GENOMIC AND TRANSCRIPTOMIC LANDSCAPE OF COLORECTAL PREMALIGNANCY

Colorectal cancer (CRC) is the third most commonly diagnosed cancer among men and women in the United States, with 3 to 5 percent of the cases diagnosed in the background of a hereditary form of the disease. Biologically, CRC is divided into two groups: microsatellite instable (MSI) and chromosomally unstable (CIN). Genomic and transcriptomic characterization of CRC has emerged from large-scale studies in recent years due to the advancement of next-generation sequencing technologies. These studies have identified key genes and pathways altered in CRC and provided insights to the discovery of therapeutic targets. Despite the wealth of knowledge acquired in the carcinoma stage, there have been insufficient efforts to systematically characterize premalignant lesions at the molecular level, which could lead to a better understanding of neoplastic initiation, risk prediction, and the development of targeted chemoprevention strategies. The challenge in characterizing premalignancy has always been the limited availability of sample material. This challenge is tackled by getting more samples, integrating public datasets, deploying better technology that use less amount of nucleic acids and in-silico tools to extract multi-layer information from the same experiment. My genomic study consisted of whole exome sequencing (WES) and high-depth targeted sequencing on 80 premalignant lesions bulk tissue and crypts to assess clonality and mutational heterogeneity. WES results showed the presence of multiple clone in premalignancy based on clustering somatic mutation allele frequency. In addition, I determined that multiple clones originate from independent crypts harboring distinct APC and KRAS alterations. In my second study, I performed immune expression profiling and assessment of mutation and neoantigen rate of 28 premalignant lesions with DNA mismatch repair (MMR) deficient and proficient background using RNAseq. My results showed an activated immune profile despite low mutational and neoantigen rate, which challenges the canonical view in MMR-deficient carcinoma stage that immune activation is largely due to high mutation and neoantigen rate. In the last study, I performed transcriptomic sub-classifications of 398 premalignant lesions that associate them with different carcinomas subtypes, and clinical and histopathological features. My results revealed two major findings: prominent immune activation and WNT and MYC activation in premalignancy. In summary, my large-scale genomic and transcriptomic analyses of colorectal adenomas have identified key molecular characteristics in early colorectal tumorigenesis and provide a foundation for discovering novel preventive strategies

High-Throughput Drug Screening Identifies a Potent Wnt Inhibitor that Promotes Airway Basal Stem Cell Homeostasis.

Mechanisms underpinning airway epithelial homeostatic maintenance and ways to prevent its dysregulation remain elusive. Herein, we identify that β-catenin phosphorylated at Y489 (p-β-cateninY489) emerges during human squamous lung cancer progression. This led us to develop a model of airway basal stem cell (ABSC) hyperproliferation by driving Wnt/β-catenin signaling, resulting in a morphology that resembles premalignant lesions and loss of ciliated cell differentiation. To identify small molecules that could reverse this process, we performed a high-throughput drug screen for inhibitors of Wnt/β-catenin signaling. Our studies unveil Wnt inhibitor compound 1 (WIC1), which suppresses T-cell factor/lymphoid enhancer-binding factor (TCF/LEF) activity, reduces ABSC proliferation, induces ciliated cell differentiation, and decreases nuclear p-β-cateninY489. Collectively, our work elucidates a dysregulated Wnt/p-β-cateninY489 axis in lung premalignancy that can be modeled in vitro and identifies a Wnt/β-catenin inhibitor that promotes airway homeostasis. WIC1 may therefore serve as a tool compound in regenerative medicine studies with implications for restoring normal airway homeostasis after injury

Accuracy of cytological examination of Tao brush endometrial sampling in diagnosing endometrial premalignancy and malignancy

