Tagged: Biomarkers

Identifying Biomarkers for Predicting Paclitaxel Response

March 28, 2024

In this research perspective, researchers discuss causal and correlative approaches to identify potential biomarkers for predicting paclitaxel response.

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Cancer therapy has come a long way from its one-size-fits-all beginning to the awakening era of personalized medicine. This change has been largely driven by the discovery of biomarkers. Biomarkers can help refine patient selection for specific therapies. A blend of causal and correlative approaches is needed to elucidate the full potential of biomarkers in cancer research. This fusion of methodologies allows for a comprehensive exploration of biomarker efficacy, leading to more accurate predictions of drug response.

In a new paper, researchers Alberto Moscona-Nissan, Karl J. Habashy, Victor A. Arrieta, Adam M. Sonabend, and Crismita Dmello from the Universidad Panamericana School of Medicine, Northwestern University and Universidad Nacional Autónoma de México discuss causal and correlative approaches to identify potential biomarkers for predicting response to paclitaxel — a commonly used chemotherapeutic agent. On February 8, 2024, their research perspective was published in Oncotarget’s Volume 15, entitled, “Combining causal and correlative approaches to discover biomarkers of response to paclitaxel.”

“[…] studying the combination of non-overlapping biomarkers’ expression, in addition to clinical and sociodemographic data could generate predictive models for paclitaxel susceptibility.”

Combining Causal and Correlative Approaches

Paclitaxel is a mainstay of treatment for various cancers, including breast, pancreatic, ovarian, and non-small cell lung carcinomas. However, the benefit derived from paclitaxel treatment varies across patients, and a significant proportion does not receive therapeutic benefit and experiences unnecessary toxicity. The variability in response to paclitaxel underscores the need for predictive biomarkers. Predictive biomarkers of response to paclitaxel can lead to improved treatment efficacy, less unnecessary toxicity, and potentially better health outcomes.

In a recent study, researchers used a whole-genome CRISPR/Cas9 knockout to identify genes that influence paclitaxel susceptibility in gliomas. They identified 51 genes that have implications in pathways such as NFkB, toll-like receptor, and MAPK signaling, transcriptional misregulation, and apoptosis. The team also identified the signal sequence receptor 3 (SSR3) gene as a predictive biomarker for paclitaxel susceptibility.

The SSR3 gene encodes the gamma subunit of the signal sequence receptor (SSR) complex, a glycosylated membrane receptor located at the endoplasmic reticulum (ER). This complex is involved in protein translocation across the ER membrane. In the study, it was found that higher SSR3 expression correlated with increased paclitaxel susceptibility in cancer cell lines. SSR3 knockout cells showed decreased susceptibility to paclitaxel, while cells overexpressing SSR3 had increased susceptibility.

The study also revealed a link between SSR3 and the unfolded protein response (UPR) pathway, which reduces the amount of unfolded proteins in the cell under stressful conditions. A positive correlation was found between SSR3 expression and IRE1a levels in glioma PDX cells. IRE1a is a serine/threonine kinase that is involved in the UPR pathway and has been implicated in various disorders.

Conclusions & Future Directions

A significant challenge in the treatment of glioblastoma is the blood-brain barrier which limits the efficacy of paclitaxel. However, innovative strategies like convection-enhanced delivery, biodegradable wafers, peptide-drug conjugates, and low-intensity pulsed ultrasound administered with microbubbles are being developed to overcome this barrier.

The researchers also wrote in their research perspective that, after identifying a potential predictive biomarker in a training cohort of patients, it is vital to validate the finding in an independent cohort. The correlation between patients’ overall survival and SSR3 expression is currently being studied in a phase 2 trial at Northwestern University. Based on the outcomes of these validations, the predictive models can be further refined by incorporating other non-overlapping histologic and molecular biomarkers along with patient demographics. The discovery of predictive biomarkers for paclitaxel response, such as SSR3, promises to significantly impact cancer treatment.

“Precision and personalized medicine can lead to a transition from a stochastic treatment response into predictable scenarios. Further identification of predictive biomarkers, validation, and study of combinations as predictive models is critical to generate a greater impact that can be translated to the bedside of patients.”

Click here to read the full research paper in Oncotarget.

