Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination Therapy.

Tumors frequently harbor isogenic yet epigenetically distinct subpopulations of multi-potent cells with high tumor-initiating potential-often called Cancer Stem-Like Cells (CSLCs). These can display preferential resistance to standard-of-care chemotherapy. Single-cell analyses can help elucidate Master Regulator (MR) proteins responsible for governing the transcriptional state of these cells, thus revealing complementary dependencies that may be leveraged via combination therapy. Interrogation of single-cell RNA sequencing profiles from seven metastatic breast cancer patients, using perturbational profiles of clinically relevant drugs, identified drugs predicted to invert the activity of MR proteins governing the transcriptional state of chemoresistant CSLCs, which were then validated by CROP-seq assays. The top drug, the anthelmintic albendazole, depleted this subpopulation in vivo without noticeable cytotoxicity. Moreover, sequential cycles of albendazole and paclitaxel-a commonly used chemotherapeutic -displayed significant synergy in a patient-derived xenograft (PDX) from a TNBC patient, suggesting that network-based approaches can help develop mechanism-based combinatorial therapies targeting complementary subpopulations.

Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.

Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. Leveraging progress in proteomic technologies and network-based methodologies, we introduce Virtual Enrichment-based Signaling Protein-activity Analysis (VESPA)-an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations-and use it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogating tumor-specific enzyme/substrate interactions accurately infers kinase and phosphatase activity, based on their substrate phosphorylation state, effectively accounting for signal crosstalk and sparse phosphoproteome coverage. The analysis elucidates time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring, experimentally confirmed by CRISPR knock-out assays, suggesting broad applicability to cancer and other diseases.

Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations.

Diffuse Midline Gliomas (DMGs) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potentially orthogonal drug sensitivities. To address this challenge, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic, non-oncogene dependencies of seven coexisting subpopulations identified by single-cell analysis-whose enrichment in essential genes was validated by pooled CRISPR/Cas9 screens. Perturbational profiles of 372 clinically relevant drugs helped identify those able to invert the activity of subpopulation-specific MRs for follow-up in vivo validation. While individual drugs predicted to target individual subpopulations-including avapritinib, larotrectinib, and ruxolitinib-produced only modest tumor growth reduction in orthotopic models, systemic co-administration induced significant survival extension, making this approach a valuable contribution to the rational design of combination therapy.

Youth With Sexual or Gender-Diverse Identities and Military Connection: Recommendations to Optimize Clinical Care.

In the United States, an estimated 1.9 million youth 13 to 17 years of age (9.5%) identify as sexual and/or gender diverse (SGD), identifying as nonheterosexual and/or having a gender identity other than the assigned sex at birth.1 Up to 7% of SGD adolescents may have at least one parent currently or previously serving in the US military, an estimated 133,000 youth nationwide.1,2 SGD adolescents are highly exposed to acute and chronic stressors, including minority stress and discrimination, resulting in elevated rates of depression, anxiety, and suicidal ideation.3,4 SGD military-connected youth (ie, SGD youth with a parent or caregiver with military service experience) were found to be at even higher risk for these negative outcomes in one published report.2 While both military connection and SGD identity may foster strengths, these youth also face well-studied stressors,2,5 and the convergence of these identities and experiences is likely to produce greater challenges. Nearly half of military-connected youth are seen by civilian clinicians in local communities for primary care, and even more are seen for specialty care.6 As a result, all clinicians, both within and outside the military health system, and especially clinicians providing mental health care, must be familiar with these unique converging stressors facing SGD military-connected youth.

Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer.

Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up To Cancer-Mark Foundation cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including (1) favorable (for example, ATM altered) and unfavorable (for example, TERT amplified) genomic subgroups, (2) a prominent association between expression of inducible components of the immunoproteasome and response and (3) a dedifferentiated tumor-intrinsic subtype with enhanced response to checkpoint blockade. Taken together, results from this cohort demonstrate the complexity of biological determinants underlying immunotherapy outcomes and reinforce the discovery potential of integrative analysis within large, well-curated, cancer-specific cohorts.

NaRnEA: An Information Theoretic Framework for Gene Set Analysis.

