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Mikhail Blagosklonny Oncotarget

Gene Mutations and Neoantigens in Head and Neck Tumors

January 13, 2022

The aim of this exploratory study was to characterize the genomic and neoantigen changes in 23 paired primary and recurrent head and neck cell squamous-cell carcinomas.

X-Ray film of neck - front and side — True colour X-Ray film of neck – front and side

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Head and neck cancer is a group of various tumors located in the oral cavity, oropharynx, larynx, and hypopharynx. Head and neck cell squamous-cell carcinomas (HNSCC) often result from tobacco use or human papillomavirus (HPV+) infection. In locally advanced HNSCC, the current therapies used are combined surgery, radiotherapy and chemotherapy. Despite the use of traditional treatments, up to 50% of patients relapse due to the increase in mutational burden as HNSCC advances. Few studies have investigated the therapeutic potential of neoantigens in HNSCC tumors.

“Prior work has characterized changes in the mutation burden between primary and recurrent tumors; however, little work has characterized the changes in neoantigen evolution.”

Neoantigens are new proteins/antigens that form on cancer cells after mutations occur in the tumor DNA. Certain neoantigens can promote anti-tumor immune responses and are potentially capable of controlling tumor progression. In an effort to characterize genomic and neoantigen changes in patients with HNSCC, researchers—from Washington University in St. Louis, Columbia University, St. Louis Children’s Hospital, and Siteman Cancer Center—investigated 23 paired primary and recurrent HNSCC tumors. Their paper, entitled, “Genomic and neoantigen evolution from primary tumor to first metastases in head and neck squamous cell carcinoma,” was chosen as the cover paper for Oncotarget’s Volume 12, Issue #6.

Patients and Samples

The researchers identified 23 biopsies from patients originally diagnosed with locally advanced HNSCC. Of the 23 patients in this study, 17 were male and 14 were tobacco smokers. The distribution of primary tumor location was nine in the oral cavity, seven in the oropharynx, six in the larynx, and one in the hypopharynx. The researchers note that all seven oropharyngeal primary tumor patients were HPV+. Each of the 23 patients received some combination of traditional treatment. Of these 23 patients, DNA and total RNA were independently extracted—totaling 69 samples. Twenty-three samples were from germlines, 23 were from primary tumors and 23 were from recurrent/metastatic tumors.

“To understand the recurrent mutation effect between primary and recurrent/metastatic tumors, we extract recurrently mutated genes (>1 sample mutated gene) from primary and recurrent/metastatic samples, separately.”

Recurrently Mutated Genes

The 23 germline blood samples were used in whole-exome sequencing (WES) data. The researchers also generated WES data using 46 paired primary and recurrent/metastatic samples from paraffin blocks and performed RNA sequencing successfully for 31 samples. After conducting RNA sequencing, they used Kallisto to predict gene expression in 16 primary tumors and 15 recurrent/metastatic tumors. A general trend showed that more mutations were within recurrent/metastatic tumors than in primary tumors. They performed KEGG pathways analysis to determine whether mutations occurred in pathways related to metastasis.

“Notably, ECM-receptor interaction pathway was extremely significant in recurrent/metastatic samples meaning that genes related to this pathway are more highly mutated than other pathway mutations in recurrent/metastatic samples.”

The TP53 gene was found to be the highest mutated driver gene in both sample groups, and the researchers identified BRCA1 and NOTCH1 as highly mutated driver genes in primary tumor samples. In recurrent/metastatic tumors, PIK3CA, ARID1A, RASA1, TSC2, and ERBB4 were mutated at higher rates than in primary tumor samples.

Infiltration of Immune Cells

To determine the infiltration of immune cells in primary tumors versus recurrent/metastatic tumors, the team performed immunohistochemistry. No significant differences in CD3+ cells, activated T cells, cytotoxic T cells, or CD3+ FOXP3+ cells were found. A significant increase of PD-L1 (an immune checkpoint protein) was found in recurrent/metastatic tumors. Upon further examination of immune checkpoint molecules, the researchers found a decrease in the expression of PDCD1 and CTLA4, with PDCD1 significantly decreased.

“We next sought to determine if genes containing neoantigens were shared between patients. Most neoantigens were unique to an individual tumor.”

Neoantigen Trends

In order to predict neoantigens among 46 tumor samples, this team utilized OptiType and MuPeXI to define the candidate neoantigens. Most patients had unique neoantigens based on the individual tumor type, however, the researchers’ analysis identified multiple patients with neoantigens in shared genes. They found neoantigens in six genes shared between four or five patients. (Three genes were among primary tumors: RYR3, DNAH7 and TTN; and three genes were among recurrent tumors: TNN, PIK3CA and USH2A.) They found that, compared to patients without them, patients who shared neoantigens in these genes tended to have increased neoantigens, CD3+ CD8+ T cell infiltration and duration of survival with HNSCC.

“These patients have increased total neoantigens, and a trend toward increased duration of survival with disease, infiltration of CD8 cells, and CTL activity. This suggests HNSCC neoantigens can stimulate an anti-tumor immune response.”

