Highlights of Whole Genome Expression Array Profiling Esophageal adenocarcinoma and Barrett's oesophagus have different mucosal defence genes
Received: 19-Dec-2022 / Manuscript No. jmir-22-84612 / Editor assigned: 22-Dec-2022 / PreQC No. jmir-22-84612 / Reviewed: 05-Jan-2023 / QC No. jmir-22-84612 / Revised: 09-Jan-2023 / Manuscript No. jmir-22-84612 / Published Date: 16-Jan-2023 DOI: 10.4172/jmir.1000168
Abstract
Esophageal adenocarcinoma (EAC) has grown significantly in prevalence while having extremely low survival rates in Western nations. Barrett’s oesophagus (BE), which is thought to form as a outcome of recurrent gastro-esophageal reflux, is one of the major risk factors for the development of this cancer. In this study, we compared genome-wide expression profiles on total RNA isolated from esophageal biopsy tissues from individuals with EAC, BE (in the absence of EAC), and those with normal squamous epithelium. We used Illumina whole-genome Beadarrays for this. To analyse significant gene and ontology discrepancies between these three tissue states, we integrated these data with publicly available raw data from three related investigations. The findings are consistent with the hypothesis that BE is a tissue with improved glycoprotein synthesis machinery (DPP4, ATP2A3, and AGR2) created to provide robust mucosal defences to fend off gastro-esophageal reflux. EAC shows indications of decreased expression of genes linked to mucosal (MUC6, CA2, TFF1) and xenobiotic (AKR1C2, AKR1B10) defences, in addition to the accelerated extracellular matrix remodelling (collagens, IGFBP7, PLAU) impacts expected in an aggressive form of cancer. Keratin, mucin, annexin, and trefoil factor gene groups are the most commonly represented differentially expressed gene families when our data are compared to earlier whole-genome expression profiling research. At least three prior profiling studies have included at least one of the eleven genes we discovered here. We employed a support vector machine left one out cross validation (LOOCV) analysis to separate squamous epithelium, BE, and EAC within the two biggest cohorts. Although this approach was effective at differentiating between squamous epithelium and BE, it highlights the necessity for more thorough research on the differences in BE and EAC’s profile.
Introduction
Esophageal adenocarcinoma (EAC) incidence has climbed significantly over the past few decades in western cultures, despite new data suggesting that the rate may have stabilised. As a outcome, this cancer now poses a considerable health burden. According to epidemiological research, variables like smoking, obesity, and gastroesophageal reflux are to blame for the rising prevalence [1].
It is unclear how biology contributes to the development of EAC. What is currently understood describes a multistep process that starts when gastro-esophageal reflux repeatedly damages the healthy squamous esophageal epithelium. A small percentage of people have intestinal metaplasia, which outcomes in Barrett’s oesophagus (BE), a columnar epithelial tissue, replacing the injured epithelium. According to estimates, 0.5-2.0% of BE patients experience a malignant progression that leads to the development of EAC each year. Histologically, the columnar phenotype exhibits increasing dysplasia as a outcome of this change. Although the general histopathological progression from BE through high grade dysplasia to EAC is well understood, the underlying biological mechanisms are still poorly understood, though they do suggest significant variation in the expression of particular gene products and the stage of the disease at which they are significant [2-5]. Additionally, even though having BE increases the risk of developing EAC significantly. Groups of genes have been jointly linked to the onset of several prevalent cancer types thanks to the use of genome-wide gene expression arrays and bioinformatics. One method of determining the biological mechanisms at play and identifying prospective therapeutic targets for the creation of innovative EAC treatments is to compare gene expression profiles between the significant histological stages in the progression towards EAC. This has been attempted by numerous study groups, but it has proven challenging due to the relatively low gene list overlap among the different profiling investigations. Although the investigations used a variety of experimental approaches, they mainly concentrated on separating squamous mucosa from BE and from EAC—the recognised histologic tissue stages. Our hypothesis was that a strong core gene list differentiating the three tissue stages under investigation would be more likely to be generated by using a uniform method to the processing of data from various research. Here, we examine gene expression data from our sample of patients drawn from a variety of Australian hospitals and contrast it with many other datasets of a similar nature that have been made available to the general public. The purpose of this work was to find a consistent collection of ontology-based gene clusters that differentiate across the important histological tissue types (squamous, BE, and EAC), as well as to highlight certain specific gene differences, using the combined expression profiling data [6-8].