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Biomarkers May Predict Neoadjuvant Chemosensitivity in Bladder Cancer

November 15, 2022

In a new study, researchers aimed to identify and validate predictive biomarkers of response to neoadjuvant chemotherapy (NAC) in patients with muscle-invasive bladder cancer (MIBC).

Biomarkers May Predict Neoadjuvant Chemosensitivity in Bladder Cancer

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Neoadjuvant chemotherapy (NAC) is a type of cancer treatment involving the administration of chemotherapy drugs before surgery. The goal of NAC is to shrink the tumor(s) in order to make it/them easier to remove during surgery and to decrease the chance of cancer recurrence after treatment. NAC is typically well tolerated by patients and has been shown to improve outcomes in patients with bladder cancer.

Predictive biomarkers are being increasingly used in oncology to identify patients who are likely to respond to chemotherapy. In the past, the decision to administer chemotherapy was based on tumor type and stage. However, it is now understood that there is considerable heterogeneity within these groups, and that not all patients will respond to the same treatment. Predictive biomarkers can help to overcome this challenge by identifying those patients who are most likely to benefit from chemotherapy.

There are a number of different types of predictive biomarkers, which can be divided into two broad categories: tumor biomarkers and host biomarkers. Tumor biomarkers are usually specific to the tumor type and can include markers of cell proliferation and DNA repair. Host biomarkers are usually found in the blood or other bodily fluids and can include markers of inflammation, immune function and metabolism. The use of predictive biomarkers has the potential to improve the efficacy of chemotherapy and reduce toxicity by avoiding its use in patients who are unlikely to benefit.

The Study

In a new study, researchers Neal Murphy, Andrew J. Shih, Paras Shah, Oksana Yaskiv, Houman Khalili, Anthony Liew, Annette T. Lee, and Xin-Hua Zhu from Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health Cancer Institute, Feinstein Institutes for Medical Research, and Mayo Clinic aimed to develop and validate a predictive biomarker panel for response to NAC in patients with muscle-invasive bladder cancer (MIBC). Their research paper was published on November 2, 2022, in Oncotarget’s Volume 13, entitled, “Predictive molecular biomarkers for determining neoadjuvant chemosensitivity in muscle invasive bladder cancer.”

“The NAC non-responders suffer from unnecessary adverse effects and a delay in time to cystectomy leading to worse overall survival [9, 10]. Subsequently, there remains a critical need to understand the molecular biology behind NAC responsiveness, in order to better tailor individual NAC therapy.”

The purpose of this research was to “develop a molecular signature that can identify MIBC NAC responders (R) and non-responders (NR) using a cohort of known NAC response phenotypes, and better understand differences in molecular pathways and subtype classifications between NAC R and NR.” Researchers identified a total of 26 patients with known NAC response for inclusion in this study. These patients were assigned at random to either the discovery or validation cohort. The discovery cohort consisted of seven NAC responders and 11 non-responders. The validation cohort consisted of three responders and five non-responders.

Transurethral resection of bladder tumor (TURBT) specimens from the Northwell Health pathology department were received as formalin-fixed, paraffin-embedded (FFPE) tissue blocks. Pathologic response was determined at the time of cystectomy. Messenger RNA (mRNA) and microRNA (miRNA) from the FFPE blocks were sequenced using RNAseq and qPCR, respectively.

“To our knowledge, our study is the first to use combined differential mRNA and miRNA expression in MIBC to identify a NAC response signature.”

The Results

“We report significant gene sets associated with NAC response phenotype, as well as three multigene and miRNA signatures generated by CCA that can be used to potentially classify NAC response.”

In the discovery cohort, the researchers found that 2309 genes were differentially expressed between the NAC responders and non-responders. In the validation cohort, 602 genes and 13 miRNA were differentially expressed. Canonical correlation (CC) analysis found that three CCs (CC13: nucleoside triphosphate metabolic process; CC16: cell cycle and cellular response to DNA damage; and CC17: DNA packaging complex) were differentiated in the discovery and validation datasets. As far as MIBC subtypes, the MD Anderson p53-like subtype, CIT MC4 subtype and Consensus Class stroma-rich subtype had the strongest correlation with a non-responder phenotype. There were no subtypes that had strong correlations with the responder phenotype.