Conclusion

In conclusion, six genes with predicted neoantigens were found in four or more HNSCC patients. The researchers explained that while there is considerably more work needed in order to expand on their results from this small sample, the observation of neoantigens in these shared genes is significant.

“This raises the possibility that the presentation of certain neoantigens are important for control of tumor growth. This small exploratory study will provide the justification for a larger study of neoantigens in HNSCC.”

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

Behind the Study: Drs. Brian Van Tine and Charles Schutt discuss this research.

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Oncotarget is a unique platform designed to house scientific studies in a journal format that is available for anyone to read without a paywall making access more difficult. This means information that has the potential to benefit our societies from the inside out can be shared with friends, neighbors, colleagues, and other researchers, far and wide.

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Oncotarget

Open-Access Oncotarget Shifts to Continuous Publishing

January 6, 2022

As of 2022, the peer-reviewed and open-access journal Oncotarget has shifted to continuous publishing.

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BUFFALO, NY, January 6, 2022 – Since its inception in 2010, Oncotarget has operated as a traditional-style journal that publishes online page numbered issues of peer-reviewed papers. Final paginated issues were then released in their permanent form to Pubmed.

As of 2022, Oncotarget has shifted to a continuous publishing model. Papers will now be published continuously within yearly volumes in their final and complete form. This means that qualified, rigorously peer-reviewed articles will be published online as soon as they are in their fully formatted and final version of record. With continuous publication, articles posted online are complete with citation details and are available in full text html and PDF formats. Additionally, research papers will appear on PubMed quickly—just days after the papers are published by Oncotarget.

Why the change? In an increasingly digital world, the open-access continuous publishing model is ideal for authors, researchers and overall readership. Continuous publishing allows for faster research dissemination, citation and clinical application, compared to a traditional format.

Oncotarget is committed to doing our part to ensure that research is available to the biomedical community as quickly as possible, while maintaining high standards of quality.

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About Impact Journals (Oncotarget’s publisher):

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Oncotarget

Can Purified Cholera Stop Obesity?

December 31, 2021

In this 2019 study, researchers investigated the effects of purified elements of cholera toxin in age-associated weight gain.

In recent years, scientists have made significant advancements to improve our understanding of the gut microbiome. This diverse environment—of somewhere around 39 trillion microorganisms living within the digestive tracts of vertebrates (including humans, and even insects)—includes bacteria, archaea, viruses, and fungi. However, a “healthy” gut microbiota remains difficult to define in humans. The contents of the gut microbiome are not only different between women and men, microbiomes differ between… everyone. Among unrelated humans, no more than 30% of the same bacterial strains are shared in the gut microbiome.

Different microbiomes can present with different biological reactions to outside factors, including infections and medications, and can even display different symptoms reacting to cancer and other diseases. Studies have repeatedly found that the gut microbiome plays important roles in human mood, sleep, metabolism, digestion, the immune and nervous systems, and in chronic inflammatory disorders, such as obesity.

“Indeed, earlier studies have shown that gut microbe-immune interactions contribute to smoldering inflammation, adiposity, and weight gain.”

The Hygiene Hypothesis

Researchers continue to find evidence to support the “hygiene hypothesis.” The hygiene hypothesis postulates that a lack of beneficial early-life microbe exposures can result in a dysregulated immune system later in life. This lack of early-life microbe exposures followed by immune imbalances may be responsible for the increase in obesity and other chronic inflammatory disorders over the past forty years.

“Systemic immune imbalances arising from the gut have been proposed as a probable cause of obesity [8].”

In 2019, researchers from Massachusetts Institute of Technology (MIT) and Aristotle University of Thessaloniki conducted a study to test using purified elements of the otherwise dangerous cholera toxin as a vaccination in mouse models. Their theory was that this safe and well-established cholera-based immune adjuvant would cause an immune system reaction that reduces the inflammation associated with age-related obesity. Their research paper was published by Oncotarget and entitled, “Consuming cholera toxin counteracts age-associated obesity.” (Go Behind the Study to learn why the researchers decided to use the cholera toxin.)

The Study

First, the researchers used both inbred and outbred mouse models to test the effects of the cholera-toxin subunit B (ctB)—a component of the Dukoral® vaccine used in humans for cholera diarrhea prevention. For each mouse model tested in the study, four different groups of eight mice each were examined: a female control group, a vaccinated female group, a male control group, and a vaccinated male group. At four weeks of age, the study mice were given three doses every-other-week of ctB at 10 micrograms. The control mice were given sham doses. The researchers found that in ctB vaccinated mice, the oral vaccination prevented age-associated weight gain compared to the control mice in both models.

Next, the researchers used an obese mouse model to test the effects of ctB dosing in early-life and to test the effects of transfering their gut flora into another mouse. The researchers found that the obese-mouse microbiome was sufficient to trigger obesity and inflammation in other mice when compared to sham-dosed control mice. In the obese mouse model, ctB dosing in early life also inhibited age-associated weight gain. This probiotic inhibited weight gain in mice dosed in early-life, and also in mice dosed in adulthood.

