Intrinsic Tumor Research Articles

Metabolism/Immunity Dual-Regulation Thermogels Potentiating Immunotherapy of Glioblastoma Through Lactate-Excretion Inhibition and PD-1/PD-L1 Blockade.

Intrinsic immunosuppressive tumor microenvironment (ITM) and insufficient tumor infiltration of T cells severely impede the progress of glioblastoma (GBM) immunotherapy. In this study, it is identify that inhibiting the expression of glucose transporter 1 (GLUT1) can facilitate the prevention of lactate excretion from tumor glycolysis, which significantly alleviates the lactate-driven ITM by reducing immunosuppressive tumor-associated macrophages (TAMs) and regulatory T cells (Tregs). Simultaneously, the findings show that the generated inflammatory cytokine IFN-γ during immune activation aggravates the immune escape by upregulating immune checkpoint programmed death-ligand 1 (PD-L1) in tumor cells and TAMs. Therefore, an injectable thermogel loaded with a GLUT1 inhibitor BAY-876 and a PD-1/PD-L1 blocker BMS-1 (Gel@B-B) for dual-regulation of metabolism and immunity of GBM is developed. Consequently, in situ injection of Gel@B-B significantly delays tumor growth and prolongs the survival of the orthotopic GBM mouse model. By actively exposing tumor antigens to antigen-presenting cells, the GBM vaccine combined with Gel@B-B is found to significantly increase the fraction of effector T cells (Th1/CTLs) in the tumor microenvironment, thereby remarkably mitigating tumor recurrence long-term. This study may provide a promising strategy for GBM immunotherapy.

Clinicopathological and Genomic Identification of Breast Cancers with No Impact on Mortality.

Implementing mammogram screening means that clinicians are seeing many breast cancers that will never develop metastases. The purpose of this study was to identify subgroups of breast cancer patients who did not present events related to long-term breast cancer mortality, taking into account diagnosis at breast screening, absence of palpability and axillary involvement, and genomic analysis with PAM50. To identify them, a retrospective observational study was carried out selecting patients without any palpable tumor and without axillary involvement, and a genomic analysis was performed with PAM50. The probability of distant metastasis-free interval (DMFI) of 337 patients was 0.92 (95% CI, 0.90-0.93) at 20 years and 0.96 (95% CI, 0.92-1.00) in 95 patients (28%) with available PAM50 tests. In 22 (23.15%) luminal A tumors and in 9 (9.47%) luminal B tumors smaller than 1 cm, and in HER2 and basal type tumors, there were no metastatic events (20-year DMFI of 1.00). Patients with nonpalpable breast cancer found at screening with negative nodes are at very low risk. It is possible to identify subgroups without metastatic events by determining the intrinsic subtype and tumor size less than 1 cm. Therefore, de-escalation of treatment should be considered.

Image-guided biopsy of intracranial lesions in children, with a small robotic device: a case series.

Robot-assisted biopsies have gained popularity in the last years. Most robotic procedures are performed with a floor-based robotic arm. Recently, Medtronic Stealth Autoguide, a miniaturized robotic arm that work together with an optical neuronavigation system, was launched. Its application in pediatric cases is relatively unexplored. In this study, we retrospectively report our experience using the Stealth Autoguide, for frameless stereotactic biopsies in pediatric patients. Pediatric patients who underwent stereotactic biopsy using the Stealth Autoguide cranial robotic platform from July 2020 to May 2023 were included in this study. Clinical, neuroradiological, surgical, and histological data were collected and analyzed. Nineteen patients underwent 20 procedures (mean age was 9-year-old, range 1-17). In four patients, biopsy was part of a more complex surgical procedure (laser interstitial thermal therapy - LITT). The most common indication was diffuse intrinsic brain stem tumor, followed by diffuse supratentorial tumor. Nine procedures were performed in prone position, eight in supine position, and three in lateral position. Facial surface registration was adopted in six procedures, skull-fixed fiducials in 14. The biopsy diagnostic tissue acquisition rate was 100% in the patients who underwent only biopsy, while in the biopsy/LITT group, one case was not diagnostic. No patients developed clinically relevant postoperative complications. The Stealth Autoguide system has proven to be safe, diagnostic, and highly accurate in performing stereotactic biopsies for both supratentorial and infratentorial lesions in the pediatric population.

