bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract B08: Identification and characterization of Rho family GTPases as drivers of drug resistance in BRAFV600 mutant melanoma
Authors: Schillo Jacob L. , Feddersen Charlotte R. , Varzavand Afshin , Vaughn Hayley R. , Wadsworth Lexy S. , Voigt Andrew P. , Zhu Eliot Y. , Riordan Jesse D. , Stipp Christopher S. , Dupuy Adam J.
Published: June 2022

The serine/threonine protein kinase BRAF is mutated in approximately 50% of cutaneous melanomas, leading to hyperactivation of the MAPK/ERK pathway. The most common mutations, BRAFV600, can be targeted by selective kinase inhibitors, such as vemurafenib. Although initial clinical response to BRAF inhibition (BRAFi) is encouraging, 90% of patients develop drug resistance within a few months. Drug resistance can be delayed, but not prevented, by combining BRAFi with an MEK inhibitor (MEKi), such as cobimetinib. While some resistance mechanisms are known, disease progression on drug cannot be explained in all patients. We performed a gain-of-function mutagenesis screen utilizing the Sleeping Beauty transposon system to identify novel drivers of resistance in BRAFV600E mutant melanoma cells sensitive to current therapies. We chose four of the top candidates from our screen and validated the ability to drive resistance to both vemurafenib and vemurafenib-cobimetinib combination treatment in multiple melanoma cell lines. In an effort to determine the broader role of candidate vemurafenib-resistance drivers, we conducted an additional in vivo mutagenesis screen, of which genetic analysis is ongoing. Our initial cell-based screen identified two members of the Dbl family of guanine nucleotide exchange factors (GEFs), VAV1 and MCF2, as candidate drivers of vemurafenib resistance. A375 melanoma cells overexpressing VAV1 or MCF2 maintain significant growth under vemurafenib treatment, while control cells do not. Functional tests of VAV1 and MCF2 identified that the active form of two Rho family members, RAC1 and CDC42, increases following treatment with vemurafenib, suggesting a PAK-mediated pathway of resistance. In addition, all candidates that were tested elevated ERK signaling in the presence of vemurafenib. Many of the extracellular signaling pathways known to drive increased vemurafenib resistance activate Rho signaling. Our results suggest that Dbl family members may play an important role in this process. Understanding how Rho activation occurs and its consequences for drug resistance in melanoma will provide critical insights into the design and validation of future targeted therapies.

Citation Format: Jacob L. Schillo, Charlotte R. Feddersen, Afshin Varzavand, Hayley R. Vaughn, Lexy S. Wadsworth, Andrew P. Voigt, Eliot Y. Zhu, Jesse D. Riordan, Christopher S. Stipp, Adam J. Dupuy. Identification and characterization of Rho family GTPases as drivers of drug resistance in BRAFV600 mutant melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B08.
Abstract B12: Potential neoantigen release and increased lymphocyte activity is facilitated by matrix metalloproteinase-dependent cleavage of mutant matrisome peptides in cutaneous melanoma
Authors: Zaman Saif , Chobrutskiy Boris I. , Patel Jay S. , Callahan Blake M. , Mihyu Moody , Diviney Andrea , Tong Wei Lue , Blanck George
Published: June 2022

Introduction: Proteases in the cancer microenvironment have been studied for decades, with a general conclusion that such proteases facilitate the spread of cancer, although there is some controversy regrading that conclusion in later stages of cancer development. More recently, a very large collection of data regarding mutant amino acids in the potential substrates of the cancer microenvironment has become available.

Methods: To better understand the potential impact of these mutant amino acids on protease function and cancer progression, we established a bioinformatics approach to assessing the impact of melanoma mutants, among a previously defined set of ECM structural proteins, on MMP2, a protease extensively associated with melanoma in terms of both protease sensitivity and MHC class I binding using original software. Additionally, T-cell receptor TRα and TRβ recombinations were bioinformatically obtained using whole-exome sequencing data from 479 melanoma tumor samples.

Results: Tumor samples with mutant amino acids adjacent to ECM structural protein, MMP2-cleavage sites represented a better survival rate and a larger proportion of mutant peptides with high HLA class I binding affinities, particularly in comparison to melanoma samples lacking a T-cell infiltrate. Furthermore, even better MHC class I binders, as a group, were identified among the sample representing ECM structural proteins mutants not adjacent to MMP2 sensitive sites and evincing a relatively poor survival rate.

Conclusion: Overall, this analysis suggested that MMP2 has the capacity of freeing mutant peptides that could facilitate an antitumor response and a better survival rate, and this analysis has the potential of resolving some of the controversy surrounding the role of cancer proteases in cancer progression.

