Current perspectives of KRAS in non-small cell lung cancer.

NSCLC has a diverse genomic background with mutations in key proto-oncogenic drivers including Kirsten rat sarcoma (KRAS) and epidermal growth factor receptor (EGFR). Roughly 40% of adenocarcinoma harbor Kras activating mutations regardless of smoking history. Most KRAS mutations are located at G12, which include G12C (roughly 40%), G12V (roughly 20%), and G12D (roughly 15%). KRAS mutated NSCLC have higher tumor mutational burden and some have increased PD-1 expression, which has resulted in better responses to immunotherapy than other oncogenes. While initial treatment for metastatic NSCLC still relies on chemo-immunotherapy, directly targeting KRAS has proven to be efficacious in treating patients with KRAS mutated metastatic NSCLC. To date, two G12C inhibitors have been FDA-approved, namely sotorasib and adagrasib. In this review, we summarize the different drug combinations used to target KRAS G12c, upcoming G12D inhibitors and novel therapies targeting KRAS.

B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation.

Protection from viral infections depends on immunoglobulin isotype switching, which endows antibodies with effector functions. Here, we find that the protein kinase DYRK1A is essential for B cell-mediated protection from viral infection and effective vaccination through regulation of class switch recombination (CSR). Dyrk1a-deficient B cells are impaired in CSR activity in vivo and in vitro. Phosphoproteomic screens and kinase-activity assays identify MSH6, a DNA mismatch repair protein, as a direct substrate for DYRK1A, and deletion of a single phosphorylation site impaired CSR. After CSR and germinal center (GC) seeding, DYRK1A is required for attenuation of B cell proliferation. These findings demonstrate DYRK1A-mediated biological mechanisms of B cell immune responses that may be used for therapeutic manipulation in antibody-mediated autoimmunity.

Vaccination as a therapeutic strategy for Nasopharyngeal carcinoma.

Patients with recurrent or metastatic NPC are left with limited treatment options. The close association between EBV and NPC make therapeutic vaccination targeting EBV-antigens an emerging new treatment modality. Therapeutic vaccination provides a stimulus to allow the patient to mount their own targeted immune response against the cancer. The two approaches that have led the field into the clinic are dendritic-cell based vaccines and virus-based vaccines. Clinical trials have shown the vaccines to be well-tolerated, and able to elicit a targeted immune response to tumor specific epitopes. Clinical efficacy data, however, is more limited given the early stage of the trials. Other approaches to developing a therapeutic vaccine for NPC include using cancer stem cell lysates, EBV-antigen peptides, and EBV-antigen plasmid DNA. Readout of ongoing trials and progression of preclinical vaccines into Phase I will shed additional light on the efficacy of vaccines and the feasibility of these different approaches to developing a therapeutic vaccine. Future studies may explore combination therapies with multiple vaccines, adoptive T-cell therapy, or checkpoint inhibitors.

The chromosome 21 kinase DYRK1A: emerging roles in cancer biology and potential as a therapeutic target.

Dual-specificity tyrosine phosphorylation-regulated kinase 1 A (DYRK1A) is a serine/threonine kinase that belongs to the DYRK family of proteins, a subgroup of the evolutionarily conserved CMGC protein kinase superfamily. Due to its localization on chromosome 21, the biological significance of DYRK1A was initially characterized in the pathogenesis of Down syndrome (DS) and related neurodegenerative diseases. However, increasing evidence has demonstrated a prominent role in cancer through its ability to regulate biologic processes including cell cycle progression, DNA damage repair, transcription, ubiquitination, tyrosine kinase activity, and cancer stem cell maintenance. DYRK1A has been identified as both an oncogene and tumor suppressor in different models, underscoring the importance of cellular context in its function. Here, we review mechanistic contributions of DYRK1A to cancer biology and its role as a potential therapeutic target.

How Convolutional Neural Network Architecture Biases Learned Opponency and Color Tuning.

Recent work suggests that changing convolutional neural network (CNN) architecture by introducing a bottleneck in the second layer can yield changes in learned function. To understand this relationship fully requires a way of quantitatively comparing trained networks. The fields of electrophysiology and psychophysics have developed a wealth of methods for characterizing visual systems that permit such comparisons. Inspired by these methods, we propose an approach to obtaining spatial and color tuning curves for convolutional neurons that can be used to classify cells in terms of their spatial and color opponency. We perform these classifications for a range of CNNs with different depths and bottleneck widths. Our key finding is that networks with a bottleneck show a strong functional organization: almost all cells in the bottleneck layer become both spatially and color opponent, and cells in the layer following the bottleneck become nonopponent. The color tuning data can further be used to form a rich understanding of how color a network encodes color. As a concrete demonstration, we show that shallower networks without a bottleneck learn a complex nonlinear color system, whereas deeper networks with tight bottlenecks learn a simple channel opponent code in the bottleneck layer. We develop a method of obtaining a hue sensitivity curve for a trained CNN that enables high-level insights that complement the low-level findings from the color tuning data. We go on to train a series of networks under different conditions to ascertain the robustness of the discussed results. Ultimately our methods and findings coalesce with prior art, strengthening our ability to interpret trained CNNs and furthering our understanding of the connection between architecture and learned representation. Trained models and code for all experiments are available at https://github.com/ecs-vlc/opponency.