Gene sets are being increasingly leveraged to make high-level biological inferences from transcriptomic data; however, existing gene set analysis methods rely on overly conservative, heuristic approaches for quantifying the statistical significance of gene set enrichment. We created Nonparametric analytical-Rank-based Enrichment Analysis (NaRnEA) to facilitate accurate and robust gene set analysis with an optimal null model derived using the information theoretic Principle of Maximum Entropy. By measuring the differential activity of ~2500 transcriptional regulatory proteins based on the differential expression of each protein's transcriptional targets between primary tumors and normal tissue samples in three cohorts from The Cancer Genome Atlas (TCGA), we demonstrate that NaRnEA critically improves in two widely used gene set analysis methods: Gene Set Enrichment Analysis (GSEA) and analytical-Rank-based Enrichment Analysis (aREA). We show that the NaRnEA-inferred differential protein activity is significantly correlated with differential protein abundance inferred from independent, phenotype-matched mass spectrometry data in the Clinical Proteomic Tumor Analysis Consortium (CPTAC), confirming the statistical and biological accuracy of our approach. Additionally, our analysis crucially demonstrates that the sample-shuffling empirical null models leveraged by GSEA and aREA for gene set analysis are overly conservative, a shortcoming that is avoided by the newly developed Maximum Entropy analytical null model employed by NaRnEA.

Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis.

Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. By leveraging progress in proteomic technologies and network-based methodologies, over the past decade, we developed VESPA-an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations-and used it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogation of tumor-specific enzyme/substrate interactions accurately inferred kinase and phosphatase activity, based on their inferred substrate phosphorylation state, effectively accounting for signal cross-talk and sparse phosphoproteome coverage. The analysis elucidated time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring that was experimentally confirmed by CRISPRko assays, suggesting broad applicability to cancer and other diseases.

A genome-wide copper-sensitized screen identifies novel regulators of mitochondrial cytochrome c oxidase activity.

Copper is essential for the activity and stability of cytochrome c oxidase (CcO), the terminal enzyme of the mitochondrial respiratory chain. Loss-of-function mutations in genes required for copper transport to CcO result in fatal human disorders. Despite the fundamental importance of copper in mitochondrial and organismal physiology, systematic identification of genes that regulate mitochondrial copper homeostasis is lacking. To discover these genes, we performed a genome-wide screen using a library of DNA-barcoded yeast deletion mutants grown in copper-supplemented media. Our screen recovered a number of genes known to be involved in cellular copper homeostasis as well as genes previously not linked to mitochondrial copper biology. These newly identified genes include the subunits of the adaptor protein 3 complex (AP-3) and components of the cellular pH-sensing pathway Rim20 and Rim21, both of which are known to affect vacuolar function. We find that AP-3 and Rim mutants exhibit decreased vacuolar acidity, which in turn perturbs mitochondrial copper homeostasis and CcO function. CcO activity of these mutants could be rescued by either restoring vacuolar pH or supplementing growth media with additional copper. Consistent with these genetic data, pharmacological inhibition of the vacuolar proton pump leads to decreased mitochondrial copper content and a concomitant decrease in CcO abundance and activity. Taken together, our study uncovered novel genetic regulators of mitochondrial copper homeostasis and provided a mechanism by which vacuolar pH impacts mitochondrial respiration through copper homeostasis.

Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.

Tumor-specific elucidation of physical and functional oncoprotein interactions could improve tumorigenic mechanism characterization and therapeutic response prediction. Current interaction models and pathways, however, lack context specificity and are not oncoprotein specific. We introduce SigMaps as context-specific networks, comprising modulators, effectors and cognate binding-partners of a specific oncoprotein. SigMaps are reconstructed de novo by integrating diverse evidence sources-including protein structure, gene expression and mutational profiles-via the OncoSig machine learning framework. We first generated a KRAS-specific SigMap for lung adenocarcinoma, which recapitulated published KRAS biology, identified novel synthetic lethal proteins that were experimentally validated in three-dimensional spheroid models and established uncharacterized crosstalk with RAB/RHO. To show that OncoSig is generalizable, we first inferred SigMaps for the ten most mutated human oncoproteins and then for the full repertoire of 715 proteins in the COSMIC Cancer Gene Census. Taken together, these SigMaps show that the cell's regulatory and signaling architecture is highly tissue specific.

Alternative therapies for chronic rhinosinusitis: A review.

The use of alternative medicine in chronic rhinosinus-itis (CRS) continues to increase in popularity, for the most part without meeting the burden of being based on sound clinical evidence. New and emerging treat-ments, both natural and developed, are numerous, and it remains a challenge for otolaryngologists as well as general practitioners to keep up to date with these therapies and their efficacy. In this systematic review, we discuss a number of alternative therapies for CRS, their proposed physiologic mechanisms, and evidence supporting their use. This analysis is based on our re-view of the English-language literature on alternative therapies for CRS (we did not include any therapies that are already recommended by accepted profession-al bodies). Data collection was performed using the PubMed database (not restricted to MEDLINE due to the nature of the subject matter), the Cochrane data-bases, and bibliography searches. We found that while many of the alternative therapies we reviewed might have a firm basis in science, they lack any clinical ev-idence to support their use specifically for CRS. Some emerging therapies, such as therapeutic ultrasonog-raphy and phonophoresis, show some promise, based on a growing body of positive evidence. In addition, the use of baby shampoo, thyme honey, and bromelain additives to saline lavage in CRS are all supported by clinical evidence, as is Sinupret, an oral preparation that contains echinacea. However, higher levels of ev-idence gleaned from large, well-designed, prospective, randomized, controlled trials are needed before any of these therapies can be recommended.