“Although we discovered dramatic benefit after early-life exposures to ctB, mice were also significantly slimmer when dosed with ctB for the first time during adulthood at 12-wks-of-age or 24-wks-of-age.”

Conclusion

The researchers found that purified elements of the cholera toxin stabilized immunity, through the gut microbiome, and inhibited age-associated obesity in multiple mouse models. Further studies are necessary to determine the degree to which an early-life microbe exposure such as this impacts immunity versus first-time adulthood exposures. Humans have been taking pre- and probiotics for quite some time without a strong grasp of exactly how these microbe infusions work. This research contributed to a better understanding of how humans can modulate our own gut microbiome to improve many aspects of our health and well-being.

“This type of microbe-immune re-programming may ultimately target other diseases linked with obesity and inflammation such as diabetes [19], multiple sclerosis [64], and cancer [25].”

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

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Oncotarget

Could Metformin and Rapamycin Replace Maintenance Chemotherapy?

December 16, 2021

Researchers explored metformin with or without rapamycin as maintenance therapy in patients with metastatic pancreatic adenocarcinoma.

Malignant fluid cytology; Malignant cells of adenocarcinoma may spread to fluid of pleural or peritoneal cavity in cancer from the breast, lung, colon, pancreas, ovary, endometrium or other sites. — Malignant cells of adenocarcinoma

Maintenance chemotherapy has previously been recommended for patients with metastatic pancreatic ductal adenocarcinoma (mPDA)—as PDA is an aggressive cancer at all stages, and treatment options are limited for later-stage mPDA. However, maintenance chemotherapy regimens often lead to toxicity and are not viable long-term options. Therefore, researchers are exploring alternative maintenance therapies for mPDA patients. In preclinical studies, the therapeutic combination of metformin and rapamycin demonstrated a potential synergy of anti-tumor activity in PDA.

“A synergistic effect of the combination of metformin with rapamycin was suggested by preclinical studies demonstrating enhanced inhibition of mTOR in a pancreatic cancer cell line and better growth inhibition of pancreatic cancer cells in a xenograft tumor model with the combination than either agent alone [21].”

Metformin is an antihyperglycemic drug that is frequently prescribed for patients with diabetes to help control blood sugar levels. Rapamycin is an immunosuppressive drug that has historically been prescribed to prevent organ rejection in kidney transplant patients. (Today, rapamycin is also being considered for its potential use in anti-aging and longevity interventions.) In animals, metformin and rapamycin both inhibit the major biological regulator of growth, named the mammalian target of rapamycin (mTOR). mTOR is thought to be a main driver of many (if not all) aging-related diseases, including cancers such as PDA.

“Mechanistic/mammalian target of rapamycin (mTOR) is a serine/threonine protein kinase which acts as a signaling node downstream of several oncogenic pathways including KRAS/MEK/ERK and PI3K/Akt, both of which are thought to be relevant drivers in a majority of PDAs [6–9].”

The Study

Given its promising potential, researchers—from Johns Hopkins University School of Medicine, Virginia Piper Cancer Center at HonorHealth, Translational Genomics Research Institute (TGen), and Shanghai Jiao Tong University School of Medicine—conducted a study exploring metformin, plus or minus rapamycin, in patients with metastatic PDA. Their priority research paper was published by Oncotarget in 2020, and entitled, “An exploratory study of metformin with or without rapamycin as maintenance therapy after induction chemotherapy in patients with metastatic pancreatic adenocarcinoma”.

A total of 22 unselected patients with mPDA were included in this randomized open-label phase 1b study between June 2014 and December 2017. Patients were at least 18 years of age and had previously been treated with chemotherapy for mPDA. At the beginning of the study, patients had either stable mPDA or responding mPDA for at least six months after induction chemotherapy. Half of the patients were randomly assigned to study Arm A, and the other 11 patients were assigned to study Arm B. Of note, the average age of the participants in Arm B was older (52–72; 66) than the participants in Arm A (34-73; 58). Otherwise, baseline characteristics between the study groups were relatively well-balanced.

Participants in study Arm A were assigned to take 850 milligrams of metformin orally, two times per day, for at least 12 months. Participants in study Arm B were assigned to take metformin and four milligrams of rapamycin once per day, for at least 12 months. The researchers conducted PET/CT scans, immunologic and metabolic analyses, statistical analysis, and continuously recorded and monitored for safety, patient tolerance, toxicity, and treatment-related adverse events.

“Treatment was continued until disease progression, intolerance of study treatments, or study closure, which occurred only after all remaining patients received a minimum of 12 months of treatment.”

Results and Conclusion

“In conclusion, the administration of metformin with or without rapamycin in patients with mPDA who achieve a response to chemotherapy is well-tolerated and was associated with better than expected overall survival in this study.”