Citation Format: Saif Zaman, Boris I. Chobrutskiy, Jay S. Patel, Blake M. Callahan, Moody Mihyu, Andrea Diviney, Wei Lue Tong, George Blanck. Potential neoantigen release and increased lymphocyte activity is facilitated by matrix metalloproteinase-dependent cleavage of mutant matrisome peptides in cutaneous melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B12.
Abstract B13: Intrinsic microsomal PGE2 synthase-1 associates with poor patient survival and T-cell infiltration, and regulates immunosuppression in human and mouse melanoma models
Authors: Kim Sun-Hee , Roszik Jason , Cho Sungnam , Ogata Dai , Ekmekcioglu Suhendan , Grimm Elizabeth A
Published: June 2022

Our research has identified microsomal prostaglandin E2 synthase 1 (mPGES1) as an important downstream effector of the cyclooxygenase 2 (COX2) pathway often expressed by melanoma cells, and largely responsible for tumor-mediated immunosuppression. We observed clear correlations in expression and co-localization of COX2 and mPGES1, for which both are associated with increased expression of immunosuppressive markers in human melanoma. In a syngeneic melanoma mouse model, mPGES1 knockout increased melanoma expression of PD-L1 showing about 25% positive cells, increased infiltration of CD8a+ T cells (around 8 fold) and CD8a+ dendritic cells (around 10 fold) into tumors and suppressed tumor growth (around 70%). Durable tumor regression was observed in mice bearing mPGES1 knockout tumors that were given anti-PD-1 therapy. Analysis of a stage III melanoma tissue microarray revealed significant associations between high mPGES1 expression and low CD8+ infiltration, which correlated with poor survival. Collectively, our results are the first to illustrate a potential role for mPGES1-inhibition and selective targeting in melanoma immune evasion and in supporting the durability of response to PD-1 checkpoint immunotherapy. Research in the development of mPGES1 inhibitors is needed to validate their use as safe treatment options, but they appear attractive and feasible based on data to date.

Citation Format: Sun-Hee Kim, Jason Roszik, Sungnam Cho, Dai Ogata, Suhendan Ekmekcioglu, Elizabeth A Grimm. Intrinsic microsomal PGE2 synthase-1 associates with poor patient survival and T-cell infiltration, and regulates immunosuppression in human and mouse melanoma models [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B13.
Abstract B26: Combinational effect of sulforaphane (SFN) and epigenetic demethylation agent 5-aza-2’-deoxycytidine (DAC) on metastatic melanoma
Authors: Chiang Tung-chin , Su L. Joseph , Koss Brian S. , Washam Charity , Byrum Stephanie , Storey Aaron , Koss Alan J.
Published: June 2022

UV exposure-induced oxidative stress is implicated as the driving mechanism of melanoma development. Increased oxidative stress results in imbalanced reactive oxygen species (ROS) that damage DNA and dysregulated epigenetic modifications and leads to melanoma progression. Sulforaphane (SFN) is the natural bioactivated product of the cruciferous vegetable family (e.g., broccoli and Brussels sprouts) and is known to play a dual role in cytoprotection and to induce apoptosis in the tumor via antioxidant regulation and histone modification of epigenetic enzymes. We investigated the combinational effect of 5-aza-2’-deoxycytidine (DAC), an FDA-approved DNA-modification epigenetic drug and SFN in melanoma cells. We found further cell growth inhibition and an increased number of altered gene expression profiles, increased survival-related cytokine expression, as well as unique histones post-translational modifications (PTMs) upon combinational treatments compared to single treatment in vitro. These results set the stage for animal studies. The long-term goal of the current study is to find an optimal dietary dose of antioxidants from SFN to reduce the burden of oxidative stress, which may contribute to melanoma recurrence, a constant problem with current treatments. In addition to recurrence, a reduced dose of epigenetic drugs applied may minimize the side effects of single-high-dose treatment.

Citation Format: Tung-chin Chiang, L. Joseph Su, Brian S. Koss, Charity Washam, Stephanie Byrum, Aaron Storey, Alan J. Koss. Combinational effect of sulforaphane (SFN) and epigenetic demethylation agent 5-aza-2’-deoxycytidine (DAC) on metastatic melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B26.
Abstract IA01: Strategies for targeted and immune therapy in melanoma
Authors: Herlyn Meenhard
Published: June 2022

Melanoma cells activate pathways that are also activated in proliferating fibroblasts, endothelial cells, or even inflammatory and immune cells. The tumor-secreted proteins and expressed cell surface receptors are associated with growth, migration, invasion, and antiapoptosis. Then there is a group of molecules that is not associated with the phenotype of differentiated cells in skin or tumor stroma but that represents re-expressed developmental genes. Several developmental pathway genes, such as those associated with noncanonical Wnt or Notch signaling, are commonly found on stem cells from the dermis that can give rise to melanocytes and on melanoma cells, but they are absent from or not activated in epidermal melanocytes. We have recently identified a G protein-coupled receptor, LPAR1, that is highly activated in neural crest-like stem cells and melanoma cells and absent from melanocytes. Expression is associated with resistance to BRAFV600E inhibition. When other subpopulations of melanoma cells were characterized that were associated with resistance to BRAF, MEK, or ERK small-molecule inhibitors, their major common property was very slow proliferation, which was in contrast to the bulk of the tumor cells. These “label-retaining cells,” characterized by expression of the H3K4 demethylase JARID1B and the protease SERPIN E2, and the EGF and NGF receptors, are not only drug resistant but also highly invasive in vitro and in experimental animal model. Nonproliferating, drug-resistant malignant cells may pre-exist in tumors. As the majority of melanoma cells are killed by kinase inhibitors, multikinase receptor-expressing cells begin proliferating to repopulate the tumor to its original heterogeneity. Thus, melanomas contain small subpopulations representing only 0.1-5% of all malignant cells that are critical for growth, invasion, and therapy resistance. To achieve total elimination of all malignant cells, we have to develop strategies to target not only the bulk of the tumor cells but also those with intrinsic resistance to common drugs. To closely mimic the conditions in patients’ tumors, we have developed >500 patient-derived xenografts. Together with the >300 permanent cell lines, they represent all clinical, genetic, and biologic groups of the disease. Since the human tumors only proliferate in immune-deficient mice, we have developed two humanized models that recapitulate the infiltration by human leukocytes into the human tumors. Inhibition of checkpoints with clinical-grade inhibitors stimulated the immune response, leading to focal or general tumor regression; thus, the models allow investigating the mechanisms of both stimulation and suppression of the immune system.