Deuteration of nonexchangeable protons on proteins affects their thermal stability, side-chain dynamics, and hydrophobicity.

We have investigated the effect of deuteration of non-exchangeable protons on protein global thermal stability, hydrophobicity, and local flexibility using well-known thermostable model systems such as the villin headpiece subdomain (HP36) and the third immunoglobulin G-binding domain of protein G (GB3). Reversed-phase high-performance liquid chromatography (RP-HPLC) measurements as a function of temperature probe global thermal stability in the presence of acetonitrile, while differential scanning calorimetry determines thermal stability in solution. Both indicate small but measurable changes in the order of several degrees. RP-HPLC also permitted quantification of the effect of deuteration of just three core phenylalanine side chains of HP36. NMR dynamics investigation has focused on methyl axes motions using cross-correlated relaxation measurements. The analysis of order parameters provided a complex picture indicating that deuteration generally increases motional amplitudes of sub-nanosecond motion in GB3 but decreases those in HP36. Combined with earlier dynamics measurements at Cα -Cß sites and backbone sites of GB3, which probed slower time scales, the results point to the need to probe multiple atoms in the protein and variety of time scales to the discern the full complexity of the effects of deuteration on dynamics.

Correlated motions of C'-N and Cα-Cß pairs in protonated and per-deuterated GB3.

We investigated correlated µs-ms time scale motions of neighboring 13C'-15N and 13Cα-13Cß nuclei in both protonated and perdeuterated samples of GB3. The techniques employed, NMR relaxation due to cross-correlated chemical shift modulations, specifically target concerted changes in the isotropic chemical shifts of the two nuclei associated with spatial fluctuations. Field-dependence of the relaxation rates permits identification of the parameters defining the chemical exchange rate constant under the assumption of a two-site exchange. The time scale of motions falls into the intermediate to fast regime (with respect to the chemical shift time scale, 100-400 s-1 range) for the 13C'-15N pairs and into the slow to intermediate regime for the 13Cα-13Cß pairs (about 150 s-1). Comparison of the results obtained for protonated and deuterated GB3 suggests that deuteration has a tendency to reduce these slow scale correlated motions, especially for the 13Cα-13Cß pairs.

Alternative therapies for chronic rhinosinusitis: A review.

The use of alternative medicine in chronic rhinosinusitis (CRS) continues to increase in popularity, for the most part without meeting the burden of being based on sound clinical evidence. New and emerging treatments, both natural and developed, are numerous, and it remains a challenge for otolaryngologists as well as general practitioners to keep up to date with these therapies and their efficacy. In this systematic review, we discuss a number of alternative therapies for CRS, their proposed physiologic mechanisms, and evidence supporting their use. This analysis is based on our review of the English-language literature on alternative therapies for CRS (we did not include any therapies that are already recommended by accepted professional bodies). Data collection was performed using the PubMed database (not restricted to MEDLINE due to the nature of the subject matter), the Cochrane databases, and bibliography searches. We found that while many of the alternative therapies we reviewed might have a firm basis in science, they lack any clinical evidence to support their use specifically for CRS. Some emerging therapies, such as therapeutic ultrasonography and phonophoresis, show some promise, based on a growing body of positive evidence. In addition, the use of baby shampoo, thyme honey, and bromelain additives to saline lavage in CRS are all supported by clinical evidence, as is Sinupret, an oral preparation that contains echinacea. However, higher levels of evidence gleaned from large, well-designed, prospective, randomized, controlled trials are needed before any of these therapies can be recommended.

Mitochondrial disease genes COA6, COX6B and SCO2 have overlapping roles in COX2 biogenesis.

