)
Carcinoma, Squamous Cell/metabolism , Chromosome Fragile Sites/genetics , Oropharynx/metabolism , Pharyngeal Neoplasms/metabolism , Acid Anhydride Hydrolases/genetics , Acid Anhydride Hydrolases/metabolism , Adult , Aged , Aged, 80 and over , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/virology , Carrier Proteins/genetics , Carrier Proteins/metabolism , Dystrophin/genetics , Dystrophin/metabolism , Female , Guanylate Kinases/genetics , Guanylate Kinases/metabolism , Humans , Male , Middle Aged , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Oropharynx/pathology , Papillomaviridae/isolation & purification , Pharyngeal Neoplasms/genetics , Pharyngeal Neoplasms/virology , Sequence Analysis, RNA , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , alpha Catenin/genetics , alpha Catenin/metabolism
19.
J Clin Virol ; 59(3): 195-200, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24440282

ABSTRACT

BACKGROUND: Human papillomavirus (HPV) is now recognized to be very important in the pathogenesis of oropharyngeal squamous cell carcinoma (OPSCC). It is not clear yet whether the physical status of HPV in OPSCC is similar to what is found in cervical cancer. STUDY DESIGN: We performed genome-wide mate pair next generation sequencing from 20 OPSCCs patients, thirteen of which were positive for HPV16 to determine the HPV physical status and its relationship to HPV oncogene E6 and E7 expression. RESULTS: This high throughput approach detected HPV integration events and also determined the bridged HPV coverage in each sample. Two of the HPV16-positive OPSCCs had HPV integration and one of the HPV16-negative OPSCCs had an HPV26 integration. We mapped the site of integration in the HPV genome in all integration events and the integrations were located at E1, E5, E6 and L2 region respectively. One HPV positive OPSCC had two integration events but also had a very high bridged HPV coverage, while the other two just had HPV integrated into the human genome. CONCLUSION: Our results are thus different from what is routinely observed in cervical cancer where HPV is almost always integrated into the human genome with loss of episomal HPV sequences. Thus more investigation should be carried out to study how episomal HPV alone can contribute to the development of most OPSCCs.


Subject(s)
Carcinoma, Squamous Cell , Oropharyngeal Neoplasms , Papillomavirus Infections , Sequence Analysis, DNA/methods , Virus Integration/genetics , Adult , Aged , Aged, 80 and over , Alphapapillomavirus/genetics , Base Sequence , Carcinoma, Squamous Cell/chemistry , Carcinoma, Squamous Cell/epidemiology , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/virology , DNA, Viral/genetics , Female , Humans , Male , Middle Aged , Molecular Sequence Data , Oropharyngeal Neoplasms/chemistry , Oropharyngeal Neoplasms/epidemiology , Oropharyngeal Neoplasms/genetics , Oropharyngeal Neoplasms/virology , Papillomavirus Infections/epidemiology , Papillomavirus Infections/genetics , Papillomavirus Infections/virology , Uterine Cervical Neoplasms
20.
Am J Hematol ; 88(9): 741-6, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23733509

ABSTRACT

We used high resolution mate-pair sequencing (HRMPS) in 15 patients with primary myelofibrosis (PMF): eight with normal karyotype and seven with PMF-characteristic cytogenetic abnormalities, including der(6)t(1;6)(q21-23;p21.3) (n = 4), der(7)t(1;7)(q10;p10) (n = 2), del(20)(q11.2q13.3) (n = 3), and complex karyotype (n = 1). We describe seven novel deletions/translocations in five patients (including two with normal karyotype) whose breakpoints were PCR-validated and involved MACROD2, CACNA2D4, TET2, SGMS2, LRBA, SH3D19, INTS3, FOP (CHTOP), SCLT1, and PHF17. Deletions with breakpoints involving MACROD2 (lysine deacetylase; 20p12.1) were recurrent and found in two of the 15 study patients. A novel fusion transcript was found in one of the study patients (INTS3-CHTOP), and also in an additional non-study patient with PMF. In two patients with der(6)t(1;6)(q21-23;p21.3), we were able to map the precise translocation breakpoints, which involved KCNN3 and GUSBP2 in one case and HYDIN2 in another. This study demonstrates the utility of HRMPS in uncovering submicroscopic deletions/translocations/fusions, and precise mapping of breakpoints in those with overt cytogenetic abnormalities. The overall results confirm the genetic heterogeneity of PMF, given the low frequency of recurrent specific abnormalities, identified by this screening strategy. Currently, we are pursuing the pathogenetic relevance of some of the aforementioned findings.


Subject(s)
Base Sequence , Oncogene Proteins, Fusion/genetics , Primary Myelofibrosis/genetics , Sequence Analysis, DNA/methods , Sequence Deletion , Translocation, Genetic , Aged , Chromosome Breakpoints , Chromosome Mapping , Chromosomes, Human, Pair 1 , Chromosomes, Human, Pair 6 , Chromosomes, Human, Pair 7 , Female , Genetic Heterogeneity , Humans , Karyotyping , Male , Middle Aged , Molecular Sequence Data , Primary Myelofibrosis/pathology
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