Citation Format: Meenhard Herlyn. Strategies for targeted and immune therapy in melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr IA01.
Abstract IA06: Concepts of cancer and metastasis: Historical perspective
Authors: Lugassy Claire , Barnhill Raymond L
Published: June 2022

In medicine, as in all of human history, there is a permanent back and forth between two principal modes of thought: (i) magical/religious/ fears/obscurantism, leading to dogma;, and (ii) intellectual activities resulting in the questioning of dogma and opening doors to new concepts. Concerning cancer, since ancient Egypt, several methods of thinking have been instituted and then rejected, influenced by new discoveries but also by the cultural context. With respect to mechanisms of cancer metastasis, after considerable debate in the 19th century, intravascular dissemination of cancer was finally imposed and is still accepted as the only mechanism for distant metastasis. However, at present, other perspectives are now taken into consideration, and in particular melanoma angiotropism, pericytic mimicry, and extravascular migratory metastasis (EVMM). This new field of cancer research may open promising new strategies for reducing or preventing melanoma metastasis.

Citation Format: Claire Lugassy, Raymond L Barnhill. Concepts of cancer and metastasis: Historical perspective [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr IA06.
Abstract IA09: Tumor cell oxidative metabolism as a barrier to antitumor immunity in melanoma
Authors: Delgoffe Greg M.
Published: June 2022

The treatment of melanoma has been fundamentally changed by immunotherapies like blockade of coinhibitory “checkpoint” molecules like CTLA-4 and PD-1. However, despite these remarkable successes, even within T cell-inflamed, high-mutational-burden tumors, response rates remain low, likely due to additional immune inhibitory mechanisms present in the tumor microenvironment. It is now generally appreciated that the tumor microenvironment is characterized by a distinct metabolic landscape, having low oxygen tension, depleted levels of essential nutrients, and buildup of toxic byproducts. We sought to determine whether this metabolic landscape was variable from patient to patient and how this landscape affected antitumor immunity and thus response to immunotherapy. Using extracellular metabolic flux analysis, we profiled the metabolic derangement of patient-derived cell lines as well as direct ex vivo patient tumor samples, revealing striking heterogeneity not only in the degree of metabolic derangement but also in the type of metabolism a tumor cell was dependent on. Analysis of the tumor infiltrate revealed that a tumor’s preference for oxidative metabolism was associated with immune dysfunction, suggesting that the ability to generate hypoxic regions in vivo is a key aspect of immune resistance. We confirmed this finding in vivo using a novel model of melanoma in which individual metabolic pathways can be selectively targeted in a single-cell derived line: loss of oxidative metabolism in tumor cells sensitizes animals to PD-1 blockade immunotherapy, while loss of glycolytic metabolism has no appreciable effect on antitumor immunity. Analysis of melanoma patient biopsy samples prior to initiation of immunotherapy revealed that increased tumor oxidative metabolism and intratumoral hypoxia was associated with poorer responses to checkpoint blockade. Our data highlight the use of tumor microenvironment hypoxia as a potential predictor of immunotherapy resistance and shed light on the use of modulators of tumor cell oxidation as a means to improve responses to checkpoint blockade.

Citation Format: Greg M. Delgoffe. Tumor cell oxidative metabolism as a barrier to antitumor immunity in melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr IA09.
Abstract IA10: Targeting melanoma metabolism to overcome resistance to treatment
Authors: Betoff Allison , Zippin Jonathan , Merghoub Taha , Chapman Paul B. , Wolchok Jedd
Published: June 2022

Despite adequate oxygen levels, cancer cells undergo anaerobic glycolysis converting glucose to lactate (the Warburg effect). It is now thought that the advantage of this for the cancer cell is that it provides the carbon and nitrogen precursors critical for macromolecule synthesis (amino acids, nucleotides, fatty acids) while still providing an adequate supply of ATP needed for growth. Understanding this metabolic landscape may provide strategies to overcome mechanisms of resistance to therapy in melanoma. AMP-activated protein kinase (AMPK) has been shown to inactivate BRAF by phosphorylating Ser 729, and in preclinical models, this can be used to enhance inhibitors of BRAFV600E. In the high ATP environment of a melanoma cell, AMPK is typically low but inducers of AMPK, such as biguanides, increase AMPK. The biguanide metformin does not enter melanoma cells efficiently due to the lack of organic cation transporter (OCT) expression on melanoma cells. However, phenformin does not require OCT for uptake. We are conducting a phase I trial in BRAF V600E-mutated melanoma patients using dabrafenib/trametinib and escalating doses of phenformin. One of the pharmacodynamic effects of phenformin is weight loss, which we are measuring. Interestingly, obesity has been associated with improved outcome in male melanoma patients treated with anti-PD1 antibodies. In contrast, our data in melanoma patients treated with anti-PD1 antibody immunotherapy do not show an association between outcome and obesity. Another consequence of anaerobic glycolysis is generation and excretion of large amounts of lactate. There is evidence that lactate can inhibit T-cell function, and we will discuss strategies to block lactate transport to enhance immunotherapy.

