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Senescence-Related TME Genes as Key Prognostic Predictors in HNSCC

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In a new study, researchers aimed to investigate the prognostic significance of senescence-related TME genes in head and neck squamous cell carcinoma (HNSCC) and their potential implications for immunotherapy response. 

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Head and neck squamous cell carcinoma (HNSCC) is a prevalent and heterogeneous form of cancer that affects thousands of individuals worldwide. The prognosis for HNSCC patients can vary greatly, depending on factors such as tumor stage and site. The tumor microenvironment (TME) plays a crucial role in tumorigenesis and disease progression, with cellular senescence being a key component. Senescent cells, characterized by cell-cycle arrest, have been shown to have both tumor-suppressive and tumor-promoting effects. However, the prognostic significance of senescence-related TME genes in HNSCC remains poorly understood.

In a new study, researchers Young Chan Lee, Yonghyun Nam, Minjeong Kim, Su Il Kim, Jung-Woo Lee, Young-Gyu Eun, and Dokyoon Kim from Kyung Hee University, Kyung Hee University Hospital at Gangdong, and the University of Pennsylvania aimed to investigate the prognostic significance of senescence-related TME genes in HNSCC and their potential implications for immunotherapy response. They utilized data from The Cancer Genome Atlas (TCGA) to identify two distinct subtypes of HNSCC based on the expression of senescence-related TME genes. The team then constructed a risk model consisting of senescence-related TME core genes (STCGs) and validated its prognostic capability in independent cohorts. Their research paper was chosen as an Aging cover paper and published in Volume 16, Issue 2, entitled, “Prognostic significance of senescence-related tumor microenvironment genes in head and neck squamous cell carcinoma.”

“To the best of our knowledge, this is the first study to offer a comprehensive evaluation of the senescence related TME status by integrating senescence related TME genes through a gene-gene network and clustering. Furthermore, we have introduced a novel risk model that utilizes a selected gene set to predict prognosis and confirmed the expression of STCGs in immune cells at single-cell levels.”

The Study

Identification of Prognostic Senescence-Related TME Genes

To identify prognostic senescence-related TME genes, the researchers screened a total of 7,878 genes in the TCGA-HNSCC dataset. They identified 288 genes that belonged to TME-related genes, tumor-associated senescence (TAS) genes, and immune-related genes. From these genes, they selected 91 prognostic senescence-related TME genes (PSTGs) based on differential expression analysis and Cox regression analysis.

Senescence-Related TME Subtypes and Characterization

Using consensus clustering analysis, the researchers classified the HNSCC samples into two distinct subtypes based on the expression of PSTGs: subtype 1 and subtype 2. The two subtypes exhibited significant differences in clinical and molecular characteristics. Subtype 2 had a higher prevalence of HPV-positive and oropharyngeal cancer cases, while subtype 1 was characterized by a higher proportion of advanced tumor stage and overall stage.

Further analysis revealed distinct differences between the subtypes in terms of genetic alterations, methylation patterns, enriched pathways, and immune infiltration. Subtype 1 had a higher mutation rate in the TP53 gene and exhibited hypomethylation in several CpG sites compared to subtype 2. Additionally, subtype 2 showed higher immune scores, stromal scores, and ESTIMATE scores, indicating a more favorable immune microenvironment.

The two subtypes also displayed differences in survival outcomes. Kaplan-Meier survival analysis showed that subtype 2 had a more favorable overall survival compared to subtype 1. This difference was enhanced in the HPV-positive cohort, suggesting that the senescence-related TME subtypes may have implications for prognosis in specific patient subgroups.

Risk Scoring Based on Senescence-Related TME Status

Using the 91 PSTGs, the researchers constructed a risk scoring model based on the LASSO Cox regression algorithm. They identified 21 STCGs that were associated with either increased risk or protection. The risk scores based on the expression levels of these genes were calculated for each patient, and the patients were classified into high- and low-risk groups.