Patients and methods
Sample collection in patients with cancer [9]
The Niigata University Medical and Dental Hospital’s and Tokyo University of Pharmacy and Life Sciences’ ethics committees gave their approval for this study (approval number 2019-0449). (approval no. 19–25 and 20–3). Before enrolment, informed consent was gathered from each of the 20 patients. Due to pre-existing OM, two individuals were disqualified, and one patient denied the post-index sample. The remaining 18 participants were cancer patients, aged 21–79, with leukaemia (n = 12) or head and neck carcinoma (n = 6), who were hospitalised for obtaining CT or RT at the Niigata University Medical and Dental Hospital between June 2020 and October 2021.
We used the Saliva Collection Aid (SalivaBio, California, USA), also known as the drooling method, or Salimetrics Oral Swab (Salimetrics, California, USA), also known as the swab method, to collect less than 0.1 mL of saliva at various points. Since the patients who were recruited would likely suffer OM, saliva was collected using the non-stimulated approach. The manufacturer’s instructions for sampling included that no food should be consumed or teeth should be brushed within one hour of the test, that lip makeup should be removed 15 minutes beforehand, and that the patient should relax for five minutes before sampling. Saliva samples were taken as needed: 1) within 14 days of the start of the TR, 2) within 3 days of an OM event, 3) if and when the OM event improved or grew worse, and 4) within 7 days of the end of the TR [10]. Two samples were obtained in the morning, and 50 samples were collected in the afternoon, all during ordinary clinical practise. Samples were kept at -80°C right away. When a patient did not experience an OM event, sampling was skipped. The first day of TR was chosen as the index date. An oral moisture-checking equipment (Mucus®; Life Co., Ltd., Saitama, Japan) was used at each sampling location in accordance with the manufacturer’s instructions by a team of oral health care professionals, including dentists, dental hygienists, nurses, and pharmacists. Each subject’s oral mucosal dryness was assessed three times, and the median value was recorded. For measuring oral mucosal dryness, no particular unit of measurement was utilised; instead, the device’s numerical value was used.
To determine the OM grade at each sample collection site using CTCAE version 5.0, the oral care support team noted the plaque control record (PCR), bleeding on probing (BOP), pocket depth, and tooth mobility before to TR. “Grade 0” was used to describe the absence of OM. The day before TR, the day of an OM event, and the day after TR were used to collect haematological and biochemical laboratory data.
Sample collection in HV
Volunteers who had oral bleeding, stomatitis, or were on medication were not allowed to participate. 33 HV in all, ranging in age from 18 to 65 (17 men and 16 women), were recruited. Mucus® was used to measure oral mucosal dryness while adhering to the techniques previously mentioned. In order to replicate the manner used to acquire more than 90% of the saliva samples from cancer patients, non-stimulated saliva from HV was collected using the drooling technique. Up until the measurement of inflammatory mediators, the saliva was maintained at -80°C. No volunteer had a history of coffee consumption, smoking, or dental treatment within one hour of sample collection. Seven samples were taken in the morning, and 26 samples were taken in the afternoon.
Result
Between August 17, 2009, and July 19, 2010, fifty patients were enlisted and monitored throughout their radiation therapy. 500 of the 520 clinical examinations conducted during this time were conducted by the first author (A.M.G.). 33 people finished the research, while 7 dropped out from tiredness. Ten participants (n = 7) had either not begun or ceased receiving cancer therapy. Others were not included because the recommended radiation dose (n = 3) was less than 54 Gray. One participant received radiation twice daily for four weeks, while the majority of participants (n = 7) and participants (n = 25) received radiation once daily for six or seven weeks.
Clinical Signs and Symptoms of Oral Mucositis
In the first week of cancer treatment, oral mucositis NCI-CTCAE scores of “1” were noted; scores of “3” began to appear at the end of the second week. By the end of the cancer treatment period, the prevalence of the score “3” was close to 50%. This may be an underestimate since some individuals were unable or unwilling to open their mouths for a full clinical assessment, making intra-oral scoring impossible. About 50% of the individuals still showed a “2” NCI-CTCAE v.3 score at the post-treatment evaluation. Participants at various time points had significantly different OMAS-Ulceration and -Erythema scores as well as TOTAL- VAS-Ulceration and -Erythema scores. However, by the conclusion of the 6-7 week period of fractionated radiation, the highest scores were routinely recorded. The average outcomes at the posttreatment examination were roughly one-third of the highest values recorded during radiation. The PROMS-aggregated scores gradually increased throughout the cancer treatment period, reaching a value of 60 on the visual analogue scale towards the end of the course of treatment. As a outcome, patterns of rising oral mucositis scores with peaks towards the conclusion of cancer treatment were evident in all assessments. When the post-treatment examination was done four to six weeks after the completion of cancer treatment, oral mucositis symptoms and signs were still present.