Citation Format: Allison Betoff, Jonathan Zippin, Taha Merghoub, Paul B. Chapman, Jedd Wolchok. Targeting melanoma metabolism to overcome resistance to treatment [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr IA10.
Abstract IA13: Opportunities and challenges in melanoma early detection
Authors: Polsky David
Published: June 2022

It is well established that survival outcomes for melanoma are highest when these tumors are diagnosed and surgically removed at their earliest stages, prior to the escape of tumor cells to regional and distant anatomic sites. Screening efforts in other malignancies such as colorectal and cervical cancers have yielded benefits in reducing the incidence of invasive cancers and their respective mortalities. Therefore, early detection through broad-based skin cancer screening appears to be a logical step to reduce melanoma mortality. To date, this strategy has not been endorsed by the United States Preventative Services Task Force (USPSTF) due to a lack of conclusive evidence. For example, the initially promising reductions in melanoma mortality observed during a skin cancer screening program in Schleswig-Holstein, Germany, were not replicated in subsequent years in Schleswig-Holstein itself or throughout Germany when the screening program was extended countrywide. The lack of solid evidence demonstrating the benefits of skin screening on melanoma mortality, coupled with the potential harms of screening, and the phenotypic heterogeneity of melanoma raise important concerns regarding the utility of broad-based skin cancer screening programs. Nevertheless, melanoma’s visibility on the skin compared to internal malignancies, and the development of new diagnostic technologies, may help balance the benefits and harms of melanoma screening when considering the varied patient populations in which screening could be deployed. In this presentation we will review current data in the context of developing early-detection strategies to reduce melanoma mortality and/or the cost of care while minimizing potential harms.

Citation Format: David Polsky. Opportunities and challenges in melanoma early detection [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr IA13.
Abstract IA14: Immunosensitivity and resistance in advanced uveal melanoma
Authors: Carvajal Richard D.
Published: June 2022

Despite the ability to effectively achieve control of uveal melanoma at the site of origin, patient outcomes have remained suboptimal due to the ultimate development of recurrent distant disease in a significant proportion of those diagnosed, together with the limited efficacy of currently available therapies in this setting. Initial insights into the tumorigenic effects of the functionally activating, mutually exclusive, early event mutations in GNAQ, GNA11, PLCB4, and CYSLTR2 led to the development of a generation of trials evaluating the effects of inhibition of single or multiple downstream pathways including the MAPK and PI3K pathways. Given the dramatic efficacy of targeted therapy in cutaneous melanoma harboring a BRAF mutation, there was initial hope that a similar strategy might demonstrate comparable effects in uveal melanoma. Unfortunately, the completed and reported clinical trials targeting these pathways have demonstrated minimal, if any, efficacy. Likewise, despite the initial enthusiasm for immunologic checkpoint blockade for the treatment of metastatic uveal melanoma given the durable antitumor responses and cures achieved in cutaneous melanoma, the activity observed thus far has been limited. Nevertheless, with the critical and clinically significant advances made over that past 10 years in precision oncology and immuno-oncology, coupled with rapidly developing advances in our understanding of the biology of uveal melanoma, there is now a new cause for hope for our patients. Trials evaluating the inhibition of alternative nodes in activated pathways alone or in preclinically synergistic combinations are ongoing, new epigenetic strategies are being explored, and preliminary promising data from novel immunologic treatment strategies including adoptive cellular therapy and T-cell redirection all provide new optimism that these innovative treatment options may meaningfully impact the course of the disease.

Citation Format: Richard D. Carvajal. Immunosensitivity and resistance in advanced uveal melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr IA14.
Abstract PR01: A cancer cell program promotes T-cell exclusion and resistance to checkpoint blockade
Authors: Shah Parin , Cuoco Michael , Su Mei-Ju , Melms Johannes , Leeson Rachel , Kanodia Abhay , Mei Shaolin , Lin Jia-Ren , Wang Shu , Rabasha Bokang , Liu David , Shalek Alex K. , Tirosh Itay , Sorger Peter K. , Wucherpfennig Kai , Van Allen Eliezer M. , Schadendorf Dirk , Johnson Bruce E. , Rotem Asaf , Rozenblatt-Rosen Orit , Garraway Levi A. , Yoon Charles H. , Izar Benjamin , Regev Aviv , Jerby-Arnon Livnat
Published: June 2022

Immune checkpoint inhibitors (ICI) produce durable responses in some melanoma patients, but many patients derive no clinical benefit, and the molecular underpinnings of such resistance remain elusive. Here, we leveraged single-cell RNA-seq (scRNA-seq) from 33 melanoma tumors and computational analyses to interrogate malignant cell states that promote immune evasion. We identified a resistance program expressed by malignant cells that is associated with T-cell exclusion and immune evasion. The program is expressed prior to immunotherapy, characterizes cold niches in situ, and predicts clinical responses to anti-PD-1 therapy in an independent cohort of 112 melanoma patients. CDK4/6-inhibition represses this program in individual malignant cells, induces senescence, and reduces melanoma tumor outgrowth in mouse models in vivo when given in combination with immunotherapy. Our study provides a high-resolution landscape of ICI resistant cell states, identifies clinically predictive signatures, and suggests new therapeutic strategies to overcome immunotherapy resistance. This study will be published on Nov. 1st in Cell (Jerby-Arnon et al., Cell 2018).