The prognostic performance of the risk scoring model was tested in independent cohorts, including the TCGA-HNSCC test set, the GSE41613 cohort, and the KHUMC cohort. The high-risk group showed significantly lower overall survival compared to the low-risk group in the TCGA-HNSCC test set and the GSE41613 cohort. Although not statistically significant, the low-risk group demonstrated a trend towards higher overall survival in the KHUMC cohort.

Immunotherapy Response Prediction and Single-Cell Analysis

The team also investigated the immunotherapy response prediction based on the risk model and the expression of STCGs. They found that the low-risk group had higher immunophenoscores and a significantly higher proportion of responders to immunotherapy compared to the high-risk group.

To further evaluate the senescence-related TME characteristics at the single-cell level, the researchers analyzed single-cell transcriptome data from HNSCC tissue. They found that STCGs were enriched in fibroblast, mono/macrophage, and T cell populations, suggesting that these cell types contribute to the senescent features of HNSCC.

Conclusion

In conclusion, the study sheds light on the prognostic significance of senescence-related TME genes in HNSCC. Their findings highlight the heterogeneity of HNSCC and the importance of the senescence-related TME in prognosis and immunotherapy response. The risk scoring model based on STCGs provides a potential prognostic biomarker for HNSCC patients, and the single-cell analysis further elucidates the association between STCGs and specific cell populations within the TME. These findings contribute to a deeper understanding of the complex interplay between senescence and the TME in HNSCC and have implications for precision medicine and personalized treatment approaches. Further research and validation are needed to fully understand the clinical implications of senescence-related TME genes in HNSCC. However, this study provides valuable insights into the role of cellular senescence in tumor progression and the potential for targeting senescence-related pathways in the development of novel therapeutic strategies for HNSCC patients.

“In conclusion, this study comprehensively investigated the prognostic and immunological features of senescence related TME genes in HNSC. By leveraging these senescence related TME genes, we successfully developed a risk model to predict HNSC prognosis and immunotherapy response, which was robustly validated using external transcriptome datasets. These findings provided evidence for the role of senescence in the TME and highlighted the potential of senescence-related biomarkers as promising therapeutic targets.”

Click here to read the full research paper published in Aging.

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Aging is an open-access, traditional, peer-reviewed journal that has published high-impact papers in all fields of aging research since 2009. All papers are available to readers (at no cost and free of subscription barriers) in bi-monthly issues at Aging-US.com.

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Investigating Susceptibility to Radiation-Induced Pulmonary Fibrosis

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Researchers evaluated three different mouse strains with varying sensitivity to radiation lung fibrosis in an effort to uncover the underlying mechanisms.

Investigating Susceptibility to Radiation-Induced Pulmonary Fibrosis

The Trending With Impact series highlights Aging publications (listed as “Aging (Albany NY)” by Medline/PubMed and “Aging-US” by Web of Science) that attract 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 Aging-US.com.

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Radiation is an effective treatment for many types of cancer. Unfortunately, this treatment has the potential to cause long-term side effects in some patients, including the thickening or scarring of lung tissue, known as pulmonary fibrosis. Radiation-induced pulmonary fibrosis (RIPF) is a serious complication that can occur after radiation therapy and can lead to death. Predicting an individual’s risk of developing RIPF remains challenging for clinicians, as little is known about the underlying mechanisms that cause it.

“Differential susceptibility to lung injury from radiation and other toxic insults across mouse strains is well described but poorly understood.”

Previous studies in mouse models have shown that there are natural variations in susceptibility to RIPF among different strains of mice. The mechanism(s) underlying this difference in susceptibility is still unknown. In a new study, researchers Eun Joo Chung, Seokjoo Kwon, Uma Shankavaram, Ayla O. White, Shaoli Das, and Deborah E. Citrin from the National Institutes of Health’s National Cancer Institute investigated differences in macrophage function across mouse strains and their potential contribution to varied RIPF susceptibility. On September 28, 2022, their research paper was published in Aging’s Volume 14, Issue 19, entitled, “Natural variation in macrophage polarization and function impact pneumocyte senescence and susceptibility to fibrosis.”