Abstract B015: CCDC80 as a novel cell intrinsic tumor suppressor protein in high grade serous ovarian cancer

Abstract B015: CCDC80 as a novel cell intrinsic tumor suppressor protein in high grade serous ovarian cancer

Pelvic Diameter is not Associated with Positive Circumferential Resection Margin in Rectal Cancer: Retrospective Analysis of 78 Cases

Abstract Objective To identify if there is an association between pelvic entry and pelvic outlet diameters with increased positive circumferential resection margin (CRM) in rectal cancer. Introduction Positive CRM in rectal cancer is a major predictor for local and distant recurrence. Pelvic diameters may be related to the difficulty of dissection, as well as intrinsic tumor characteristics such as tumor size, location, distance from the anal margin, and T stage, which may compromise the integrity of the mesorectum and circumferential margin involvement. Methods A retrospective review of the patient's medical records who underwent surgical resection of rectal adenocarcinoma from January 2012 to June 2022 was performed. The patient's preoperative staging, operative characteristics, and histopathologic outcomes were gathered from the medical records. Preoperative MRI scanning was done in all patients. MRI pelvimetry was done by two observers. CRM involvement was recorded as stated in the pathology report. Pelvimetry variables were dichotomized according to their mean values for correlation analysis. The odds ratio (OR) was calculated from a binary logistics regression model to assess the relation between the positive CRM and the independent variables. Results A total of 78 patients were included in this study. A positive CRM was reported in 10 patients (12.8%). BMI >27.4 + 6.6 (p = 0.02), positive extramural vascular invasion (p = 0.027), positive CRM by MRI scanning (p = 0.004), and anal sphincter involvement (p = 0.03) were associated with positive CRM. Pelvimetry values were not associated with a positive CRM. Conclusion No association was found between the pelvic diameters measured by MRI pelvimetry with a positive CRM.

Immunological subtyping of salivary gland cancer identifies histological origin-specific tumor immune microenvironment

Gene expression analysis enhances proper cancer subtyping, a better understanding of the molecular characteristics of cancer, and strategies for precision medicine. However, salivary gland cancer (SGC) subtyping remains largely unexplored because of its rarity and diverse histopathological and immunological characteristics. This study aimed to determine whether the histological origin and immunological characteristics of SGC subtypes are intrinsic tumor immunity factors. We performed immune profiling of 94 RNA-seq of SGC tissues and found that the SGCs that originated from the excretory duct (ED), such as the salivary duct and mucoepidermoid carcinomas, exhibit higher immunity than those from the intercalated duct (ID), such as the adenoid cystic and myoepithelial carcinomas, based on the computationally predicted immune score (p < 0.001), immune cell enrichment in the tumor immune microenvironment (TIME) (p < 0.001), T-cell receptor diversity (p < 0.001), and expression of signal I (major histocompatibility complex, MHC, p < 0.001) and signal II (co-stimulatory, p < 0.001 and co-inhibitory, p < 0.001) genes. Further analysis revealed that tolerogenic dendritic cell-induced dysfunctional T-cell populations and T-cell exclusion in the TIME are the major immune evasive mechanisms of the ED-and ID-derived SGCs, respectively.

Abstract B003: Advancing biomarker discovery using a novel window of opportunity (WOO) trial for pancreatic ductal adenocarcinoma: Trial updates

Abstract Background: There are a growing number of targeted agents that have the potential to greatly improve the clinical outcomes of patients with PDAC beyond current standard of care chemotherapy. However, there is a lack in our understanding of which patients and intrinsic PDAC tumor types will best respond to a given targeted agent(s). In order to optimizing their clinical utility, it is crucial that we a deep understanding of the biological impact that these targeted agents (alone or combination) have within the human system. As such, we designed and implemented the WOO trial to provide a highly adaptable discovery platform for the preliminary assessment of biological activity of one or more targeted agents in patients with PDAC. Utilizing paired, pre- and on-treatment biopsies, along with a robust multiomics pipeline, the WOO trial enables independent assessment of the biological impact of targeted agent(s) on key signaling pathways that can be used to explore novel therapeutic strategies. Methods: WOO is a multi-arm early phase I trial platform designed to assess the pharmacodynamic (PD) effects of one or more study agent(s) alone or in combination in patients with PDAC. A Master Protocol is used to describe overarching design and logistics, and sub-protocols separately describe each study arm comprising the different investigational agent(s). Each participants undergoes a baseline tumor biopsy, then receives their assigned study agent(s) for a specified timeframe (not exceeding 30 days), before undergoing a repeated tumor biopsy, after which they continue to receive therapy per standard of care or clinical trials. Spatially-resolved, single cell multiplex assays are used to compare the effects of the study agent(s) on tumor cell state and heterogeneity between the paired samples. The primary study objective is to independently assess the PD feasibility of detecting a measurable change in tumor biology at post-treatment from baseline for participants within a study arm. The WOO trial uses a 2-stage Bayesian efficacy monitoring approach with a futility-stopping rule for each study arm. In stage 1 of each study arm, if 6 or more of the first 10 participants have a detectable change in tumor biology measurements (i.e., pre vs. post-treatment), then the study arm may continue to enroll an additional 10 participants. To date, 4 study arms are being evaluated: 1) poly (ADP-ribose) polymerase inhibitor (PARPi), olaparib (300 mg PO BID for 10 days), 2) MEK inhibitor (MEKi), cobimetinib (60 mg PO QD for 10 days), 3) ERK inhibitor, LY3214996 (400 mg PO QD for 10 days), and 4) PLK1 inhibitor, onvansertib (12 mg/m2 PO QD for 10 days). To date, a total of 34 participants have been enrolled and treated: n = 14 cobimetinib, n= 15 olaparib, n=2 onvansertib. Future arms to be added. Trial ID: NCT04005690. Citation Format: Charles D. Lopez, Adel Kardosh, Emerson Chen, Guillame Pegna, Alexander Guimaraes, Bryan Foster, Brian Brinkerhoff, Shaun M. Goodyear, Erin Taber, Brindha Rajagopalan, Johnson Vo, Kiara Siex, Brett Johnson, Danielle Galipeau, Dove Keith, Brett Sheppard, Brody Jonathan, Rosalie Sears, Gordon Mills. Advancing biomarker discovery using a novel window of opportunity (WOO) trial for pancreatic ductal adenocarcinoma: Trial updates [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B003.