The researchers observed “remarkably longer than expected” progression free survival and overall survival in this typically poor-prognosis population of patients. In this cohort, a low neutrophil-to-lymphocyte ratio and decreased fluorodeoxyglucose-avidity and/or decreased CA19-9 from baseline predicted improved outcomes among the long-term survivors. Overall, metformin and rapamycin were well-tolerated and their safety profiles were found to be comparable to previous reports. The researchers were forthcoming about limitations of their study—as their cohort was relatively small and the study was not powered to detect differences in clinical activity between the treatment arms.

“To this end, we identified several factors which may be used to select for patients with improved outcomes; however, whether good prognosis patients need any further treatment at all and whether poor prognosis patients will benefit from continued chemotherapy rather than a maintenance approach are not known and additional prospective studies are needed to answer these questions.”

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

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Oncotarget

Chemical in Sunscreen Promotes Breast Cancer in Diet-Dependent Manner

November 18, 2021

The bioactivity of oxybenzone—a harmful chemical often found in sunscreens—was examined within mouse models of breast cancer in high- and low-fat dietary contexts.

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Oxybenzone (benzophenone-3; BP-3) is a toxic endocrine-disrupting chemical (EDC). Alarmingly, this chemical has been identified as a common ingredient in some brands of sunscreen. Oxybenzone can often be found in humans, household dust, fish and, due to its widespread human use, the water environment—causing harm to coral reefs and other murine life. Previous studies have shown that environmental toxins and estrogenic chemicals have emerged as potential culprits in the promotion of breast cancer. Furthermore, oxybenzone has been known to have estrogenic and anti-estrogenic properties.

“Although BP-3 has a very short half-life, its presence is widespread in human urine [9], in as much as 98% of the general U.S. population [13].”

Researchers from the Breast Cancer and the Environment Research Program at Michigan State University studied the diet-dependent effects of oxybenzone in mouse models of mammary tumorigenesis during puberty and adulthood. Their paper was published by Oncotarget in 2020, and entitled, “Benzophenone-3 promotion of mammary tumorigenesis is diet-dependent.”

“We [previously] demonstrated enhancement of mammary tumorigenesis by a diet high in saturated animal fat (HFD) [5–8]. Thus, examination of the activity of EDCs in a dietary context may provide additional insight into the potential role of EDCs in promoting breast cancer.”

The Study

In the current study, the team employed the Trp53–null transplantation of a basal-like breast cancer mouse model. The researchers previously demonstrated that proliferative, inflammatory and angiogenic activity in the mammary gland can be modulated by estrogen and a high-fat diet (HFD). Therefore, both pubertal and adult mice were placed on either low- or high-fat diets. After one week, study mice were ovariectomized, given time for recovery and the natural dissipation of endogenous hormones, and then treated for five days with either saline (control) or 17β-estradiol (E2).

Next, the estrogenic or anti-estrogenic effects of oxybenzone were examined in these mice under three dietary conditions: mice fed a life-long low-fat diet (LFD), mice fed a LFD during puberty and then a HFD in adulthood (LFD-HFD) and finally, mice fed a HFD during puberty and then a LFD in adulthood (HFD-LFD). Mice in LFD-HFD and HFD-LFD groups were fed their initial diet from three to 10 weeks of age, and were then switched to the alternative diet. Half of these mice were injected with oxybenzone and the other half (control) were injected with saline.

“We found that BP-3 had complex effects that were dependent upon dietary regimen and tumor histopathology.”

Results

Consistent with their previous studies, the researchers found that most of the tumors developed were epithelial in histological composition, and few were spindle cell carcinomas. They found that oxybenzone reduced the tumorigenesis of epithelial tumors in LFD mice. The LFD-HFD combination resulted in more spindle cell tumors compared to the life-long LFD mice. Oxybenzone treatment increased the tumorigenesis of epithelial tumors in mice fed the LFD-HFD.

“Kaplan-Meier analysis revealed that BP-3 reduced tumorigenesis of epithelial tumors in mice fed LFD (Figure 3A). On the other hand, consistent with the increased proportion of epithelial tumors, BP-3 was promotional for epithelial tumorigenesis in mice fed LFD-HFD (Figure 3C), while reducing spindle cell tumorigenesis (Figure 3D).”

Researchers saw that proliferation was increased by oxybenzone treatment most significantly in the mammary glands of 26-week-old HFD mice. Curiously, oxybenzone treatment increased the number of lesions only in mice fed the HFD-LFD. The researchers note that, in this study and others, a “pubertal window of susceptibility” was observed, reinforcing the important notion that puberty is a highly sensitive window of time for poor diets and adverse exposures to environmental toxins. Ultimately, the team found that oxybenzone enhances estrogen-stimulated breast cancer cell proliferation in pubertal mice fed a HFD.

“Benzophenone-3 increased tumor cell proliferation, decreased tumor cell apoptosis, and increased tumor vascularity dependent on specific dietary regimen and tumor histopathology.”

Conclusion

Collectively, the researchers’ findings suggest that exposure to oxybenzone has adverse consequences in mammary tumorigenesis. The degree of severity appeared to be modulated differently among the three dietary regimens studied. Mice fed a HFD in adulthood experienced a decrease in tumor cell apoptosis and an increase in tumor vascularity and tumor cell proliferation. They note that there is future value in exploring the differences between pubertal and adult exposure to oxybenzone on a constant diet regimen.