The Study

While the precise mechanisms underlying RIPF are not fully understood, it is thought that senescent pneumocytes (or alveolar cells) play a key role. Pneumocytes are a type of cell in the lung that are essential for gas exchange. Type II pneumocytes (AECII) function as alveolar stem cells after lung injury. The researchers hypothesized that macrophages (a type of white blood cell that play an important role in immune responses) may contribute to promoting AECII senescence.

“AECII are known to be in close contact with alveolar macrophages, and, in this fashion, to contribute to lung homeostasis [11].”

The researchers hypothesized that natural variations in macrophage function contribute to differences in RIPF susceptibility. To explore their hypothesis, they evaluated three different mouse strains with varying sensitivity to radiation lung fibrosis: C57L mice (RIPF-prone), C57BL6/J mice (intermediate) and C3H/HeN mice (RIPF-resistant). Female mice (to avoid sex-based differences in results) underwent thoracic irradiation (IR). Changes in macrophages and pneumocytes were assessed.

The Results

The team found that susceptibility to radiation-induced lung injury and premature AECII senescence varied by mouse strain. Pulmonary irradiation led to varied macrophage phenotypes and accumulation in each strain. In responses to polarizing stimuli, macrophages demonstrated strain-dependent responses. M2 macrophages induced AECII senescence via NOX2-derived superoxide production in a strain-dependent manner. Finally, macrophages expressing NOX2 accumulated in fibrotic lungs after radiation.

“NOX1 and NOX2 protein were expressed at the highest levels in C57L BMDM, with intermediate expression in C57BL6/J BMDM and the lowest expression in C3H/HeN BMDM (Figure 6B).”

The researchers demonstrated that the C57L mice (the strain with the greatest sensitivity to RIPF) exhibited the greatest rate of accumulation of senescent AECII cells. At the same time, they found that the fibrosis-sensitive (C57L and C57Bl6/J) mouse strains exhibit a greater accumulation of M2 polarized macrophages than the fibrosis-resistant strain (C3H/HeN).

“However, until now, the impact of M2 polarization on AECII senescence was unexplored. In this study, we identified that M2 macrophage polarization can contribute to AECII senescence, potentially leading to a positive feedback loop that furthers pulmonary injury.”

Conclusion

This study provides new insights into the role of macrophages in RIPF susceptibility. The findings suggest that natural variations in macrophage function contribute to differences in RIPF susceptibility. The different macrophage polarization profiles across strains may contribute to their varying susceptibilities to RIPF by promoting AECII senescence. These findings may help to develop new strategies for the prevention and treatment of RIPF.

“In this study, variation in the accumulation of senescent cells across strains with varying sensitivity to fibrosis has been established. Further, strain variation in macrophage response to polarizing stimuli and capacity to produce superoxide and induce senescence in epithelial cells is described. Together, these data highlight the importance of macrophage-epithelial interactions in the context of lung fibrosis and identify NOX2 as a possible therapeutic target in radiation lung injury.”

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

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Aging is an open-access journal that publishes research papers bi-monthly in all fields of aging research. These papers are available at no cost to readers on Aging-us.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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Trending With Impact: Underlying Mechanisms of Replicative Senescence

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Published on the cover of Aging’s Volume 14, Issue 7, researchers conducted a new study investigating the role of IGFBP5 in replicative senescence.

cell division illustration

The Trending With Impact series highlights Aging (Aging-US) publications that attract 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 Aging-US.com.

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In 1961, Leonard Hayflick and Paul Moorhead proposed a theory later named the Hayflick Limit. They discovered that a normal human cell can divide between 50 and 70 times before it can no longer proliferate and eventually dies. Researchers have since continued to explore this phenomenon and, today, this aging process is known as cellular (replicative) senescence.

“There are currently several experimental models of cellular senescence. Hayflick and Moorhead observed that primary human fibroblasts in culture exhibit a limited proliferative capacity [6]. This growth arrest during passages is called replicative senescence.”

This permanent cessation of the cell cycle is universally found in biology due to known and unknown causes, including the shortening of telomeres. While telomere shortening plays an important role, it is not the only event responsible for inducing cellular senescence. Thus, researchers have spent decades under the microscope experimenting with cellular models of replicative senescence.