“In conclusion, our results identify molecular signatures that can be used to differentiate MIBC NAC responders versus non-responders. We have presented the salient molecular pathways and relevant genes, including mitochondrial response gene expression (MRPS12, MRPS34, MRPS28, MRPS14, and MRPS2), DNA replication initiation, and DNA unwinding and DNA damage (MCM2-3, MCM5-6 and XAP , ELK4, and FOXA3) that can be further analyzed to better understand NAC response. The above mentioned genes derived from their respective three pathways may be selected as part of a NAC response biomarker panel. In addition, we have highlighted the utility of molecular subtyping in relation to NAC response. If validated in a larger cohort, these findings may help deliver chemotherapy to those patients most likely to respond.”

Conclusion

Neoadjuvant chemotherapy is a promising treatment option for muscle-invasive bladder cancer patients, however, there is a class of patients who do not respond to chemotherapy. The results of this study implicate several different types of biomarkers that may be associated with chemosensitivity in MIBC patients. Further research is needed to validate these findings. Ultimately, if validated, these biomarkers could help to spare non-responders from side effects associated with ineffective and unnecessary chemotherapy.

“Our results identify molecular signatures that can be used to differentiate MIBC NAC R versus NR, salient molecular pathway differences, and highlight the utility of molecular subtyping in relation to NAC response.”

Click here to read the full research paper published by Oncotarget.

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Oncotarget is an open-access journal that publishes primarily oncology-focused research papers in a continuous publishing format. These papers are available at no cost to readers on Oncotarget.com. Open-access journals have the power to benefit humanity from the inside out by rapidly disseminating information that may be freely shared with researchers, colleagues, family, and friends around the world.

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Protein-Based Risk Model Predicts Esophageal Cancer Recurrence

September 23, 2022

Researchers developed a multi-protein expression-based risk model to predict recurrence-free survival for ESCC patients.

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The Trending With Impact series highlights Oncotarget publications attracting higher visibility among readers around the world online, in the news, and on social media—beyond normal readership levels. Look for future science news about the latest trending publications here, and at Oncotarget.com.

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Esophageal cancer is the sixth most common cause of death from cancer worldwide. The two main types of esophageal cancer are adenocarcinoma and esophageal squamous cell carcinoma (ESCC). ESCC arises from the cells lining the esophagus, and it is most common in areas of the world where tobacco use and alcohol consumption are high.

“Biomarkers to predict the risk of disease recurrence in Esophageal squamous cell carcinoma (ESCC) patients are urgently needed to improve treatment.”

Researchers Raghibul Hasan, Gunjan Srivastava, Akram Alyass, Rinu Sharma, Anoop Saraya, Tushar K. Chattopadhyay, Siddartha DattaGupta, Paul G. Walfish, Shyam S. Chauhan, and Ranju Ralhan from All India Institute of Medical Sciences, Mount Sinai Hospital Toronto, McMaster University, Guru Gobind Singh Indraprastha University, and the University of Toronto conducted a new study on the protein expression-based risk model they developed to predict recurrence-free survival for ESCC patients. On September 14, 2022, their research paper was published in Oncotarget’s Volume 13, and entitled, “Prediction of recurrence free survival for esophageal cancer patients using a protein signature based risk model.”

The Study

“Our study is important because: (i) it is based on changes in expression levels of the biomarker proteins in different subcellular compartments and is not limited to alterations in the overall protein expression levels; (ii) investigates the comprehensive clinical relevance of subcellular alterations in expression of multiple key components of Wnt pathway in the same ESCC patients’ cohort; (iii) correlates these findings with disease outcome and (iv) develops a Biomarker risk score for defining the risk of recurrence of ESCCs.”

Figure 1: Immunohistochemical analysis of Wnt protein in esophageal tissues.

The researchers aimed to develop and validate a panel of biomarkers with the potential to predict tumor recurrence in patients with ESCC, as well as to generate a risk model for clinical decision-making. This study enrolled 80 ESCC cases, 61 esophageal dysplastic tissues and 47 normal tissues. A multi-protein signature was generated from microarray data using the Cox proportional hazard model which was then internally validated on an independent set of samples by immunohistochemistry. The researchers demonstrated that a panel of four biomarkers (cytoplasmic β-catenin, nuclear c-Myc, nuclear DVL and membrane α-catenin) constituted the prognostic molecular signature for ESCC patients. They found that this protein signature could predict disease recurrence in patients with ESCC.