“This points to a need for further studies of benzophenone-3 in both animal models and humans as a potential breast cancer risk factor, as well as a more general need to evaluate endocrine disrupting chemicals in varying dietary contexts.”

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

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Oncotarget

New Study: ALK Rearrangement Among Lung Cancer Patients

November 10, 2021

In Oncotarget’s Volume 12, Issue 23, cover paper, researchers retrospectively assessed the prevalence of anaplastic lymphoma kinase (ALK) gene rearrangement among nearly 20,000 patients with advanced non-small cell lung cancer.

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The identification of an actionable gene mutation or translocation in patients with cancer can give researchers a target for new drug therapies. One such mutation, found in some patients with non-small cell lung cancer (NSCLC), is anaplastic lymphoma kinase (ALK) gene rearrangement. However, the exact population of patients that present with ALK rearrangement has not been fully characterized. Identifying the subpopulation of patients who present with ALK rearrangement may lead to better overall treatment outcomes.

Researchers—from University of Mississippi Medical Center, Roche Information Solutions, Roche Diagnostics Corporation, Genesis Research, and Houston Methodist Hospital—conducted a retrospective study of nearly 20,000 patients with advanced NSCLC (aNSCLC). The researchers assessed ALK rearrangement prevalence in the cohort overall and then categorized the data using patient characteristics. Their paper was published on the cover of Oncotarget’s Volume 12, Issue 23, and entitled, “Anaplastic lymphoma kinase rearrangement prevalence in patients with advanced non-small cell lung cancer in the United States – retrospective real world data”.

“We performed a retrospective study of a database to acquire real-world clinical data on the frequency of the translocation in a large pool of patients drawn primarily from community hospitals and practices.”

The Study

This cross-sectional, observational study used de-identified data from Flatiron Health’s database, which included 19,895 patients who were diagnosed with aNSCLC in the United States between 2015 and 2019. The average age of patients was 68.5, plus or minus 10 years. The distribution of gender was nearly equal, with men comprising 50.4% (10,029) of the patient cohort, and 68.4% of patients were Caucasian. A large proportion of patients had a non-squamous histology type (80.5%) and smoking history (85.5%).

“Prevalence of ALK rearrangement was assessed overall and then stratified by patient characteristics such as age, gender, race, smoking status and histology.”

The researchers used descriptive statistics to summarize patient characteristics. Characteristics included age, gender, race, geographic location, smoking status, histology, practice type (community or academic), PD-L1 status, prevalence of ALK rearrangement and other biomarkers.

“Regardless of documented histology, a higher ALK rearrangement rate (8.9%) was observed among patients who had no smoking history compared to patients with a smoking history (1.5% ALK positivity) which represent the largest number of patients in this cohort (17,003).”

Conclusion

Results from the study concluded that ALK rearrangement was present in 2.6% of the total cohort, or 517 patients. The researchers found that ALK rearrangement prevalence varied based on the patients’ demographic characteristics. The rate of ALK rearrangement was the highest among patients younger than 40 years old, and decreased with age. Researchers found no significant difference in ALK rearrangement between men and women. However, when compared to other patients, Asian patients had a higher ALK rearrangement rate (39 out of 623, or 6.3%). Interestingly, the ALK positivity rate was greatest (9.3%) among non-smoking patients with non-squamous histology.

“In summary, this retrospective review of nearly 20,000 patients with aNSCLC and tested for ALK in the United States confirms that ALK rearrangements are found more commonly in younger nonsmokers and patients of Asian descent.”

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

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Oncotarget is a unique platform designed to house scientific studies in a journal format that is available for anyone to read—without a paywall making access more difficult. This means information that has the potential to benefit our societies from the inside out can be shared with friends, neighbors, colleagues, and other researchers, far and wide.

For media inquiries, please contact media@impactjournals.com.

Oncotarget

New Study: Vaccine Enhances Breast Cancer Treatment

October 27, 2021

Researchers conducted a study to examine the efficacy of adding the P10s-PADRE vaccine to chemotherapy treatments for patients with HR+/HER2− breast cancer.

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The most common type of breast cancer in the United States is HR+/HER2− breast cancer. Patients with HR+/HER2− breast cancer often face the threat of distant recurrence—long after the completion of their treatment. Previous studies have found that high levels of tumor infiltrating lymphocytes (TILs) were associated with improved outcomes and recurrence-free survival in patients with HR+/HER2− breast cancer. These studies and many others have prompted researchers to further develop and test cancer vaccinesin an effort to elicit anti-tumor immune responses in these patients.

“Therefore, a rational combination therapy that enhances the immune-stimulatory properties of NAC [neoadjuvant chemotherapy], can provide long-term survival benefits for this patient population.”