In a new study released on April 4, 2022, researchers from Sapporo Medical University in Sapporo, Japan, investigated mechanisms of replicative senescence in vitro. Their trending research paper was published on the cover of Aging (Aging-US) Volume 14, Issue 7, and entitled, “Downregulation of IGFBP5 contributes to replicative senescence via ERK2 activation in mouse embryonic fibroblasts.”

The Study

Cellular senescence is typically characterized by cell growth arrest, an increase of cells positive for SA-β -gal staining, and upregulation of p16 and p19. To begin this study, the team cultured embryonic mouse fibroblasts (MEFs) and conducted cell passages according to the 3T3 method. They found that the MEFs underwent senescence after the 5th passage (P5). The team also found that at P8, the expression of insulin-like growth factor binding protein 5 (IGFBP5) mRNA was significantly reduced when compared with that of P2 MEFs.

Next, the team performed a knockdown of IGFBP5 in the MEF cells. Results showed that IGFBP5 knockdown induced premature cellular senescence in P2 MEFs. Knockdown of IGFBP5 increased phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) but did not affect expression levels of Akt or p16 repressors. The researchers also found that supplementing the cell culture growth medium with additional exogenous IGFBP5 delayed growth arrest and reduced replicative senescence in the MEF cells.

“To examine whether activated ERK1 and ERK2 by IGFBP5 knockdown are involved in the induction of senescent phenotypes, we examined effects of knockdown of ERK1 and ERK2 using a combination with IGFBP5 siRNA in P2 MEFs.”

Upon further analysis of ERK1/2’s role in IGFBP5-knockdown cells, the team found that the silencing of ERK2, and not ERK1, blocked the increase in the number of SA-β-GAL-positive cells. ERK2 knockdown attenuated the reduction in the cell number and upregulation of p16 and p21 in IGFBP5-knockdown cells. This study provides evidence that downregulation of IGFBP5 contributes to replicative senescence via ERK2 activation in mouse embryonic fibroblasts.

Conclusion

For the first time, the role of IGFBP5 in replicative senescence was demonstrated in MEFs. Their findings suggest that ERK2 underlies cellular senescence induced by IGFBP5 downregulation. Cellular senescence appears to be a complex process with many moving parts. While more research is needed to fully understand the role of IGFBP5 in replicative senescence, this study provides new insights into the underlying mechanisms involved in this complex process.

“In conclusion, the results of the present study demonstrated that downregulation of IGFBP5 during serial passage contributes to replicative senescence via an ERK2-dependent mechanism (Figure 6). The results suggest that IGFBP5 counteracts replicative senescence in MEFs.”

Figure 6. Schematic summary of our findings. MEFs at early passage secrete certain levels of IGFBP5. Secreted IGFBP5 proteins inhibit MEK/ERK2 by attenuating their phosphorylation (P) in the neighboring cell, leading to suppression of cellular senescence. IGFBP5 secretion is decreased during serial passage, causing activation of ERK2 and cellular senescence.
Figure 6. Schematic summary of our findings. MEFs at early passage secrete certain levels of IGFBP5. Secreted IGFBP5 proteins inhibit MEK/ERK2 by attenuating their phosphorylation (P) in the neighboring cell, leading to suppression of cellular senescence. IGFBP5 secretion is decreased during serial passage, causing activation of ERK2 and cellular senescence.

Click here to read the full research paper published by Aging (Aging-US).

AGING (AGING-US) VIDEOS: YouTube | LabTube | Aging-US.com

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Aging (Aging-US) is an open-access journal that publishes research papers bi-monthly in all fields of aging research. These papers are available at no cost to readers on Aging-us.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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Trending With Impact: A New Marker of Aging and Cellular Senescence

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Researchers from the Campisi Lab discovered new insights while investigating Cdkn1a transcript variants 1 and 2.

Embryonic stem cell colony

The Trending with Impact series highlights Aging publications that attract 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 Aging-US.com.