“Our panel of biomarkers predicted disease recurrence more effectively as compared to individual biomarkers analyzed in this study and demonstrated the strong predictive power of this panel of biomarkers for ESCC patients.”

Conclusion

The research team found that a panel of four biomarkers could predict disease recurrence in patients with ESCC. Furthermore, they showed that this protein signature could be used to stratify patients into high- and low-risk groups. This study provides valuable insights into the role of these proteins in the development and progression of esophageal cancer. The development of this risk model may help to tailor treatment and follow-up strategies for patients with ESCC.

“In conclusion, integrated analysis of expression of the panel of 4 proteins in ESCC patients has allowed us to validate the robustness of our biomarker panel in stratification of patients at high or low risk of disease recurrence. This risk classifier has the potential to identify the high risk patients for more rigorous personalized treatment and the low risk patients may be spared from the harmful side effects of toxic therapy as well reduce the burden on health care providers. The findings of our study set the foundations for external validation of the prognostic signature as a step forward in translation of this panel of protein markers for ESCC patients and establish their clinical relevance for larger worldwide application in future studies.”

Click here to read the full research paper published by Oncotarget.

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How Heartburn Can Turn Into Esophageal Cancer, and a Possible Biomarker

July 15, 2022

In a recent Oncotarget paper, researchers investigated telomere shortening in patients with Barrett’s esophagus as a potential biomarker of high risk for esophageal cancer.

The Trending With Impact series highlights Oncotarget publications attracting higher visibility among readers around the world online, in the news, and on social media—beyond normal readership levels. Look for future science news about the latest trending publications here, and at Oncotarget.com.

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Smokers are significantly more likely than nonsmokers to have acid reflux. In many Western countries, a popular diet—known for its convenience, availability and, frankly, its lack of nutritional value—is also known to cause acid reflux. Some of the affordable foods and beverages easily accessible to Western consumers include fried food, fast foods, pizza, potato chips (and other processed snacks), high-fat meats (bacon, sausage), cheese, alcohol, soda, energy drinks, and etcetera. Unfortunately, this indulgent type of diet is accompanied by consequences beyond oily skin and an expanding waistband.

Barrett’s Esophagus

Chronic acid reflux can lead to gastroesophageal reflux disease. Gastroesophageal reflux disease can lead to Barrett’s esophagus (BE). BE is a premalignant condition in which the lining of the esophagus becomes damaged by acid reflux. BE can lead to the onset of a type of cancer called esophageal adenocarcinoma (EAC). Over the past few decades, statistics have reported that the incidence of EAC in Western populations is increasing.

“Esophageal adenocarcinoma (EAC) is on the rise in western countries with increased incidence and high mortality [1, 2].”

Since the popularity of smoking and a heartburn-inducing diet is likely to continue in the West, the early detection of EAC is critical for improving patient outcomes. If a biomarker could indicate a BE patient’s present risk of EAC, early EAC treatment could curb incidence and mortality rates. However, such a biomarker has yet to be confirmed. On February 14, 2022, researchers from Technische Universität München, Columbia University Irving Medical Center and Universitätsklinikum Freiburg published the research paper, “Telomere shortening accelerates tumor initiation in the L2-IL1B mouse model of Barrett esophagus and emerges as a possible biomarker,” in Oncotarget.

“Here we aimed to provide functional evidence for the hypothesis that telomere shortening can directly contribute to tumor initiation, and thus serve as a potential biomarker for BE cancer risk stratification [22, 24].”

Telomere Shortening and Tumor Initiation

“Shortened telomeres is a common sight in epithelial cancers and has also been described in EAC and its precancerous lesions.”

In this study, researchers investigated the impact of shortened telomeres in a mouse model for Barrett’s esophagus (L2-IL1B). The L2-IL1B mouse model is characterized by inflammation that leads to a Barrett-like metaplasia. The team knocked out the mTERC gene (mTERC−/−), which is the catalytic subunit of telomerase in the L2-IL1B mice.