This abstract is also being presented as Poster A25.

Citation Format: Parin Shah, Michael Cuoco, Mei-Ju Su, Johannes Melms, Rachel Leeson, Abhay Kanodia, Shaolin Mei, Jia-Ren Lin, Shu Wang, Bokang Rabasha, David Liu, Alex K. Shalek, Itay Tirosh, Peter K. Sorger, Kai Wucherpfennig, Eliezer M. Van Allen, Dirk Schadendorf, Bruce E. Johnson, Asaf Rotem, Orit Rozenblatt-Rosen, Levi A. Garraway, Charles H. Yoon, Benjamin Izar, Aviv Regev, Livnat Jerby-Arnon. A cancer cell program promotes T-cell exclusion and resistance to checkpoint blockade [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR01.
Abstract PR12: Regulation of the tumor-suppressive miR-29 family by oncogenic MAPK signaling in melanoma
Authors: Vera Olga , Bok Ilah , Jasani Neel , Balogun Oluwashanu , Nakamura Koji , Karreth Florian
Published: June 2022

MicroRNAs are a group of noncoding RNAs that can regulate gene expression by targeting the mRNA of a gene. Many microRNAs respond to different stimuli such as growth signals or cellular stress. The tumor-suppressive miR-29 family (miR-29a, b and c), for example, is induced during aging and senescence as a p53-dependent response to DNA damage. Given the tumor-suppressive potential of miR-29, we sought to examine if its expression is induced by oncogenic stress in a p53-dependent manner. Ectopic overexpression of oncogenic Braf-V600E and Kras-G12D in mouse embryonic fibroblasts (MEFs) using retroviral transduction resulted in increased expression of pri-miR-29a-b1 and, to a lesser extent, pri-miR-29b2~c. While ectopic Kras-G12D overexpression stimulated p53 activity, Braf-V600E failed to elicit a p53 response, suggesting that this oncogene provokes miR-29 expression in a p53-independent manner. Moreover, expression of Braf-V600E at physiologic levels induced miR-29 in the absence of a p53 response. Accordingly, expression of endogenous Braf-V600E stimulated miR-29 in MEFs even when p53 was silenced by RNAi. When Braf-V600E MEFs were treated with a MEK inhibitor, miR-29 levels decreased in both the presence and absence of p53, suggesting that the MAPK pathway downstream of Braf-V600E directly regulates miR-29 transcription. Importantly, TPA-mediated stimulation of the MAPK pathway increased miR-29 levels in human melanocytes. Similarly, expression of Braf-V600E induced miR-29 in human melanocytes and MEK inhibition rescued this effect. These results strongly support the notion that miR-29 transcription is induced by MAPK signaling and suggest that oncogenic BRAF provokes a tumor-suppressive miR-29 checkpoint that needs to be inactivated for further tumor progression. Indeed, human melanoma cells lines express lower levels of miR-29 compared to human melanocytes, and inactivation of miR-29 by a lentiviral sponge in Braf-V600E mutant melanocytes and melanoma cells promotes cell transformation. We are now utilizing our ESC-GEMM platform to generate Braf-V600E; Pten-deficient mice expressing the miR-29 sponge and will assess if counteracting the induction of miR-29 by Braf-V600E promotes melanoma formation in vivo. Our results suggest a biphasic role of miR-29 during melanomagenesis where Braf-V600E-induced miR-29 upregulation prevents the progression of early lesions until miR-29 is downregulated, likely by inactivation of the ARF-p53 axis.

This abstract is also being presented as Poster B24.

Citation Format: Olga Vera, Ilah Bok, Neel Jasani, Oluwashanu Balogun, Koji Nakamura, Florian Karreth. Regulation of the tumor-suppressive miR-29 family by oncogenic MAPK signaling in melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR12.
Abstract PR14: Defining isoform-specific roles for AKTs in BRAFV600E-driven melanoma
Authors: Farrell Jaymes , Pietruska Jodie , McRee Siobhan , Tsichlis Philip , Hinds Philip
Published: June 2022

The PI3K/AKT pathway is frequently dysregulated in cutaneous melanoma and impacts both tumor aggression and resistance to BRAFV600E/K inhibitors. While current clinical approaches to AKT inhibition are severely limited by the toxicity of pan-AKT inhibitors, selective inhibition of individual AKT isoforms (AKT1, AKT2, or AKT3) remains an attractive, if yet unattainable, approach. A critical gap in our understanding concerns how the three highly homologous yet functionally distinct AKT isoforms contribute to melanomagenesis and treatment response. To address this question, we are employing RNAi and gene editing approaches to interrogate the effect of selective suppression or CRISPR/Cas9-mediated deletion of each isoform in vitro, as well as the impact of AKT isoform loss on 1) the growth of melanoma xenografts and 2) the development of spontaneous tumors in a melanoma-prone mouse model. In addition, we are interrogating tumor-promoting functions of AKT isoform-selective substrates recently identified in a phospho-proteomic screen of mouse fibroblasts, a system that allows us to identify downstream actionable targets that may mediate the effects of AKT isoforms in tumorigenesis. Broadly, we are focusing on the importance of AKTs in tumor cell growth, metastasis, and response to inhibitors of BRAFV600E/K or CDK4/6. We find that loss of AKT1 impacts growth of BRAF mutant human melanoma cells both in vitro and in vivo. Additionally, AKT1 appears to play an isoform-specific role in response to pharmacologic CDK4/6 inhibition, impacting transcriptional and morphologic changes typically associated with permanent cell cycle arrest. In contrast, loss of AKT2 has a minimal impact on melanoma cell growth or response to CDK4/6 inhibition, but severely limits the development of metastatic disease, potentially through a combination of impaired seeding at the metastatic site and defects in glycolysis. While AKT3 loss does not appreciably impact the above-mentioned cellular phenotypes, the protumorigenic role of AKT3 may involve activation of broadly-acting neutral proteases previously implicated in cell cycle progression, cell migration, and CDK5 regulation. Taken together, we provide evidence for distinct roles for AKT isoforms in several aspects of the tumorigenic process as well as response to current therapies. Future studies will focus on identification and targeting of the relevant downstream mediators of these phenotypes.