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The phenomenon in which cells are still metabolically active but can no longer proliferate is known as cellular senescence. Cellular senescence is a normal mechanism in development and tissue homeostasis—and a hallmark of aging.

“Most of my lab works on a process called cellular senescence, which is a cellular response to stresses and damage, many of which increase with age,” Dr. Judy Campisi, Professor at the Buck Institute for Research on Aging and Senior Scientist at the Lawrence Berkeley National Lab, said in a recent Aging interview. 

An international team of researchers from Dr. Campisi’s lab are in search of new biological markers of cellular senescence and aging. Understanding mechanisms of aging such as senescence is key for developing new, safe interventions that may extend human life—with compounding socioeconomic and cultural impacts. Researchers from this lab come from institutions including the Buck Institute, the University of California, Berkeley’s Lawrence Berkeley National Lab, Universidad de Córdoba, Universidad Mayor, Geroscience Center for Brain Health and Metabolism, and Unity Biotechnology. The team published a trending 2021 paper in Aging‘s Volume 13, Issue 10, entitled, “Cdkn1a transcript variant 2 is a marker of aging and cellular senescence.” 

“Our results are, to our knowledge, the first to study Ckdn1a transcript variants in the context of aging.”

THE STUDY

There are a number of mechanisms that drive cellular senescence. Previously, mRNA and protein coding gene Cdkn1a transcript variant 1 (p21var1) has been better-studied compared to Cdkn1a transcript variant 2 (p21var2). The authors of this paper explain that this is likely because the encoded protein is identical to that encoded by variant 1, and both variants are regulated by p53. However, neither variants have ever before been studied in the context of aging. In this study, the researchers explored the expression levels of both Cdkn1a transcript variants 1 and 2 in the context of cellular senescence using several tissues from aged mice and a cell culture model of mouse cells.

“The stringent cell growth arrest associated with cellular senescence is determined, among other mechanisms, by activities of cyclin-dependent kinase inhibitor proteins p16Ink4a and p21Cip1/Waf1, encoded by the Cdkn2a and Cdkn1a loci, respectively [1].”

Study results showed that both variants are induced during cellular senescence. They showed that p21var1 and p21var2 are equally sensitive to transcriptional upregulation after p53 stabilization. The in vitro models also found that p21var2 is preferentially induced with age.

“In sum, p21var2 expression is consistently elevated with age, in contrast with an absence of age-related change in p21var1 levels.”

The researchers conducted further tests in vivo to examine the expression pattern of p21var2 and their results suggested that the circadian regulation of p21Cip1/Waf1 is driven solely by expression of Cdkn1a transcript variant 1. The team also induced cellular senescence in vivo with doxorubicin and ABT-263 (navitoclax) and evaluated the variants’ expression. These results confirmed their in vitro findings that p21var2 is more prone to cellular senescence than p21var1, thus making it a better marker for assessing the presence of senescent cells in vivo.

CONCLUSION

“We show that, although tissue-specific exceptions may arise, p21var2 but not p21var1 is a better candidate marker of aging and senescence in mice.”

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

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Aging is an open-access journal that publishes research papers monthly in all fields of aging research and other topics. These papers are available to read at no cost to readers on Aging-us.com. Open-access journals offer information that has the potential to benefit our societies from the inside out and may be shared with friends, neighbors, colleagues, and other researchers, far and wide.

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2021 Ride for Roswell
2021 Ride for Roswell
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Behind the Study: COVID-19 and Chronological Aging

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Dr. Michael P. Lisanti from The University of Salford describes his 2020 paper published by Aging, entitled, “COVID-19 and chronological aging: senolytics and other anti-aging drugs for the treatment or prevention of corona virus infection?“

Researchers explain their studies that were published in Aging

Behind the Study is a series of transcribed videos from researchers elaborating on their recent oncology-focused studies published by Aging. A new Behind the Study is released each Monday. Visit the Aging YouTube channel for more insights from outstanding authors.