From complexity to clarity: unravelling tumor heterogeneity through the lens of tumor microenvironment for innovative cancer therapy.

Despite the tremendous clinical successes recorded in the landscape of cancer therapy, tumor heterogeneity remains a formidable challenge to successful cancer treatment. In recent years, the emergence of high-throughput technologies has advanced our understanding of the variables influencing tumor heterogeneity beyond intrinsic tumor characteristics. Emerging knowledge shows that drivers of tumor heterogeneity are not only intrinsic to cancer cells but can also emanate from their microenvironment, which significantly favors tumor progression and impairs therapeutic response. Although much has been explored to understand the fundamentals of the influence of innate tumor factors on cancer diversity, the roles of the tumor microenvironment (TME) are oftenundervalued. It is therefore imperative that a clear understanding of the interactions between the TME and other tumor intrinsic factors underlying the plastic molecular behaviors of cancers be identified to develop patient-specific treatment strategies. This review highlights the roles of the TME as an emerging factor in tumor heterogeneity. More particularly, we discuss the role of the TME in the context of tumor heterogeneity and explore the cutting-edge diagnostic and therapeutic approaches that could be used to resolve this recurring clinical conundrum. We conclude by speculating onexciting research questions that can advance our understanding of tumor heterogeneity with the goal of developing customized therapeutic solutions.

Sleep apnoea increases biomarkers of immune evasion, lymphangiogenesis and tumour cell aggressiveness in high-risk patients and those with established lung cancer.

Intermittent hypoxaemia and obstructive sleep apnoea (OSA) have been linked to lung cancer through as yet unidentified pathophysiological mechanisms. This study evaluates the effect of OSA on serum levels of biomarkers of immunosurveillance, lymphangiogenesis and intrinsic tumour cell aggressiveness in high-risk individuals screened for lung cancer and patients with established lung cancer. Serum samples from individuals participating in a lung cancer screening cohort (SAILS study) or with newly diagnosed lung cancer (SAIL study) were analysed. All patients underwent home sleep apnoea testing. Soluble levels of programmed cell death-1 (PD-1), programmed cell death ligand-1 (PD-L1), cytotoxic T-lymphocyte antigen-4, midkine (MDK), paraspeckle component-1 (PSPC1), transforming growth factor-β1 (TGF-β1), SMAD3, matrix metalloproteinase-2 and co-stimulus receptor of the tumour necrosis factor family of receptors (CD137) were determined by ELISA. The presence of moderate-to-severe OSA was associated with increased levels of PSPC1, MDK, PD-L1 and PD-1 in screened individuals, and with higher values of PSPC1, TGF-β1, PD-L1 and PD-1 in patients with established lung cancer. The findings correlated with nocturnal intermittent hypoxaemia indices. Moderate-to-severe OSA is associated with increased expression of serum biomarkers of immune evasion, lymphangiogenesis and tumour cell aggressiveness in high-risk individuals screened for lung cancer and those with established disease.

The role of extracellular vesicles in cancer.