Researchers from University of Arkansas for Medical Sciences, University of Texas Southwestern, Highlands Oncology Group, and Université Claude Bernard Lyon 1 conducted a new single-arm Phase Ib clinical trial. Early-stage HR+/HER2− breast cancer patients were treated with carbohydrate-mimetic peptides, the P10s-PADRE vaccine, in combination with chemotherapy treatments. Their paper was chosen as the cover of Oncotarget’s Volume 12, Issue 22, and entitled, “P10s-PADRE vaccine combined with neoadjuvant chemotherapy in ER-positive breast cancer patients induces humoral and cellular immune responses.”

“The main objective of our study was to determine an appropriate schedule to be used for adding the P10s-PADRE vaccine to cancer chemotherapy in the neoadjuvant setting considering the ability of the vaccine to elicit adequate antibody response.”

The Study

After meeting the study’s detailed inclusion/exclusion criteria, a total of 25 patients with HR+/HER2− breast cancer were selected to partake in this single-arm Phase Ib clinical trial. Patients were divided into five cohorts (five patients per cohort): A, B, C, D, and E. Each patient was treated with a combination of four therapies over the course of 22-25 weeks, including three doses of thepeptide-based P10s-PADRE cancer vaccine, four doses of Cyclophosphamide (chemotherapy), four doses of Doxorubicin (chemotherapy) and four doses of Docetaxel (chemotherapy). Using a cohort-specific treatment schedule for the previously stated combination of therapies, the researchers assessed the feasibility, safety and immunogenicity achieved in each cohort and each patient.

Additionally, patients underwent surgery between weeks 26 and 33 (four to eight weeks after their last chemotherapy treatment). Each cohort also had a cohort-specific blood draw schedule—blood was drawn at eight different times in the 73-week time frame. Blood draws were used to conduct flow cytometry, measure the concentration of cytokines, natural killer (NK) cells and antibodies, and to determine the presence of anti-peptide antibody response and the percentage of TILs. The researchers observed that all five cohorts saw a significant reduction in tumor size.

“The data suggest that subjects enrolled in schedule C generated a more consistent and robust antibody response, therefore schedule C appears as the schedule of choice for future combination therapy.”

Their findings concluded that, in combination with chemotherapy, P10s-PADRE immunization in HR+/HER2− breast cancer patients induced “acceptable” antibody responses in study cohorts C and E. The treatment schedule in cohort C demonstrated the strongest antibody response by affecting the expression levels of NK-cell markers, stimulating the production of cytokines, T-cells and TILs. However, the researchers note that continued analysis of the blood samples collected could show serum antibodies may begin to appear later on in patients enrolled in the other treatment schedules.

Conclusion

“This Phase Ib clinical trial of the P10s-PADRE vaccine shows that immunization in combination with a standard-of-care NAC is feasible and well-tolerated. Combination therapy induces antibody response, stimulates activation of NK cells, and is associated with infiltration of T cells in tumor microenvironment. Randomized phase II trials focusing on treatment schedule C are needed to validate current findings and evaluate clinical efficacy.”

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

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Oncotarget

EMT Resistance in Cancer Cells and Two Potential Causes

October 21, 2021

Researchers used mathematical modeling to investigate mechanisms that drive the elusive phenomenon of cancer cell resistance to epithelial-mesenchymal transition (EMT).

Epithelial–mesenchymal transition (EMT): losing cell polarity and cell adhesion to gain migratory and invasive properties.

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Cancer cells have been known to use sagacious methods of evading apoptosis and mysteriously overcoming powerful anti-cancer therapies. One such method of evasion has recently been identified as the process of epithelial-mesenchymal transition (EMT) and its reverse process, mesenchymal-epithelial transition (MET). These transitions enable epithelial cells (structural/fixed) to gain mesenchymal cell (differentiating/mobile) functions, and vice versa. Researchers believe that epithelial-mesenchymal plasticity (EMP) allows cancers to become therapy resistant, determines cancer aggressiveness and allows metastatic cancer to mobilize and spread.

“Such dynamic and reversible switching can help tumor cells to overcome various challenges during disease progression such as anoikis [6], and assaults by the immune system [7].”

These processes and their characterization in cancer have been studied, however, questions remain about their molecular determinants and degree of reversibility, or irreversibility, in different cell populations and environments. To further elucidate EMT, researchers from Rice University, Northeastern University and the Indian Institute of Science used mechanistic mathematical models to identify possible mechanisms that may drive EMT response to an EMT-inducing signal in a given isogenic cell population. Their paper was published by Oncotarget in 2020, and entitled, “Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT.”

EMT/MET Reversibility/Irreversibility

In the introduction of this paper, the authors discuss results from previous research about the reversibility and irreversibility of EMT/MET. EMT can be triggered by various EMT-inducing external signals, such as TGFβ or by adjusting the levels of EMT-specific transcription factors (EMT-TFs). They report that, in cells stimulated over shorter durations (between two and six days), cells may revert back to an epithelial state after withdrawal of the signal/stimulus. They also explain that cells that have been stimulated over longer durations (10+ days) may render EMT irreversible and to become “locked” in a mesenchymal state.