Although Tao brush has become one of the most studied and used endometrial cytological samplers, concerns remain about the adequacy of the cytological sample compared with definitive histology. We aimed to assess accuracy of cytological examination from Tao brush sampling in diagnosing endometrial premalignancy and malignancy through a systematic review and meta-analysis. Seven electronic databases were searched from January 2000 to July 2021 for all studies which allowed assessment of accuracy of Tao brush in diagnosing endometrial premalignancy and malignancy. We calculated sensitivity, specificity, positive and negative likelihood ratios (LR+ and LR−), diagnostic odds ratio (DOR) and area under the curve (AUC) on summary receiver operating characteristic (SROC) curve. Five studies with 774 patients were included. In diagnosing endometrial premalignancy and malignancy, cytological examination from Tao brush endometrial sampling showed pooled sensitivity of 0.95 (95% CI, 0.90–0.98), specificity of 0.92 (95% CI, 0.90–0.94), LR+ of 12.73 (95% CI, 3.94–41.18), LR− of 0.09 (95% CI, 0.05–0.18), DOR of 184.84 (95% CI, 24.37–1401.79), AUC of 0.9757 (standard error: 0.013). In conclusion, cytological examination from Tao brush seems to have a high diagnostic accuracy and might be proposed as both screening and diagnostic tool. However, further studies are necessary to confirm these findings

STING expression and response to treatment with STING ligands in premalignant and malignant disease.

Human papilloma virus positive (HPV+) tumors represent a large proportion of anal, vulvar, vaginal, cervical and head and neck squamous carcinomas (HNSCC) and late stage invasive disease is thought to originate from a premalignant state. Cyclic dinucleotides that activate STimulator of INterferon Genes (STING) have been shown to cause rapid regression of a range of advanced tumors. We aimed to investigate STING ligands as a novel treatment for papilloma. We tested therapies in a spontaneous mouse model of papilloma of the face and anogenital region that histologically resembles human HPV-associated papilloma. We demonstrate that STING ligands cause rapid regression of papilloma, associated with T cell infiltration, and are significantly more effective than Imiquimod, a current immunotherapy for papilloma. In humans, we show that STING is expressed in the basal layer of normal skin and lost during keratinocyte differentiation. We found STING was expressed in all HPV-associated cervical and anal dysplasia and was strongly expressed in the cancer cells of HPV+ HNSCC but not in HPV-unrelated HNSCC. We found no strong association between STING expression and progressive disease in non-HPV oral dysplasia and oral pre-malignancies that are not HPV-related. These data demonstrate that STING is expressed in basal cells of the skin and is retained in HPV+ pre-malignancies and advanced cancers, but not in HPV-unrelated HNSCC. However, using a murine HNSCC model that does not express STING, we demonstrate that STING ligands are an effective therapy regardless of expression of STING by the cancer cells

FOXM1 coming of age: time for translation into clinical benefits?

A decade since the first evidence implicating the cell cycle transcription factor Forkhead Box M1 (FOXM1) in human tumorigenesis, a slew of subsequent studies revealed an oncogenic role of FOXM1 in the majority of human cancers including oral, nasopharynx, oropharynx, esophagus, breast, ovary, prostate, lung, liver, pancreas, kidney, colon, brain, cervix, thyroid, bladder, uterus, testis, stomach, skin, and blood. Its aberrant upregulation in almost all different cancer types suggests a fundamental role for FOXM1 in tumorigenesis. Its dose-dependent expression pattern correlated well with tumor progression starting from cancer predisposition and initiation, early premalignancy and progression, to metastatic invasion. In addition, emerging studies have demonstrated a causal link between FOXM1 and chemotherapeutic drug resistance. Despite the well-established multifaceted roles for FOXM1 in all stages of oncogenesis, its translation into clinical benefit is yet to materialize. In this contribution, I reviewed and discussed how our current knowledge on the oncogenic mechanisms of FOXM1 could be exploited for clinical use as biomarker for risk prediction, early cancer screening, molecular diagnostics/prognostics, and/or companion diagnostics for personalized cancer therapy

Frequent and specific immunity to the embryonal stem cell–associated antigen SOX2 in patients with monoclonal gammopathy

Specific targets of cellular immunity in human premalignancy are largely unknown. Monoclonal gammopathy of undetermined significance (MGUS) represents a precursor lesion to myeloma (MM). We show that antigenic targets of spontaneous immunity in MGUS differ from MM. MGUS patients frequently mount a humoral and cellular immune response against SOX2, a gene critical for self-renewal in embryonal stem cells. Intranuclear expression of SOX2 marks the clonogenic CD138− compartment in MGUS. SOX2 expression is also detected in a proportion of CD138+ cells in MM patients. However, these patients lack anti-SOX2 immunity. Cellular immunity to SOX2 inhibits the clonogenic growth of MGUS cells in vitro. Detection of anti-SOX2 T cells predicts favorable clinical outcome in patients with asymptomatic plasmaproliferative disorders. Harnessing immunity to antigens expressed by tumor progenitor cells may be critical for prevention and therapy of human cancer