Extracellular vesicles (EVs), which include small EVs such as exosomes, play a critical role in intercellular communication and are produced by both cancer and non-cancer cells. Several studies have shown that cancer cells exploit various strategies to regulate the biogenesis, composition, and functions of EVs primarily to promote cancer progression. Given that exosomes originate from major sorting hubs at the limiting membrane of endosomes, they are central to a signaling network that connects external stimuli with intrinsic tumor cell features. Exosomes contain diverse repertoires of molecular cargos, such as proteins, lipids, and nucleic acids, which determine their heterogeneity and functional properties in cancer progression. Therefore, targeting exosome biogenesis will enhance our understanding of tumorigenesis and also promote the discovery of novel approaches for cancer therapy. In this chapter we summarize the machinery of exosome biogenesis and the local, distant, and systemic effects of exosomes released by cancer cells. Furthermore, we explore how these exosomes regulate the anti-tumor immune response and epigenetic mechanisms to sustain cancer progression and their implications in cancer prevention and treatment.

Presence of crown-like structures in breast adipose tissue; differences between healthy controls, BRCA1/2 gene mutation carriers and breast cancer patients.

Crown-like structures (CLS) in breast adipose tissue are associated with inflammation and a potential factor in breast cancer behaviour. Whether this effect varies between breast cancer subtypes and is influenced by BMI and BRCA mutation status is presently unknown. Therefore, we compared CLS presence between adipose tissue of healthy controls, BRCA1/2 gene mutation carriers and breast cancer patients, and assessed the relation of CLS with clinical outcome in breast cancer patients. Immunohistochemical staining for CD68 was performed on breast adipose tissue sections of 48 healthy controls, 78 BRCA1/2 gene mutation carriers and 259 breast cancer patients. CLS presence and index (CLS/cm2) were correlated with BMI, BRCA status, tumour presence, intrinsic tumour subtype and tumour characteristics. Associations with clinical outcome were assessed. CLS were more often present in breast cancer patients compared to BRCA carriers and healthy controls. CLS presence was associated with the presence of breast cancer and high BMI. CLS were more often present in Luminal-B-like tumours compared to the other subtypes. No correlations between CLS and BRCA status or age was found. In TNBC, CLS were related to lymphovascular invasion. No association with survival was found. In conclusion, CLS were more frequently present in breast adipose tissue of breast cancer patients compared to BRCA1/2 gene mutation carriers and healthy controls. Furthermore, our study provides evidence of the association between obesity and presence of CLS. The prognostic significance and impact on clinical outcome of differences in CLS numbers should be further assessed in prospective studies.

Abstract B070: Characterizing breast cancer etiologic subtypes in the Ghana Breast Health Study

Abstract Background: Breast cancer subtyping has largely been based on immunohistochemical markers of estrogen receptor status. However, RNA-based intrinsic subtypes, including luminal (hormone receptor-positive) and non-luminal (hormone receptor-negative) have been shown to be etiologically relevant, with studies also suggesting other tumor markers (e.g., TP53 status) to be important contributors to etiologic heterogeneity. Compared to luminal tumors, non-luminal tumors are more likely to be TP53 mutant than wildtype-like. TP53 mutant breast cancers are associated with more aggressive tumor features and these mutations are more common among cases of African descent. However, few RNA-based subtyping studies have described etiologic heterogeneity in indigenous African populations. Therefore, we evaluated associations between established breast cancer risk factors and risk of PAM50 intrinsic subtypes and tumor subtypes defined by RNA-based TP53 functional status in the population-based Ghana Breast Health Study (GBHS). Methods: We analyzed data from 600 invasive breast cancer cases and 2,528 controls in the GBHS. RNA was extracted from formalin-fixed paraffin-embedded tumor samples and run on the nCounter® Breast Cancer 360™ Panel. Samples were then classified for intrinsic subtype (N=285 luminal, N=315 non-luminal) using a research version of the PAM50 assay and for TP53 functional status (N=333 wildtype-like, N=300 mutant-like) using a validated RNA signature. Odds ratios (OR) and 95% confidence intervals (CI) were estimated for risk factors using polytomous logistic regression models adjusted for potential confounders. Results: About 1 in 4 tumors classified as ER-positive by immunohistochemistry were non-luminal by RNA expression. Similarly, about 1 in 5 ER-negative tumors were reclassified as luminal. Etiologic heterogeneity was observed by luminal subtype for certain reproductive factors. Higher parity (≥3 vs. &amp;lt;3 births) was associated with lower risk of luminal tumors (OR [95% CI] = 0.68 [0.49, 0.92]), but not with non-luminal tumors (0.95 [0.69, 1.30]). Likewise, later age at first birth (≥26 vs. &amp;lt;19 years) was more strongly associated with risk of luminal than non-luminal tumors (2.16 [1.37, 3.40] and 1.30 [0.84, 2.00], respectively). Consistent with previous findings, TP53 status was also an important etiologic factor and risk factor patterns mirrored those for luminal/non-luminal subtypes. Finally, we evaluated cross-classification of these two etiologic markers to identify risk factors that represent the dual action of both an estrogenic and a DNA-repair pathway. Age at first birth seems to suggest dual action. Conclusions: This study used high-quality RNA expression data to show that intrinsic subtype and TP53 status are useful breast tumor markers for describing etiologic heterogeneity, with cross-classification leading to improved understanding of the etiologic underpinnings of certain risk factors. This work has important implications for the use of gene-expression-based subtyping for breast cancer classification in this population. Citation Format: Amber N. Hurson, Ebonee N. Butler, Alina M. Hamilton, Bernard Petershie, Thomas U. Ahearn, Melissa A. Troester, Jonine Figueroa, Nicolas Titiloye, Montserrat Garcia-Closas, Mustapha Abubakar. Characterizing breast cancer etiologic subtypes in the Ghana Breast Health Study [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr B070.