Researchers suspect the existence of a “tipping point” after continued signal/stimulus exposure is what results in irreversible EMT. Multiple mechanisms have been proposed as responsible for this tipping point, including epigenetic alterations and self-stabilizing feedback loops in regulatory circuits. However, there remains a need for studies to investigate the mechanistic basis that causes epithelial cells to be resistant to undergoing EMT, or the irreversibility of MET.

“Some sporadic observations about the resistance of epithelial cells to undergo EMT have been reported [14, 24], but a causative mechanistic understanding still remains elusive.”

The Study

To investigate the mechanisms that enable the irreversibility of MET, or lack of EMP, the researchers in this study used mechanism-based mathematical modeling. Their experimental observations indicated that a global epigenetic program limiting the action of ZEB1 was found to underlie epithelial trait retention in cells exposed to persistent Twist1 activation for 21 days. They demonstrated a possible underlying mechanism by which GRHL2 overexpression can resist EMT. Importantly, the researchers found that, from a single isogenic cell population, two subpopulations of cells emerged and responded differently to the EMT-signalling.

“Here, we propose two independent mechanism[s] that may explain the resistance of epithelial tumor cells to undergo EMT: 1) epigenetic feedback mediated via GRHL2—an MET-inducing transcription factor (MET-TF) [25–27]; and 2) stochastic partitioning of parent cell biomolecules among the daughter cells at the time of cell division [28–30].”

Aside from epigenetic mediation involving GRHL2, the researchers believe varying EMT-signal responses within isogenic cell populations are caused by stochastic partitioning of molecules during cell division. The researcher described this phenomenon as a type of incongruent “noise” that takes place when cells divide.

“Such noise in the distribution of molecules may affect cell-fate and drive non-genetic heterogeneity [28–30], leading to different phenotypic distributions in terms of EMT [3].”

Conclusion

The team concluded that MET should not only be considered the reverse process of EMT, as important and distinct processes may be involved in both EMT and MET transformations. The authors are forthcoming about limitations in their study—indicating that a more detailed molecular mechanism-based epigenetic model would provide better insights into EMT. They also note that they did not consider spatial effects in their model, where more dense or spread out cell populations and access to signal strength, nutrients and oxygen may change outcomes.

“Future efforts should decode the molecular mechanisms of any such epigenetic feedback of GRHL2 on ZEB1 expression as well as track the distribution of molecules during cell divisions happening while cells are being induced to undergo EMT/MET.”

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

Watch, read or listen to an Oncotarget Interview with Drs. Herbert Levine and Mohit Kumar Jolly as they discuss this paper.

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Oncotarget

Trending With Impact: Unconventional Method Effectively Targets NSCLC

October 4, 2021

Researchers developed a divergent strategy to treat non-small cell lung cancer (NSCLC).

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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The mammalian target of rapamycin (mTOR) operates within two distinct protein complexes—mTOR complex 1 (mTORC1) and complex 2 (mTORC2). These protein complexes are not yet fully understood, as they were only recently identified in humans in 1994. What researchers do know is that mTORC1 is involved in the regulation of many cellular processes and is a key mediator of cell growth and proliferation. mTORC1 is activated by growth factor receptor signals through the PI3K–AKT and RAS–ERK mitogen-activated protein kinase (MAPK) pathways.

The PI3K/AKT/mTOR pathway may be an efficacious target in the treatment of patients with non-small cell lung cancer (NSCLC). This theory is based on the identification of particular gene mutations in NSCLC that are associated with the PI3K/AKT/mTOR pathway. However, previous studies have not yet succeeded in defining an effective monotherapy or combination of therapies that targets this pathway while improving NSCLC patient outcome.

Researchers from Institut Curie, PSL University, Xentech, BioPôle Alfort, Hôpital Foch, and Centre Léon Bérard designed a study using a new methodology to test treatment combinations based on specific targets identified as biomarkers of resistance to PI3K-targeting treatments, and not based on the NSCLC mutations themselves. Their trending research paper was published by Oncotarget in 2021 and entitled, “High in vitro and in vivo synergistic activity between mTORC1 and PLK1 inhibition in adenocarcinoma NSCLC.”

“Our main strategy was therefore, using a panel of NSCLC PDXs, (i) to define predictive markers of response to RAD001 therapy and (ii) to identify possible combinations of treatments that may be able to reverse RAD001 resistance.”

THE STUDY

Researchers tested RAD001/Everolimus (an mTORC1 inhibitor) in vivo using NSCLC Patient-Derived Xenografts (PDXs), which demonstrated high antitumor efficacy. They next aimed to define predictive markers of response to RAD001 using real-time quantitative RT-PCR assays.

“In order to define predictive markers of response to RAD001, we used real-time quantitative RT-PCR assays to quantify the mRNA expression of a large number of selected genes.”