DYRK1A regulates B cell acute lymphoblastic leukemia through phosphorylation of FOXO1 and STAT3.

DYRK1A is a serine/threonine kinase encoded on human chromosome 21 (HSA21) that has been implicated in several pathologies of Down syndrome (DS), including cognitive deficits and Alzheimer's disease. Although children with DS are predisposed to developing leukemia, especially B cell acute lymphoblastic leukemia (B-ALL), the HSA21 genes that contribute to malignancies remain largely undefined. Here, we report that DYRK1A is overexpressed and required for B-ALL. Genetic and pharmacologic inhibition of DYRK1A decreased leukemic cell expansion and suppressed B-ALL development in vitro and in vivo. Furthermore, we found that FOXO1 and STAT3, transcription factors that are indispensable for B cell development, are critical substrates of DYRK1A. Loss of DYRK1A-mediated FOXO1 and STAT3 signaling disrupted DNA damage and ROS regulation, respectively, leading to preferential cell death in leukemic B cells. Thus, we reveal a DYRK1A/FOXO1/STAT3 axis that facilitates the development and maintenance of B-ALL.

Circulating tumor cell analysis in locally advanced and metastatic squamous cell carcinoma of the head and neck.

BACKGROUND: Circulating tumors cells (CTCs) are considered an early step towards metastasis and have been linked to poor prognosis in several types of cancer. CTCs in squamous cell carcinoma of the head and neck (SCCHN) have an unclear role. METHODS: In this prospective study, patients with locally advanced or metastatic SCCHN had CTC counts assessed before starting systemic treatment using the CellSearch System. Select cases also had sequential CTC evaluation. Presence of CTCs was correlated with patient characteristics and outcomes. RESULTS: Forty-eight patients enrolled, and 36 had evaluable clinical data and baseline CTC counts. Twenty-five patients had locally advanced disease (LAD) and 11 had metastatic disease. ≥1 CTCs were detected in six patients with LAD (24%) and four with metastatic disease (36%). On univariate analysis, smoking was associated with CTCs. CONCLUSION: CTCs are not associated with prognosis in patients with LAD and metastatic disease; however, they are present in this patient population, and ≥1 CTCs is associated with a history of smoking. LEVEL OF EVIDENCE: 1b; individual prospective cohort study.

Chemotherapy after immune checkpoint blockade in patients with recurrent, metastatic squamous cell carcinoma of the head and neck.

OBJECTIVES: Given that immune checkpoint inhibitors (ICIs) are now preferred agents in first-line treatment of recurrent/metastatic (R/M) squamous cell carcinoma of the head and neck (SCCHN), we retrospectively studied outcomes on post-ICI therapies. MATERIALS AND METHODS: We collected data from the medical records of 60 patients with R/M SCCHN who received ICIs followed by at least one further line of cytotoxic or biologic therapy at our institution from 2014 to 2019. We also compared outcomes with those of historical trials in the ICI-naïve, second-line or greater setting. RESULTS: Patients who received platinum-based regimens as their post-ICI therapies experienced improved overall response (ORR) (50% versus 10%, p < 0.01) and improved overall survival (OS) (15.1 months versus 7.3 months, HR 0.46, p = 0.04) compared to the rest of the cohort. Patients receiving platinum re-challenge were more likely to respond than all other patients in the cohort (OR 8.37, p = 0.01). The ORR for patients on 5-fluorouracil (5-FU)-containing regimens (63%) was also higher than other patients in the cohort (p = 0.03). Immunotherapy-based regimens compared favorably to historical data of first exposure to ICIs (disease control rate 54% versus 36%). Singlet regimens were associated with shorter OS than other regimens (HR = 2.38, p = 0.01). CONCLUSIONS: Platinum- and 5-FU-based doublet or triplet regimens may be superior options in the post-ICI setting. Immunotherapy re-challenge following ICI therapy may also be a reasonable option.

Treatment of Aggressive Thyroid Cancer.

Although thyroid cancer generally has a good prognosis, there is a subset of patients for whom standard care (ie, treatment limited to surgery or surgery plus radioactive iodine) is either not appropriate because of the aggressive nature of their disease or not sufficient because of disease progression through standard treatment. Most of these tumors are in 3 groups: radioactive iodine-refractory differentiated thyroid carcinoma including poorly differentiated thyroid carcinoma anaplastic thyroid carcinoma, and progressive medullary thyroid carcinoma. Major classes of treatments in clinical development for these aggressive thyroid tumors include tyrosine kinase inhibitors, mammalian target of rapamycin inhibitors, and mitogen-activated protein kinase kinase inhibitors.

Chromosome 3q arm gain linked to immunotherapy response in advanced cutaneous squamous cell carcinoma.