Abstract B004: Molecular crosstalk between NF-κB and NRF2 signaling affects prognosis in HPV-associated head and neck cancer

Abstract The incidence of head and neck squamous cell carcinoma (HNSCC) is on the rise and is expected to increase by 50% by 2030. Around half of the patient population affected are diagnosed when the tumor is at a locally advanced stage. These patients are usually treated with intense radiotherapy, leading to severe side-effects. Precision medicine would revolutionize the treatment of head and neck cancer by accurately identifying patients that are at low risk of recurrence, reduce treatment related side-effects and aid in overall improvement in quality of life of patients after treatment. This generates the need to develop biomarkers to identify patients with less aggressive tumors as candidates for treatment de-escalation. We applied an unbiased approach (weighted gene correlation network analysis (WGCNA)) that allows detection of autocorrelated gene sets on 3 independent cohorts of HPV+ HNSCC and created 22 consensus transcriptional modules by selecting genes that grouped together in WGCNA analyses from all 3 cohorts. Interestingly, only 1 module intrinsically divided HPV+ HNSCC into 2 subtypes, displaying different mutational profiles, mutational signatures, HPV gene expression patterns, HPV integration status, and patient survival. Gene set enrichment analysis revealed that this module was enriched in NF-kB genes and strongly associated with NF-κB signaling, confirming our prior findings that defined HPV+ HNSCC subtypes by presence or absence of NF-kB regulators, TRAF3 or CYLD defects and by the NF-κB activity classifier. We hypothesized that NF-kB-driven intrinsic tumor characteristics contribute to increased sensitivity of NF-kB active HPV+ head and neck tumors to radiation, providing patients survival benefits. Indeed, TRAF3 or CYLD deletion dramatically increased radiation sensitivity of HPV+ head and neck cancer cells. As we began to investigate mechanisms of radiation sensitization associated with TRAF3 and CYLD deletion, we found that activation of NF-κB significantly correlated with marked downregulation of nuclear factor erythroid 2-related factor 2 (NRF2) activity in tumors from 3 independent cohorts, as well as in HPV+ HNSCC cells that harbor constitutively active NF-kB due to deletion of TRAF3 or CYLD. Interestingly, TRAF3 CRISPR KO cells had lower NRF2 protein levels that were restored by MG132 treatment, indicating an involvement of KEAP1/CUL3 mediated proteasomal degradation of NRF2. In summary, our data showcases an inverse correlation between NF-kB and NRF2 pathways in HPV+ HNSCC. Currently, there are no prognostic biomarkers to distinguish patients who require aggressive therapy versus those that are appropriate for reduced intensity treatment. Identification of markers distinguishing the 2 subtypes of HPV+ HNSCC (high NF-kB and low NRF2 activity) may serve as prognostic biomarkers to help clinicians with therapeutic decisions. Citation Format: Aditi Kothari, Travis Schrank, Wendell Yarbrough, Natalia Isaeva. Molecular crosstalk between NF-κB and NRF2 signaling affects prognosis in HPV-associated head and neck cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B004.

Lessons learned from phase 3 trials of immunotherapy for glioblastoma: Time for longitudinal sampling?

Glioblastoma (GBM)'s median overall survival is almost 21 months. Six phase 3 immunotherapy clinical trials have recently been published, yet 5/6 did not meet approval by regulatory bodies. For the sixth, approval is uncertain. Trial failures result from multiple factors, ranging from intrinsic tumor biology to clinical trial design. Understanding the clinical and basic science of these 6 trials is compelled by other immunotherapies reaching the point of advanced phase 3 clinical trial testing. We need to understand more of the science in human GBMs in early trials: the "window of opportunity" design may not be best to understand complex changes brought about by immunotherapeutic perturbations of the GBM microenvironment. The convergence of increased safety of image-guided biopsies with "multi-omics" of small cell numbers now permits longitudinal sampling of tumor and biofluids to dissect the complex temporal changes in the GBM microenvironment as a function of the immunotherapy.