This abstract is also being presented as Poster A16.

Citation Format: Jaymes Farrell, Jodie Pietruska, Siobhan McRee, Philip Tsichlis, Philip Hinds. Defining isoform-specific roles for AKTs in BRAFV600E-driven melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR14.
Zusätzlicher Nutzen von Necitumumab bei Chemotherapie mit Gemcitabin und Cisplatin?
Authors: Reinmuth Niels
Published: June 2022

Hintergrund: In der SQUIRE-Studie konnte durch das Hinzufügen von Necitumumab, einem IgG1-Antikörper gegen den epidermalen Wachstumsfaktor-Rezeptor (EGFR), zur Erstlinientherapie mit Gemcitabin und Cisplatin (GC+N) bei fortgeschrittenem nicht-kleinzelligem Plattenepithelkarzinom der Lunge (squamous non-small-cell lung cancer; sqNSCLC) das Gesamtüberleben (OS) signifikant verbessert werden; das Sicherheitsprofil war akzeptabel. Wir untersuchten Daten für die deutsche Subpopulation (N = 96) von SQUIRE-Patienten mit EGFR-exprimierenden Tumoren. Patienten und Methoden: Patienten mit sqNSCLC im Stadium IV wurden im Verhältnis 1:1 randomisiert auf bis zu 6 Zyklen von offenem GC+N oder GC allein. GC+N-Patienten ohne Progression erhielten anschließend eine Necitumumab-Monotherapie bis zur Krankheitsprogression oder einer inakzeptablen Toxizität. Der primäre Endpunkt war OS; zu den sekundären Endpunkten gehörten progressionsfreies Überleben (PFS), Sicherheit und gesundheitsbezogene Lebensqualität (EQ-5D, Lung Cancer Symptom Scale; LCSS). Ergebnisse: Die 96 deutschen SQUIRE-Patienten mit EGFR-exprimierenden Tumoren (GC+N: 42; GC: 54) erhielten im Median 4 GC-Zyklen; die GC+N-Patienten erhielten 5 Zyklen Necitumumab. Die zusätzliche Gabe von Necitumumab war mit einer Reduktion des Mortalitätsrisikos um 41% (Hazard Ratio (HR): 0,59, 95%-Konfidenzintervall (KI) 0,37-0,94%, p = 0,026) assoziiert sowie mit einer Reduktion des Progressionsrisikos um 44% (HR: 0,56, 95%-KI 0,33-0,95%, p = 0,029). Die unerwünschten Ereignisse, die typischerweise mit einer EGFR-Antikörper-Behandlung einhergehen (u.a. Hautausschlag, Hypomagnesiämie), kamen bei GC+N häufiger vor. Im Zeitraum bis zur Verschlechterung der EQ-5D- und LCSS-Scores gab es keine nennenswerten Unterschiede zwischen den Behandlungsarmen, mit Ausnahme des Appetitverlusts (verzögert bei GC+N). Schlussfolgerung: Der Überlebensvorteil durch das Hinzufügen von Necitumumab zu Erstlinien-GC war in der deutschen SQUIRE-Subpopulation mit EGFR-exprimierenden Tumoren stärker ausgeprägt als in der Gesamtpopulation (Intention-to-treat-Population); die Toxizität war beherrschbar und entsprach der in der Gesamtpopulation.
Nur wer testet, kann profitieren
Authors: Reinmuth Niels
Published: June 2022

Objective: Latin American countries are heterogeneous in terms of lung cancer incidence and exposure to potential carcinogens. We evaluated the frequency and clinical characteristics of ALK rearrangements (ALKr) in Latin America. Methods: A total of 5,130 lung cancer patients from 10 Latin American countries were screened for inclusion. ALKr detection was performed by fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and real-time reverse transcriptase-polymerase chain reaction (RT-PCR) to assess method variability. Demographic and clinicopathologic characteristics were analyzed. Results: Among the 5,130 patients screened, 8.4% (n = 433) had nonevaluable FISH tests. Evaluable FISH analyses revealed positive ALKr in 6.8% (320/4,697) of the study population, which included patients from 9 countries. ALKr distribution for each country was: Mexico 7.6% (79/1,034), Colombia 4.1% (10/242), Argentina 6.0% (153/2,534), Costa Rica 9.5% (13/137), Panama 4.4% (5/114), Uruguay 5.4% (2/37), Chile 8.6% (16/185), Venezuela 8.9% (13/146), and Peru 10.8% (29/268). RT-PCR showed high positive (83.6%) and negative (99.7%) predictive values when compared to the gold standard FISH. In contrast, IHC only showed a high negative predictive value (94.6%). Conclusions: Although there is a clear country and continental variability in terms of ALKr frequency, this difference is not significant and the overall incidence of ALKr in Latin America does not differ from the rest of the world.
The Role of Copy Number Variations and FHIT Gene on Phenotypic Characteristics of Cases Diagnosed with Autism Spectrum Disorder
Authors: Ünsel Bolat Gül , Bolat Hilmi
Published: June 2022