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Hi, I’m professor Michael Lisanti and I’m the Chair of Translational Medicine at the University of Salford, and today I want to talk about our new prospective article, which links COVID-19 and chronological aging, and is focused on potential treatments and prevention strategies. I got interested in this topic because there seems to be an association between COVID-19 fatalities and aging, especially in patients with advanced chronological age. Patients over 65, and their 70s and 80s, are more likely to have increased morbidity and mortality. And so, I thought there may be a link there, between aging and senescence and the viral replication, as well as the potential therapy.

What I’d like to highlight about this particular article is that it proposes potential treatment strategies as well as prevention strategies. The reason is because it appears that this disease, the virus itself, may target senescent cells and senescent cells have been rewired to increase protein synthesis and also to increase the secretion of inflammatory mediators, which is known as the SASP, the senescence-associated secretory phenotype.

And so, one idea would be to use drugs that are senolytics. Senolytics are drugs that target and lyse senescent cells, but also to use protein synthesis inhibitors. The reason is because proteins synthesis inhibitors and senolytic drugs would prevent viral replication, which would reduce viral transmission. And so this could be used as a preventative strategy. I’ll just give you a couple of examples. If you have a drug which is an FDA-approved protein synthesis inhibitor, it should inhibit the secretion of inflammatory mediators, like IL-6. It should inhibit the fibrosis by preventing the secretion and production of collagen. And most importantly, the virus is also made of protein, so if you have a protein synthesis inhibitor, it will also inhibit viral replication.

Figure 1. What is the relationship between COVID-19 and advanced chronological age?
Figure 1. What is the relationship between COVID-19 and advanced chronological age?

There are three drugs I’d like to mention in particular. One is azithromycin, which is a senolytic. The others are also protein synthesis inhibitors, like doxycycline and rapamycin. All three have been shown to reduce IL-6 production because of their inhibition of protein synthesis activity. And also, all three of them have been shown to inhibit viral replication, not specifically of COVID 19, but since this effect on protein synthesis is a generalized effect, it should work for any virus. For example, azithromycin has been shown to inhibit the replication of Zika virus and Ebola virus, doxycycline has been shown to inhibit the replication of dengue virus, and rapamycin, which is another protein synthesis inhibitor with anti-aging properties, has been shown to inhibit replication of the HIV virus.

So, it seems to me that it’s a no-brainer that we should be repurposing FDA-approved drugs that are protein synthesis inhibitors, both for prevention, to prevent the inflammation fibrosis that’s occurring that’s killing people with COVID-19, and also to prevent the contagion by inhibiting viral replication. So I think this could provide a very inexpensive way forward because drugs like doxycyclin are only less than 10 cents a day, and could be used, as I said, for both prophylaxis and treatment. But, I think we need to use it early in the disease to prevent the fibrosis and inflammation, which makes them long, very inflexible and unable to expand and contract, and leads them to a fibrotic lung disease, which prevents patient recovery and could explain lethality of the disease.

I would like to directly engage with people to pick this up, to bring this forward as potential clinical trials. These clinical trials could be done directly in healthcare workers because they are the most vulnerable. In addition, they could be done in patients with advanced chronological age, or even with patients that are asymptomatic, that have been identified as the virus-positive. And it would be like a window trial where you would do viral titers first, and then you would give the drug and then you could also look at the viral titers after administering the drugs. So this would be a very easy, straightforward trial.

All the diagnostic tools for COVID-19 have already been identified and perfected, so all we need to do is interject FDA-approved drugs, which are protein synthesis inhibitors, to look at the eradication, the virus. So this would also be a very inexpensive clinical trial. But I would like to engage with infectious disease experts and virologists to help facilitate. Thank you.

Of course, I would like to thank two foundations which have supported our work: The Fox Point Foundation in Canada and The Healthy Life Foundation in the UK for providing the equipment and infrastructure at the University of Salford.

Click here to read the full paper, published by Aging.

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Aging is an open-access journal that publishes research papers monthly in all fields of aging research and other topics. These papers are available to read at no cost to readers on Aging-us.com. Open-access journals offer information that has the potential to benefit our societies from the inside out and may be shared with friends, neighbors, colleagues, and other researchers, far and wide.

For media inquiries, please contact [email protected].

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