Teratoma pathology and genomics in anti-NMDA receptor encephalitis.

Ovarian teratoma is a common occurrence in patients with anti-NMDA receptor encephalitis (NMDARe), and its removal is crucial for a favorable prognosis. However, the initial pathogenesis of autoimmunity in the encephalitic teratoma remains unclear. In this study, we aimed to investigate the genomic landscape and microscopic findings by comparing NMDARe-associated teratomas and non-encephalitic control teratomas. A prospective consecutive cohort of 84 patients with NMDARe was recruited from January 2014 to April 2020, and among them, patients who received teratoma removal surgery at Seoul National University Hospital were enrolled. We conducted a comparison of whole-exome sequencing data and pathologic findings between NMDARe-associated teratomas and control teratomas. We found 18 NMDARe-associated teratomas from 15 patients and compared them with 17 non-encephalitic control teratomas. Interestingly, the genomic analysis revealed no significant differences in mutations between encephalitic and non-encephalitic teratomas. Pathologic analysis showed no discrepancies in terms of the presence of neuronal tissue and lymphocytic infiltration between the encephalitic teratomas (n = 14) and non-encephalitic teratomas (n = 18). However, rituximab-naïve encephalitic teratomas exhibited a higher frequency of germinal center formation compared to non-encephalitic teratomas (80% vs. 16.7%, P = 0.017). Additionally, rituximab-treated encephalitic teratomas demonstrated a reduced number of CD20+ cells and germinal centers in comparison to rituximab-naïve encephalitic teratomas (P = 0.048 and 0.023, respectively). These results suggest that the initiation of immunopathogenesis in NMDARe-associated teratoma is not primarily attributed to intrinsic tumor mutations, but rather to immune factors present in the encephalitic patient group, ultimately leading to germinal center formation within the teratoma.

Stratification of Multiple Myeloma Patients in the Commpass Study By Single Cell Transcriptomics of Plasma Cells Associates with Clinical Outcome

Introduction: There is substantial variation in the prognosis and response to therapy among multiple myeloma (MM) patients. This diversity is influenced by both intrinsic tumor features and the tumor microenvironment. We hypothesize that the clinical outcomes post IMiD and/or PI are linked to molecular subtypes dictated by tumor sample transcriptomics. We previously showed that molecular subtyping based on the CoMMpass bulk RNAseq data has an association with time to second-line therapy (log rank p = 0.0018; Hamidi et al., Blood 140: 7208-7210). Here, we applied the same molecular subtyping schema to single cell RNAseq isolated plasma cell transcriptomic profiles. Methods: Bone marrow biopsies from newly diagnosed MM patients (N = 200) in the MMRF CoMMpass study (NCT01454297) were collected, enriched by CD138 negative bead selection, and scRNAseq was performed by MMRF Immune Profiling Consortium, a collaboration between MMRF and laboratories at Beth Israel Deaconess Medical Center, Icahn School of Medicine at Mt. Sinai, Mayo Clinic, Washington University in St. Louis, and Emory University. After quality control and unsupervised clustering, plasma cells were subset out and pseudo-bulk expression profiles were generated for baseline samples with more than 100 plasma cells (N = 95). Unsupervised machine learning approach based on consensus non-negative matrix factorization (cNMF) was applied to identify the transcriptomics-based molecular subtypes. A random forest model, built from scRNAseq-based molecular subtypes (scNMF), was applied to bulk RNAseq data with a larger sample size (N = 754) to train a predictive molecular subtyping (pNMF). Potential cell-cell communication events based on scRNAseq were also predicted by LIgand-receptor ANalysis frAmework (LIANA). Results: 705,959 single cells passed the quality control and were broadly annotated as T/NK cells, B cells, plasma cells, myeloid cells, erythroid, progenitor, and stromal cells. Consistent with previous reports, CD138 negative bead selection did not completely remove plasma cells, resulting in an average of 18.5% plasma cells (n = 130,213). Subsequent unsupervised clustering of plasma cells exhibited a patient specific clustering pattern, suggestive of the heterogeneity of these tumor-derived cells. Unsupervised NMF on the pseudo-bulk expressions of baseline plasma cells identified five patient subsets. In the same cohort of patients (N = 95), subtypes assigned by the single cell had a better association with time to second-line therapy ( p-value = 0.0027 in scNMF as compared to p = 0.13 in bulk NMF). The median time to 2nd line of 2,443 days in scNMF5.1 versus 585 days in scNMF5.4; and the median time to 2nd line of 1,597 days in NMF5.2 versus 850 days in NMF5.3. A predicted subtyping based on scRNAseq data (pNMF) had a significantly better association with time to second-line therapy (Figure 1A, log rank p = 0.00088), compared to the published molecular subtyping based on bulk RNAseq (log rank p = 0.0018). The median time to 2nd line of 1,342 days in pNMF5.1 versus 597 days in pNMF5.5; compared to the median time to 2nd line of 1,347 days in NMF5.2 versus 850 days in NMF5.3. The best clinical outcome subset pNMF5.1 was characterized with higher levels of IFN pathways (Figure 1B, Hallmark interferon gamma and alpha pathways Wilcoxon p = 0.003 and p = 0.010, respectively) and higher levels of tumor-promoting inflammatory microenvironment (Hallmarks inflammatory response and TNFα signaling via NF-κB p = 0.003 and p = 0.010, respectively). The worst outcome subset pNMF5.5, on the other hand, displayed higher levels of glycolysis, a promoting factor of tumor development ( p &amp;lt; 0.001). Moreover, the total number of cell-cell interactions between the major cell types differed based on scRNAseq subtypes, informing the underlying biology driving the molecular heterogeneity. We identified a positive feedback loop of CXCL12/CXCR4 signaling between stromal and plasma cells, enhancing tumor cell proliferation. Conclusions: The identification of molecular subtypes based on single-cell data through an innovative unsupervised machine learning approach can have significant implications for determining which NDMM patients are likely to respond to established therapies; and the cellular level resolution allows deconvolution of cell-cell signaling, enhancing our understanding of the underlying molecular biology and mechanisms of resistance.