Copy number variations (CNVs) have been implied in the etiology of autism spectrum disorder (ASD), and microarray-based techniques are performed as a first-step genetic test. Our aim was to present clinical features and CNV profiles of patients with ASD and their parents. Array-CGH was applied to detect CNVs. Previously as likely pathogenic reported duplications were detected at 16p13.11 and 11p15.2p15.1. Other variants were found in 16p11.2p11.1, 3p14.2, 15q11.2, 10q11.22, 3p26.3, 4q13.3, 22q13.32q13.33, and 1q44 and were classified as variants of unknown significance. Deletion of the FHIT gene was associated with the regression of language and social skills without mental impairment. Paternal inheritance of difficulty in social skills and the FHIT gene was documented. In addition, varying olfactory receptor family genes were implicated in de novo and hereditary CNVs. In this study, we aimed to present the clinical characteristics of the cases and parents in more detail, especially in pathogenic CNV cases, which enables us to increase our knowledge on inherited CNVs and genotype-phenotype correlation. We suggest that both genetic and psychiatric evaluation of the parents of the cases is important for better understanding the clinical relevance of the CNV results.
Prediction of Acute Kidney Injury for Acute Type A Aortic Dissection Patients Who Underwent Sun’s Procedure by a Perioperative Nomogram
Authors: Zhang Yuhui , Lan Yongrong , Chen Tongyun , Chen Qingliang , Guo Zhigang , Jiang Nan
Published: June 2022

Introduction: Postoperative acute kidney injury (AKI) occurs in 20–40% of acute type A aortic dissection (ATAAD) patients undergoing cardiac surgery. A predictive model could be developed to assess the probability of AKI in patients with ATAAD before and after cardiac surgery in a timely manner. Methods: This retrospective study enrolled a total of 224 patients with ATAAD. Patients were subjected to total arch replacement using a tetrafurcate graft with stented elephant trunk implantation according to Sun’s procedure. Statistical comparison for the collected data was done with Student’s t test or Mann-Whitney U test (continuous variables) and χ2 test (categorical variables). The independent predictors were screened by multivariate logistic regression analysis and then incorporated into a nomogram. The reliability of cardiac surgery-associated AKI (CSA-AKI) models was evaluated using the area under the receiver operating characteristic curve (AUC). Results: This study enrolled 224 ATAAD patients, including 53 patients with AKI and 171 patients without AKI. The incidence of ATAAD-induced AKI in the cohort was 23.66%. The screened predictors for AKI include iliac artery involvement, creatinine, D-dimer, autotransfusion, platelet-rich plasma reinfusion, nasal temperature, red blood cells, fresh frozen plasma, drainage, and mechanical ventilation. The calculated AUC values for model 1, model 2, model 3, and model 4 were 0.710, 0.777, 0.827, and 0.848, respectively. Model 4 was optimum for AKI risk scoring compared with model 1, model 2, and model 3. Conclusions: AKI prediction models were established for ATAAD patients using preoperative, intraoperative, and postoperative information. Particularly, model 4 shows superiority in risk prediction for CSA-AKI.
Cytopathological Findings in Bronchoalveolar Lavage from Patients with COVID-19
Authors: Galeano Reyes Silvio Antonio , Dhimes Tejeda Patricia , Steen Bárbara , Arcos Orozco Hansely Keret , Ramos Pontón Paloma
Published: June 2022

Information on cellular analysis of bronchoalveolar lavage (BAL) in patients with COVID-19 is limited. Some studies have described an increase in lymphocyte percentage or exuberant plasmacytosis. Some reports addressed the importance of molecular testing on BAL samples to confirm COVID-19 pneumonia, in clinically highly suspected patients with consecutive negative nasopharyngeal swab results. In addition to atypical lymphocytes in the peripheral blood, morphologic findings of atypical lymphocytes in BAL were also reported in a few patients. The objective of this study was to describe the cytopathic characteristics identified, any data presented here are descriptives and intended to trigger further research. Three general aspects have been evaluated in each sample: reactive changes, virus-related pathological changes, and differential leukocyte count. Seventeen samples were collected. All samples were negative for malignancy, with an inflammatory background, predominantly lymphohistiocytic in 5 samples, histiocytic in 9, and 3 with predominantly neutrophilic. Hemosiderin-laden macrophages were observed in 12/17. Nonspecific reactive cell changes were identified in 4 samples, including bronchial, alveolar, and reserve cell hyperplasia. Virus-related pathological changes were observed in 14 samples, such as loss of nuclear chromatin pattern, lymphocytes with atypical nuclei, nuclear and cytoplasmic inclusions, multinucleations in bronchial cells and macrophages, or multinucleated giant cells. The identification of multinucleated giant cells could represent a cytopathic effect induced by the virus, at the same time the nuclear clearance of pneumocytes as a possible direct effect. BAL is a procedure aimed at obtaining cells from the respiratory tract that can provide valuable and rapid information. It is important to collect and describe as many cytopathological findings as possible, which can provide relevant information for future studies.
Intraventricular Bone Dust Migration after Endoscopic Third Ventriculostomy: Illustrative Report of 2 Cases
Authors: Chan Kevin Ivan Peñaverde , Hong Manilyn Ann Constantino , Legaspi Gerardo Dizon , Khu Kathleen Joy Ong Lopez
Published: June 2022