The team found three significantly highly expressed and targetable genes in NSCLC tumors resistant to RAD001: PLK1, CXCR4 and AXL. They then analyzed these genes for their prognostic value among NSCLC patients that were found in the publicly available database KMPLOT. This analysis revealed that of the three genes evaluated, only one high-gene expression was correlated with a negative impact on overall survival of patients with adenocarcinoma: PLK1. Given this data, the researchers next evaluated the in vivo efficacy of RAD001 combined with a PLK1 inhibitor, volasertib, in four PDX models. The RAD001 + volasertib combination demonstrated dramatic efficacy in three of the four models.

“In all tested PDXs, except LCF29, we have observed a significant, but variable, improvement of the antitumor efficacy of RAD001 + volasertib in comparison to each monotherapy (Figure 2A).”

To define this RAD001 + volasertib drug combination’s mechanism of action, the researchers conducted a pharmacodynamics (PD) study. The team then evaluated post-therapeutic proteins involved in the cell cycle, vascularization and carbonic anhydrase IX expression. These results were then validated using in vitro studies.

CONCLUSION

“Our determination of relevant Pi3K-based therapeutic combination(s) was not supported, by the presence of actual molecular abnormalities, nor by physician therapeutic practices, but by the identification of predictive markers of resistance to Pi3K-based monotherapies.”

In summary, the researchers conclude that their study demonstrates that inhibiting both mTORC1 and PLK1 proteins induces synergistic antitumor activity in multiple models of NSCLC. In the discussion section of this paper, the authors detailed the divergent methodology they used to come to their conclusion.

“This methodology may promote more relevant clinical trials and avoid non-efficient combinations, inacceptable toxicities, and expensive and time-consuming studies.”

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

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Oncotarget

Trending With Impact: Promising Non-Small Cell Lung Cancer Prodrug

August 26, 2021

Researchers examined the preclinical prodrug LP-184 and its efficacy in treating non-small cell lung cancers that lack actionable targets or resistance-related genes.

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Between 20 and 40% of adults with non-small cell lung cancer (NSCLC) eventually go on to develop brain metastases. Over 40% of patients with NSCLC have limited treatment options due to a lack of actionable therapeutic targets. Treatment for such patients has been limited to non-targeted chemotherapy—an approach which increases the risk of developing drug-resistance due to underlying resistance-associated mutations.

“Newer drugs that will be more potent and remain efficacious in NSCLC with such mutations could lead to better alternate or combinatorial therapies.”

Lantern Pharma (a pharmaceutical company developing targeted cancer therapies) created a new drug candidate and next generation member of the acylfulvene class of prodrugs, named LP-184. Researchers from Lantern Pharma and REPROCELL (a commercial contract research organization) conducted a study to test the anti-tumor activity of this preclinical compound in a variety of NSCLC cell lines. In 2021, Oncotarget published team’s pape, entitled, “The acylfulvene alkylating agent, LP-184, retains nanomolar potency in non-small cell lung cancer carrying otherwise therapy-refractory mutations.”

The Study

Despite LP-184’s highly-synthetic sounding name, the lead product in this acylfulvene prodrug (Illudins) is derived from, you guessed it, Jack-o-Lantern mushrooms.

“Acylfulvenes have been derived from cytotoxic agents called Illudins, isolated from Jack-o-Lantern mushroom (Omphalotus illudens), that retain and improve the cytotoxicity of parent Illudins for use as anticancer agents.”

The anti-tumor activity of this compound is based on activation through reductive mechanisms, mediated by enzymes such as Prostaglandin Reductase 1 (PTGR1). PTGR1 is known to be upregulated in some tumors, including in tumors with mutations in KEAP1. LP-184 sensitivity was investigated in NSCLC cell lines with individual or combined mutations in KEAP1, KRAS, TP53, and STK11.

“There is a high unmet need for effective therapies for NSCLC harboring mutations in these genes that have not only been considered undruggable till date but also are associated with loss of efficacy or resistance to multiple therapeutic strategies, at least in frontline regimens.”

The researchers tested LP-184 in vitro in 19 primary and metastatic NSCLC cell lines to determine the range of NSCLC settings that this compound might work best in. Clinical data analyses were also conducted by the researchers to predict tumor responsiveness to LP-184. In addition, the compound was examined in two mouse models of primary lung cancer. Mouse models were tested for sensitivity to LP-184 in both two- and three-dimensional culture systems.

“We sought to assess LP-184 activity in a panel of selected NSCLC adenocarcinoma cell lines, determine associations between genomic and transcriptomic profiles and responses of cell lines tested, and compare in vitro potency of LP-184 with that of approved chemotherapy agents.”

Conclusion

Among their many findings, the researchers demonstrated that LP-184 has high nanomolar potency in 11 of the 19 NSCLC cell lines tested—indicating broad NSCLC anti-tumor activity. In vivo, LP-184 showed efficacy in terms of tumor regression in one of the two mouse models.

“We propose further evaluation of LP-184 in multiple PTGR1 high NSCLC settings that may not necessarily be mutually exclusive, including in highly prevalent KEAP1 and KRAS mutant tumors (Figure 6), and in patients with lack of actionable targets or resistance-related genes with no effective therapy options available.”

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

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