The pathologists’ eyes on foregut: histopathological relations in the experimental and routine diagnostics

SUMMARY I. The study aimed to investigate the incidence of duodeno-gastroesophageal reflux-induced malignoma formation in a series of duodeno-esophageal anastomosis operations in rats. This surgical method provided a model for the reflux-induced esophageal pathologies, without carcinogen administration. 30 weeks of duodeno-gastroesophageal reflux disease significantly increased the risk of the development of BE, and reflux-induced EAC formation was evident in 4 animals. In one of these particular cases, a superficial squamous cell cancer was noted in close vicinity to the adenocarcinoma formation. The results of the applied rat model afford evidence of the simultaneous activation of more than one possible carcinogenetic pathway in experimental GERD. Synchronous neoplasm formation with different growth pattern characteristics is a rarity in humans, and this phenomenon suggests that the presented model is a suitable means of mimicking the whole spectrum of human GERD pathology. II/1. The study aimed to carry out standardized histopathological analysis focusing not only on SIM but also on the presence of additional glands in the metaplastic process at 826 consecutive patients. According to standardized histopathological dataset the cases were classified and recorded by computerized method. The obtained data proved that 1) pure SIM is very rare in the Hungarian population, 2) cardiac and superficial mucous glands are good predictors for SIM, 3) pancreatic acinar and fundic metaplasias carry less severe metaplastic process, and 4) superficial mucous glands can be responsible for creating foregut-derived tissues and thus can be the origin of BE. II/2. The study aimed to assess the value of forceps biopsy sampling in establishing the correct diagnosis revealed by EMR as well as to evaluate the efficacy of this method. Fifty-six subjects with sessile gastric polyps of epithelial origin, at least 0.5 cm in diameter, and not associated with polyposis syndromes, were included. The obtained data showed that forceps biopsy is not fully representative of the entire lesion, and a simple biopsy may therefore lead to a faulty differentiation between the neoplastic and non-neoplastic lesions. EMR proposes diagnostic and staging advantage in assessing patients with EGC as compared to forceps biopsy, because it provides more intact mucosa and submucosa for histological analysis. Sessile gastric polyps should be fully resected by EMR for a final diagnosis and (depending on the lesion size and type) possibly definitive treatment

The dynamics of gene expression changes in a mouse model of oral tumorigenesis may help refine prevention and treatment strategies in patients with oral cancer.

A better understanding of the dynamics of molecular changes occurring during the early stages of oral tumorigenesis may help refine prevention and treatment strategies. We generated genome-wide expression profiles of microdissected normal mucosa, hyperplasia, dysplasia and tumors derived from the 4-NQO mouse model of oral tumorigenesis. Genes differentially expressed between tumor and normal mucosa defined the "tumor gene set" (TGS), including 4 non-overlapping gene subsets that characterize the dynamics of gene expression changes through different stages of disease progression. The majority of gene expression changes occurred early or progressively. The relevance of these mouse gene sets to human disease was tested in multiple datasets including the TCGA and the Genomics of Drug Sensitivity in Cancer project. The TGS was able to discriminate oral squamous cell carcinoma (OSCC) from normal oral mucosa in 3 independent datasets. The OSCC samples enriched in the mouse TGS displayed high frequency of CASP8 mutations, 11q13.3 amplifications and low frequency of PIK3CA mutations. Early changes observed in the 4-NQO model were associated with a trend toward a shorter oral cancer-free survival in patients with oral preneoplasia that was not seen in multivariate analysis. Progressive changes observed in the 4-NQO model were associated with an increased sensitivity to 4 different MEK inhibitors in a panel of 51 squamous cell carcinoma cell lines of the areodigestive tract. In conclusion, the dynamics of molecular changes in the 4-NQO model reveal that MEK inhibition may be relevant to prevention and treatment of a specific molecularly-defined subgroup of OSCC