A weakly supervised NMF method to decipher molecular subtype-related dynamic patterns in breast DCE-MR images

Objective. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is an important imaging modality for breast cancer diagnosis. Intratumoral heterogeneity causes a major challenge in the interpretation of breast DCE-MRI. Previous studies have introduced decomposition methods on DCE-MRI to reveal intratumoral heterogeneity by analyzing distinct dynamic patterns within each tumor. However, these methods estimated the dynamic patterns and their corresponding component coefficients in an unsupervised manner, without considering any clinically relevant information. Approach. To decipher molecular subtype-related dynamic patterns, we propose a weakly supervised nonnegative matrix factorization method (WSNMF), which is able to decompose the pixel kinetics of DCE-MRI with image-level subtype labels. The WSNMF is developed based on a discriminant nonnegative matrix factorization (NMF) to utilize coarse-grained subtype information, in which between- and within-class scatters are defined on the mean vector of component coefficients over all pixels in each tumor, rather than directly on the vector of component coefficients of each pixel. Main results. Experiments demonstrated that the dynamic patterns identified by WSNMF had superior performance in distinguishing between luminal A and the other subtype tumors. The classification performance was evaluated using the area under the receiver operating characteristic curve (AUC). WSNMF yielded better classification performance (AUC = 0.822) than other heterogeneity analysis methods, including two partitioning-based methods (KPC with AUC = 0.697 and TTP with AUC = 0.760) and two unsupervised decomposition-based methods (PCA with AUC = 0.774 and NMF with AUC = 0.797). Significance. Our method adds a valuable new perspective into DCE-MRI decomposition-based heterogeneity analysis by taking advantage of intrinsic tumor characteristics to improve the diagnosis of breast cancer.

Mathematical modeling of radiotherapy: impact of model selection on estimating minimum radiation dose for tumor control.

Radiation therapy (RT) is one of the most common anticancer therapies. Yet, current radiation oncology practice does not adapt RT dose for individual patients, despite wide interpatient variability in radiosensitivity and accompanying treatment response. We have previously shown that mechanistic mathematical modeling of tumor volume dynamics can simulate volumetric response to RT for individual patients and estimation personalized RT dose for optimal tumor volume reduction. However, understanding the implications of the choice of the underlying RT response model is critical when calculating personalized RT dose. In this study, we evaluate the mathematical implications and biological effects of 2 models of RT response on dose personalization: (1) cytotoxicity to cancer cells that lead to direct tumor volume reduction (DVR) and (2) radiation responses to the tumor microenvironment that lead to tumor carrying capacity reduction (CCR) and subsequent tumor shrinkage. Tumor growth was simulated as logistic growth with pre-treatment dynamics being described in the proliferation saturation index (PSI). The effect of RT was simulated according to each respective model for a standard schedule of fractionated RT with 2 Gy weekday fractions. Parameter sweeps were evaluated for the intrinsic tumor growth rate and the radiosensitivity parameter for both models to observe the qualitative impact of each model parameter. We then calculated the minimum RT dose required for locoregional tumor control (LRC) across all combinations of the full range of radiosensitvity and proliferation saturation values. Both models estimate that patients with higher radiosensitivity will require a lower RT dose to achieve LRC. However, the two models make opposite estimates on the impact of PSI on the minimum RT dose for LRC: the DVR model estimates that tumors with higher PSI values will require a higher RT dose to achieve LRC, while the CCR model estimates that higher PSI values will require a lower RT dose to achieve LRC. Ultimately, these results show the importance of understanding which model best describes tumor growth and treatment response in a particular setting, before using any such model to make estimates for personalized treatment recommendations.