After mTERC knockout, the researchers found that the telomeres shortened and the mice displayed signs of DNA damage. The tumor area along the squamocolumnar junction (SCJ) was increased in the second generation of these mice, and histopathological dysplasia (abnormal changes) was also increased. In vitro studies indicated that organoid formation capacity increased in BE tissue from the L2-IL1B mTERC−/− G2 mice.

“In summary, we here demonstrated a functional role of telomere shortening, a well observed property of BE, in promoting early onset esophageal tumor initiation in the L2-IL1B mouse model.”

Additional results of the study found that the telomeres in human BE epithelial cells lining the stomach with or without dysplasia were shorter than in gastric cardia tissue (the junction between the lower esophagus and the stomach). The study also found that differentiated cells that make mucus (goblet cells, which help protect the stomach lining) had longer telomeres than cells actively dividing (and more likely to become cancerous) in the columnar lined BE epithelium.

“Moreover, besides the importance during early carcinogenesis in the mouse model, shortening of telomeres was specifically decreased in dysplastic columnar-type tissue rather than in differentiated goblet cells in human BE- and LGD tissue samples.”

Conclusion

“Here, we demonstrate that telomere dysfunction aggravates the histological phenotype, extends the tumor area in the inflammation-based L2-IL1B mouse model for BE and acts as a driver for early dysplasia development.”

In summary, these findings suggest that shortened telomeres may play a role in tumor development in a mouse model of BE and are associated with proliferating columnar epithelium in human BE. The study suggests that shortened telomeres should be evaluated further as a possible biomarker for predicting EAC cancer risk in people with BE.

“It is plausible that with our measurements we could emulate this with shortened telomeres being at higher risk of genome instability and lowered cell-to-cell variability marking clonal expansion. However, larger studies are needed to test these hypotheses.”

Click here to read the full research paper published by Oncotarget.

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Trending With Impact: Analysis of Breast Cancer in Nigerian Women

August 16, 2021

In this trending paper published by Oncotarget in 2021, a cohort of Nigerian women were assessed for a useful biomarker in aggressive molecular subtypes of breast cancer.

The Trending with Impact series highlights Oncotarget publications attracting higher visibility among readers around the world online, in the news, and on social media—beyond normal readership levels. Look for future science news about the latest trending publications here, and at Oncotarget.com.

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Forms of cancer can vary in prevalence and aggression in different populations of people around the world. For instance, incidence rates of breast cancer (BC) have been rising in Africa over the past few decades. Research finds that Nigerian women have the highest age-standardized mortality rate of breast cancer on the African continent. This population in particular also faces disproportionately aggressive molecular subtypes of breast cancer.

“BC in Nigeria is characterized by disproportionately aggressive molecular subtypes, with exceptionally high rates of triple-negative (TN) BC [4], similar to BC in other countries in West Africa [5] and among African American women in the United States [6].”

In order to develop better treatment strategies, there is a distinct need to identify biomarkers that indicate, and even predict, these aggressive subtypes of breast cancer in Nigerian women. In 2021, a new study was conducted by researchers from Duke University, University of Lagos, Obafemi Awolowo University Teaching Hospital, University of Ibadan, Federal Medical Center Abeokuta, UNC Gillings School of Global Public Health, Our Lady of Apostle Catholic Hospital in Ibadan, University of Alabama at Birmingham, University of Kentucky, and University of Kansas Medical Center. Their trending research paper was published by Oncotarget and entitled, “Association of high-sensitivity C-reactive protein and odds of breast cancer by molecular subtype: analysis of the MEND study.”

C-Reactive Protein

“C-reactive protein (CRP) is associated with risk and aggressiveness for several types of cancer.”

When there is inflammation in the body, levels of the C-reactive protein (CRP) increase. This easily measurable protein can be a useful biomarker of systemic inflammation, infection, or tissue damage. Previous studies show that circulating CRP has been elevated in various types of cancers; it has also been associated with tumor prognosis. Past studies about CRP’s association in breast cancer subtypes have been notably few, and none have focused on isolating subpopulations in Africa.

“Additionally, it is worth noting that most of these past studies have been conducted in populations from the United States and Europe, among mostly White study populations, and to our knowledge, none have been conducted in populations from Africa.”