Discussion
When under acute psychological stress, oncology patients undergoing cancer treatment require supportive care. In order for the patient to tolerate and ultimately benefit from the cancer therapy, it is crucial to prevent and manage oral mucositis as a side effect of the treatment. The optimum method for determining the severity of oral mucositis, rather than depending solely on one or the other, appears to be the combination of clinician-observed oral mucositis symptoms and patient-reported experiences of those symptoms. According to the outcomes of the current investigation, the PROMS scale can supplement standard clinical examinations of oral mucositis. Additionally, in cases where patients are unable to open their mouths, suffer a thorough clinical oral examination, or are otherwise unable to travel to the treatment facility, the PROMS can also take the place of the usual clinician-determined assessments of oral mucositis. While data based on PROMS assessment may nearly always be collected, there are a few situations where full clinical examinations of oral mucositis may be impossible. On a patient-by-patient basis, the PROMS score may be utilised in several circumstances to fill in for missing clinical data. If necessary, the PROMS questionnaires could be finished online using telecommunications technology (such as the Internet) in place of a clinical oral mucositis assessment during the course of cancer treatment.
It should be made clear that the PROMS was created with the aim of illuminating the potential efficacy of any therapeutic measures against oral mucositis rather than serving as a gauge of quality of life or addressing psychological duress. Only a few questions are asked to make the system more user-friendly, and these are focused on routine daily activities that are objectively recognised as radiation side effects. Since the patient will have to work harder to complete the questionnaire, adding more questions is not always a good idea. The focus of future research will be on any questions that may be redundant. Additionally, integrating inquiries on the frequency of burning feelings and the likelihood of bleeding would be unreliable due to the need for good cognitive function the patients’ extraordinary emotional circumstances.
In general, participants seemed to grasp the items on the PROMS questionnaire quite fast and with little difficulty. Additionally, most people thought it was quick and simple to complete the questionnaire and didn’t feel it was a hardship when they were receiving cancer treatments. In the early stages of cancer treatment, patients should be made aware that the PROMS data may end up being the only way their intraoral oral mucositis status can be evaluated at later stages of the cancer treatment period. This is especially important if the PROMS scale is implemented in routine care or as an outcome in a clinical trial.
Over all the time periods, including the crucial sixth and seventh weeks of cancer therapy, when oral mucositis is at its worst, there was a reasonably strong association between the PROMS data and the clinician-based scoring methods. The severity of the ulceration did not adequately reflect the patient burdens endured during the initiation and progression of oral mucositis. Yet, rather than what would be less significant clinical assessments of lesion appearance and size, shouldn’t the patient burden direct modifications in cancer therapy (varying from reduction in treatment intensity to complete discontinuation of treatment)? The optimum endpoint or outcome metric for making decisions regarding further treatment of the condition, in this case oral mucositis, is the patient burden, much as it is with management of other chronic conditions characterised by pain, including “chronic pain” itself. As a outcome, determining the extent of ulceration is the most crucial—and in some cases, the only—measure of success. However, while understanding a patient’s behaviour during cancer treatment and the relative level of stress they are experiencing during treatment is important, it seems much more crucial so that the right actions can be taken. In contrast to a patient with greater ulcerations but few symptoms, a patient with “small” patches of ulceration but extreme levels of discomfort may not need intervention. The size and/ or extent of the ulcers simply cannot capture this, especially given that the pain associated with this illness is thought to be complicated and possibly neuropathological in origin.
Conclusion
The current research shows that the PROMS scale and other regularly used instruments for evaluating oral mucositis in patients with head and neck cancer have good correlations with assessments of oral mucositis experience. Therefore, patient-based experiences of oral mucositis as described by the PROMS scale may be a useful tool to supplement clinical assessment of oral mucositis or to serve as a substitute assessment in circumstances where patients are unable to tolerate oral examinations.
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Citation: Nacarow DJ (2023) Highlights of Whole Genome Expression Array Profiling Esophageal adenocarcinoma and Barrett’s oesophagus have different Mucosal Defense Genes. J Mucosal Immunol Res 7: 168. DOI: 10.4172/jmir.1000168
Copyright: © 2023 Nacarow DJ. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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