Introduction: Autologous bone dust replacement is a commonly used technique to seal a defect created from a burr hole. However, postoperative migration of these bone fragments may occur as an uncommon complication of endoscopic third ventriculostomy (ETV). Case Presentation: We report 2 cases of intraventricular bone dust migration resulting in acute hydrocephalus from physical obstruction of the stoma and infection. Discussion/Conclusion: From our 2 cases as well as other reported cases, the bone dust may have acted as a foreign body and served as a nidus of infection, in addition to causing physical obstruction. A lumbar puncture performed after ETV may have resulted in a suction effect of the bone dust from the burr hole into the ventricular system. Both our cases necessitated urgent surgical intervention to extract the bone fragments and restore CSF flow. Because of its potential complications, we recommend against using autologous bone dust for closure of a burr hole defect after ETV.
Blending of three-dimensional geometric model shapes
Authors: Ng Seng-Beng , Ng Kok-Why , Rahmat Rahmita Wirza O.K. , Yoong Yih-Jian
Published: June 2022

Three-dimensional (3D) geometric model shapes blending method can create various in-between models from two inputs of models shapes. Though, many blended shapes are implausible due to different inputs of model type, inappropriate matching-parts, improper parts-segmentation, and non-tally number of segmentation parts. are crucial and should be taken into account. The objective of this paper is to study the strengths and weaknesses of some prominent shapes blending methods and the 3D reconstruction methods. An interpolated shape blending program using the Laplacian-based contraction and Slinky-based segmentation method is developed to illustrate the critical problems arise in the shape blending process. Output results are to be compared with some prominent existing methods and one will observe the potential research direction in the blending research work
Short-term uncleaned signal to noise threshold ratio based end-to-end time domain speech enhancement in digital hearing aids
Authors: Nimmagadda Padmaja , Swamy Kondru Ayyappa , Prathima Samuda , Chintha Sushma , Alex Zachariah Callottu
Published: June 2022

This paper presents the improvements in the combined solution for the noise estimation and the speech enhancement in digital hearing aids in time domain. This study focuses on the single channel statistical temporal speech enhancement using adaptive Wiener filtering. In this technique, the noise is updated based on the short-term uncleaned signal to noise threshold ratio (ST-USNTR) of the frame. It works best if and only if the back ground noise level is low compared to that of speech of interest. We considered the time domain algorithms in order to consider the time varying nature of speech signal. The performance of the proposed algorithm is evaluated for speech signal with seven ty pes of noises and three signal to noise ratios (SNR) levels in each type of noise. From the results, it is clear that the basic level of adaptive speech enhancement is obtained using statistical parameters of noisy speech without the need for reference input.
Performance analysis of the application of convolutional neural networks architectures in the agricultural diagnosis
Authors: Belattar Sara , Abdoun Otman , Haimoudi El khatir
Published: June 2022

Agriculture is an important sector for developing countries and farmers. Recently, numerous techniques for increasing agricultural productivity have been utilized. However, different issues are still encountered by farmers including various plant diseases. Plant diseases diagnoses are challenging research, and they should be analyzed and treated by detecting the diseased plant leaves. For that reason, in this paper, we develop our proposed architecture using convolutional neural networks (OP-CNN) as a computer-aided to detect and diagnose plant diseases. The proposed architecture can assist farmers in increasing both the quantity and quality of their agricultural productivity. Besides this, the OP-CNN helps to reduce disease prevalence through early detection. The performance of our proposed model is compared with other convolutional neural networks (CNN) architectures in order to validate its capability. The strawberry dataset was employed to train and test the models since the strawberry is one of the main crops in the Larache Province (Morocco). The experimental tests demonstrate that our proposed OP-CNN reaches the highest values versus DenseNet121, VGG19, and ResNet50 with 100%, 99%, 97%, and 63% respectively for classification accuracy, 100%, 100%, 98% and, 79% respectively for precision, 100%, 99%, 97%, and 63% respectively for recall, and 100%, 99%, 97%, and 58% respectively for "F" _1Score.
A comparative study to predict breast cancer using machine learning techniques
Authors: Shankar Reddy Shiva , Pilli Neelima , Voosala Priyadarshini , Ravi Chigurupati Swaroop
Published: June 2022

Detection of disease at the starting stage is a very crucial problem. As the population growth increases, the risk of death incurred by breast cancer rises exponentially. Breast cancer is the most common cancer in women, and it is also the most dangerous of all cancers. Deaths because of breast cancer have b een increasing in recent times. Earlier detection of the disease followed by treatment can reduce the risk and increase survival chances. There will be cases where even medical professionals can make mistakes in identifying the disease. This project deals with the detection of Breast cancer using the cell data of the tumor present in the breast. So, with the help of technologies in machine learning and artificial intelligence can substantially improve the diagnosis accuracy. The development of this project is beneficial in medical decision support systems. Several machine learning techniques, namely Adaboost, multi-layer perceptron (MLP) and stacking classifier; were used, and among all the algorithms, the stacking classifier results in the best accuracy. The accuracies 95.6%, 97.1%, and 99.2% respectively.