The Study

In this study, 555 Nigerian participants were assembled—of which 296 were confirmed breast cancer cases, and 259 were controls. The researchers collected clinical and reproductive characteristics of each participant, including the controls. In their first analysis, the researchers observed that newly diagnosed cases of Nigerian breast cancer were significantly more likely to have high levels of highly-sensitive CRP (hsCRP) compared to the controls. After adjusting for socio-demographic, clinical, and reproductive variables, the team still observed significant statistical significance for high levels of hsCRP associated with Nigerian BC. The findings from this cohort study also showed that high hsCRP was associated with a four-fold increased odds of BC.

“We also provide novel evidence of associations between hsCRP and BC molecular subtypes, with significant associations observed for luminal A, TN, and HER-enriched subtypes.”

Conclusion

“In conclusion, our analysis revealed a positive association between hsCRP and odds of BC, overall and for all molecular subtypes. Because CRP is an easily measured biomarker in the blood, it may represent a useful predictor of BC in the Nigerian context. We urge larger studies, preferably prospective cohort studies, among women of African descent to further characterize this association.”

Click here to read the full research paper, published by Oncotarget.

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Trending With Impact: Novel Biomarkers in Bladder Cancer

June 4, 2021

Researchers from the University of Houston and UT Southwestern Medical Center conducted a study which aimed to screen urine for potentially useful protein biomarkers of bladder cancer.

The Trending with Impact series highlights Oncotarget publications attracting higher visibility among readers around the world online, in the news, and on social media—beyond normal readership levels. Look for future science news about the latest trending publications here, and at Oncotarget.com.

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Bladder cancer is four times more common among men than women, and it is the sixth most common cancer diagnosis in the United States. However, researchers have found that cystoscopy—the primary method physicians use to diagnose patients with bladder cancer—is relatively invasive, expensive, and has the potential to cause urinary tract infections.

“In contrast, urine is a noninvasive and readily available biological fluid that can be used for diagnostic tests.”

In 2021, researchers from the University of H ouston and UT Southwestern Medical Center conducted a study which aimed to screen urine for possibly useful protein biomarkers of bladder cancer. The paper they authored was published in Oncotarget’s Volume 12, Issue 8, and entitled: “Urine protein biomarkers of bladder cancer arising from 16-plex antibody-based screens.”

“Urine biomarkers could potentially provide preliminary confirmation of low-grade BC [bladder cancer] before invasive procedures are performed and facilitate surveillance of BC, as reviewed [9].”

The Study

Patients may benefit in a number of different ways by using urine as fluid in diagnostic testing for bladder cancer. Urine is readily bioavailable, non-invasive, and it can also be collected and tested on a regular basis. Patients can even use various cost-effective point-of-care diagnostic tools, including at-home testing. First, the researchers assessed whether there were useful biomarkers of bladder cancer to be found in this fluid. The team used Luminex screening to test for both low and high levels of 16 proteins utilizing highly specific antibody-protein interactions.

“In this study, Luminex screening was used to simultaneously assay the protein abundances of 16 potential biomarkers in different stages of bladder cancer and then compared to urology clinic controls.”

ELISA validation was then used to determine which proteins were significantly elevated in bladder cancer. They found that levels of three urine proteins were capable of distinguishing between control and bladder cancer urine. One protein was also found to be capable of discriminating between high- and low-grade disease, and the successive clinical stages of bladder cancer.

“Upon ELISA validation, urine IL-1α, IL-1ra, and IL-8 were able to distinguish control urine from urine drawn from various bladder cancer stages, with IL-8 being the best discriminator.”

Conclusion

“These studies indicate that urine IL-1α, IL-1ra, and IL-8 are potential biomarkers of BC, two of which re-affirm previous reports.”

The researchers note that these newer urine biomarkers must be analyzed in larger cohorts, in specific clinical contexts, and compared to the performance of current diagnostic tools, such as the Bladderchek and UroVysion FISH assay.

“Looking forward, systematic studies in larger patient cohorts are warranted to establish the specific clinical contexts in which these markers may be used, including the following: (i) for initial diagnosis of BC, (ii) for surveillance of tumor recurrence, and/or (ii) for assessing treatment response following BCG therapy or other therapeutic modalities.”

Click here to read the full scientific study, published by Oncotarget.

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