Intracellular Salmonella delivery of an exogenous immunization antigen refocuses CD8 T cells against cancer cells, eliminates pancreatic tumors and forms antitumor immunity.

Immunotherapies have shown great promise, but are not effective for all tumors types and are effective in less than 3% of patients with pancreatic ductal adenocarcinomas (PDAC). To make an immune treatment that is effective for more cancer patients and those with PDAC specifically, we genetically engineered Salmonella to deliver exogenous antigens directly into the cytoplasm of tumor cells. We hypothesized that intracellular delivery of an exogenous immunization antigen would activate antigen-specific CD8 T cells and reduce tumors in immunized mice. To test this hypothesis, we administered intracellular delivering (ID) Salmonella that deliver ovalbumin as a model antigen into tumor-bearing, ovalbumin-vaccinated mice. ID Salmonella delivers antigens by autonomously lysing in cells after the induction of cell invasion. We showed that the delivered ovalbumin disperses throughout the cytoplasm of cells in culture and in tumors. This delivery into the cytoplasm is essential for antigen cross-presentation. We showed that co-culture of ovalbumin-recipient cancer cells with ovalbumin-specific CD8 T cells triggered a cytotoxic T cell response. After the adoptive transfer of OT-I CD8 T cells, intracellular delivery of ovalbumin reduced tumor growth and eliminated tumors. This effect was dependent on the presence of the ovalbumin-specific T cells. Following vaccination with the exogenous antigen in mice, intracellular delivery of the antigen cleared 43% of established KPC pancreatic tumors, increased survival, and prevented tumor re-implantation. This response in the immunosuppressive KPC model demonstrates the potential to treat tumors that do not respond to checkpoint inhibitors, and the response to re-challenge indicates that new immunity was established against intrinsic tumor antigens. In the clinic, ID Salmonella could be used to deliver a protein antigen from a childhood immunization to refocus pre-existing T cell immunity against tumors. As an off-the-shelf immunotherapy, this bacterial system has the potential to be effective in a broad range of cancer patients.

Immunohistochemical expression of SOX2 in OKC and ameloblastoma: A comparative study.

Odontogenic, non-inflammatory maxillofacial cysts and tumours vary greatly in their ability to grow and cause local tissue destruction. Despite their common embryologic origin, the biologic mechanisms responsible for this diverse array of clinical behaviour are largely unknown. Unfortunately, even with accurate tissue diagnosis and appropriate surgical management, these tumours have relatively high recurrence rates. While this may be related to surgical technique, it may also be due to intrinsic tumour biology. SOX2 is differentially expressed in odontogenic cysts and tumours, which has an impact over patient prognosis. This could be related to their diverse cells of origin or stages of histogenesis. SOX2 is expressed in OKC and ameloblastoma, and in this study, we look forward to find altered levels and intensity of SOX2 in the above-mentioned lesions. To profile the expression of SOX2 in odontogenic keratocyst (OKC) and ameloblastomaTo compare the intensity of these lesions, analyse their intrinsic feature and predict their recurrence. Histopathologically diagnosed cases of OKC and ameloblastoma will be selected (n = 40). Paraffin-embedded, formalin-fixed sections of these lesions will be stained for SOX2 marker using a standard immunohistochemical technique. Positive control will be taken as oral squamous cell carcinoma and negative control will be taken as normal oral mucosa. A comparison between the stained cell types in odontogenic keratocyst and ameloblastoma revealed statistically significant differences. The immunoreactivity scores of SOX2 were analysed in both groups. The results indicated that 45% of OKC cases exhibited strongly positive reactivity, while 65% of ameloblastoma cases were negative. Statistical analysis demonstrated highly significant differences in the frequency of SOX2 expression between the two groups, with a higher frequency of negative expression in ameloblastoma. Stem cell markers have been observed in these lesions, suggesting the acquisition of stem-like properties by tumour cells, which can affect patient prognosis. Specifically, the marker SOX2 shows differential expression in odontogenic cysts and tumours. High expression of SOX2 in OKC indicates the presence of stem cells with significant self-renewal and proliferative properties, potentially signifying neoplastic behaviour. In contrast, weak or absent expression of SOX2 in ameloblastoma suggests different molecular pathways involved in its neoplastic behaviour.