AIMS: The activity that the immune checkpoint inhibitor (ICI) cemiplimab has recently demonstrated has led to a paradigm shift in the management of patients with advanced cutaneous squamous cell carcinoma (cSCC). To identify predictive biomarkers of response to ICIs in advanced cSCC, we studied 33 patients who received ICI therapy at the Dana-Farber/Harvard Cancer Center (DF/HCC) and analysed sequencing data for a subset of these patients. METHODS: We collected clinical data using electronic health records and genomic data using the institutional OncoPanel platform of the DF/HCC. We compared tumour genomics with data from previously sequenced cSCC cohorts. RESULTS: We observed high tumour mutational burden regardless of smoking status and response to ICI and longer median overall survival among those patients who achieved an ICI response. We compared the genetic data from our cohort with data from other cohorts that included fewer patients with distant metastatic disease. Although our cohort had a similar genetic landscape to those of comparator cohorts, mutations in PIK3C2B were more common in our study. In our cohort, copy number alterations (CNAs) in the 3q chromosomal arm appeared to predict response to ICI therapy. CONCLUSION: CNAs in the 21-27 bands of chromosome arm 3q, a region that includes PIK3CA, ETV5 and BCL6, may represent predictors of response to ICI and may be candidates for drug targeting in combination or sequence with ICI agents.

Everolimus in Anaplastic Thyroid Cancer: A Case Series.

Background: Anaplastic thyroid cancer (ATC) is a very aggressive disease and accounts for over 50% of thyroid-cancer related deaths. mTOR inhibition has shown anti-tumor activity in ATC. We report our experience treating patients with ATC with everolimus off-protocol. Methods: Patients with confirmed ATC and treated with everolimus at DFCI were identified and reviewed retrospectively. NexGen sequencing was performed, and radiologic responses were correlated with mutational profile. Results: Five patients were treated from 2013 to 2016. Three patients had a response, which included one patient who achieved a partial response for 27.9 months, and two patients who had stable disease for 3.7 and 5.9 months, respectively. Genomic analysis was available in two patients and revealed that the partial responder had mutations involving the PI3K/mTOR pathway. Conclusion: Everolimus has anti-tumor activity in ATC, and responses may correlate with mutations involving the PI3K/mTOR pathway. Further studies are warranted.

Pretreatment serum xanthophyll concentrations as predictors of head and neck cancer recurrence and survival.

BACKGROUND: The purpose of this study was to examine associations of pretreatment serum carotenoids, tocopherols, and quercetin with prognosis in 154 patients newly diagnosed with head and neck cancer. METHODS: Pretreatment blood and health surveys were collected. Serum micronutrients were measured by high performance liquid chromatography. Data on recurrence and death were collected annually. Cox proportional hazards models measured associations of serum nutrient concentrations with recurrence and overall survival. RESULTS: During a median follow-up time of 37 months, there were 32 recurrences and 27 deaths. After controlling for covariates, subjects with high versus low serum xanthophyll and total carotenoid concentrations had significantly longer recurrence-free time (p = .002 and p = .02, respectively). Overall survival time was significantly longer in patients with high versus low serum xanthophyll concentrations (p = .02). CONCLUSION: Future research should evaluate the possible benefits of interventions to increase intakes of rich food sources of xanthophylls in this patient population. © 2015 Wiley Periodicals, Inc. Head Neck 38: E1591-E1597, 2016.

Vitamin A depletion induced by cigarette smoke is associated with an increase in lung cancer-related markers in rats.

BACKGROUND: We have previously demonstrated that cigarette smoke is associated with a significant reduction of retinoic acid in rat lungs and the formation of tracheal precancerous lesions. However, the underlying mechanism of cancer risk induced by vitamin A deficiency is unclear. The purpose of this study was to determine whether the cigarette smoke-induced depletion of vitamin A is related to changes in lung cancer risk-related molecular markers. RESULTS: We investigated the roles of the retinoic acid receptors (RARs) as well as other biomarkers for potential cancer risk in the lungs of rats exposed to cigarette smoke. Twenty-four male weanling rats were fed a purified diet and divided equally into four groups. Three experimental groups were exposed to increasing doses of cigarette smoke from 20, 40 or 60 commercial cigarettes/day for 5 days/week. After 6 weeks, the retinoic acid concentrations in the lung tissue as measured via high performance liquid chromatography (HPLC) significantly decreased (P < 0.01) in cigarette smoke exposed groups. Western Blot analysis revealed that cigarette smoke exposure increased lung protein expression of RAR α in a threshold manner and decreased RAR ß and RAR γ expression in a dose-dependent fashion. Protein expressions of cyclin E and proliferating cell nuclear antigen (PCNA) were increased significantly in a dose-dependent manner in cigarette smoke exposed-groups. Additionally, there was a significant increase in protein expression of cJun and cyclin D1 demonstrating a threshold effect similar to that exhibited by RARα, suggesting a potential independent signaling pathway for RARα in lung carcinogenesis. CONCLUSIONS: Findings from this study suggest that cigarette smoke-induced lung retinoic acid depletion may involve two independent pathways, RARα- and RARß-mediated, responsible for the increased cancer risk associated with cigarette smoke-induced vitamin A deficiency.