Biogenesis of cytochrome c oxidase (CcO), the terminal enzyme of the mitochondrial respiratory chain, is a complex process facilitated by several assembly factors. Pathogenic mutations were recently reported in one such assembly factor, COA6, and our previous work linked Coa6 function to mitochondrial copper metabolism and expression of Cox2, a copper-containing subunit of CcO. However, the precise role of Coa6 in Cox2 biogenesis remained unknown. Here we show that yeast Coa6 is an orthologue of human COA6, and like Cox2, is regulated by copper availability, further implicating it in copper delivery to Cox2. In order to place Coa6 in the Cox2 copper delivery pathway, we performed a comprehensive genetic epistasis analysis in the yeast Saccharomyces cerevisiae and found that simultaneous deletion of Coa6 and Sco2, a mitochondrial copper metallochaperone, or Coa6 and Cox12/COX6B, a structural subunit of CcO, completely abrogates Cox2 biogenesis. Unlike Coa6 deficient cells, copper supplementation fails to rescue Cox2 levels of these double mutants. Overexpression of Cox12 or Sco proteins partially rescues the coa6Δ phenotype, suggesting their overlapping but non-redundant roles in copper delivery to Cox2. These genetic data are strongly corroborated by biochemical studies demonstrating physical interactions between Coa6, Cox2, Cox12 and Sco proteins. Furthermore, we show that patient mutations in Coa6 disrupt Coa6-Cox2 interaction, providing the biochemical basis for disease pathogenesis. Taken together, these results place COA6 in the copper delivery pathway to CcO and, surprisingly, link it to a previously unidentified function of CcO subunit Cox12 in Cox2 biogenesis.

An Unusual Cause of Dysphagia: A Large Expectorated Arteriovenous Malformation.

BACKGROUND: Vascular malformations are generally detected in childhood or adolescence with first presentations in adulthood being rare. CASE REPORT: We report the case of a 52-year-old female with threatened compromise of her airway after expectorating a massive arteriovenous malformation anchored at the supraglottis. The only preceding symptom was dysphagia. The lesion was resected, the patient had a quick recovery, and she has shown no evidence of recurrence. CONCLUSION: Although uncommon, vascular malformations of the supraglottis or hypopharynx should be considered in the differential diagnosis of a patient presenting with dysphagia because of the potential to cause disastrous airway compromise. Although a lesion presenting acutely mandates a definitive airway plan, when clinically possible, computed tomography scan and indirect laryngoscopy can provide useful information for the airway and operative teams.

Transtympanic Facial Nerve Paralysis: A Review of the Literature.

Facial nerve paralysis because of penetrating trauma through the external auditory canal is extremely rare, with a paucity of published literature. The objective of this study is to review the literature on transtympanic facial nerve paralysis and increase physician awareness of this uncommon injury through discussion of its clinical presentation, management and prognosis. We also aim to improve patient outcomes in those that have sustained this type of injury by suggesting an optimal management plan. In this case report, we present the case of a 46-year-old white woman who sustained a unilateral facial nerve paresis because of a garfish penetrating her tympanic membrane and causing direct damage to the tympanic portion of her facial nerve. On follow-up after 12 months, her facial nerve function has largely returned to normal. Transtympanic facial nerve paralysis is a rare injury but can have a favorable prognosis if managed effectively.

Concurrent Spigelian hernia and falciform ligament hernia in a 67-year-old female.

INTRODUCTION: Internal abdominal hernias account for 1% of all hernias but 5.8% of all bowel obstructions and hence are of significant clinical importance. Similarly Spigelian hernias account for only 0.12-2% of all abdominal wall hernias. CASE PRESENTATION: We present and discuss the management of a case that presented with concurrent falciform ligament internal abdominal hernia and Spigelian hernia. We believe this is the first reported case of such an occurrence in the literature. CONCLUSION: Due to the advancements in computer topography (CT) imaging many internal and Spigelian hernias are diagnosed pre-operatively though these scan are not always available or indicated in cases of suspected small bowel obstruction. Due to the high mortality rate of undiagnosed internal hernias a high clinical suspicion must be maintained. The authors recommend laparoscopic trans-abdominal repair of Spigelian hernias in order to examine the abdominal contents and exclude rare, though potentially serious internal hernias.

Schneiderian-Type Papilloma of the Middle Ear: A Review of the Literature.

Schneiderian-type papilloma of the middle ear is a rare finding. We present a 46-year-old Aboriginal man with a large tympanic membrane perforation and a Schneiderian-type papilloma filling the middle ear. The aim of this study is to familiarize clinicians with this uncommon disease through discussion of its clinical presentation, diagnostic considerations and management. A search of English-language peer-reviewed literature was undertaken using the key words "Schneiderian-type papilloma," "inverted papilloma," and "middle ear." A total of 29 cases (including the present case) of Schneiderian-type papilloma involving the middle ear were reviewed. Common presenting symptoms include hearing loss, otalgia, and otorrhea. Middle ear disease is associated with higher rates of recurrence and malignant transformation than its sinonasal counterpart. Radical surgical resection is the only curative treatment. Schneiderian-type papilloma is a benign, but locally aggressive, epithelial neoplasm most commonly arising in the sinonasal tract. Whilst involvement of the middle ear is extremely rare, knowledge of this condition is important due to its propensity to recur and the high rate of malignant transformation.

Early recognition and management of laryngeal fracture: a case report.

BACKGROUND: Laryngeal fracture is a rare condition that can lead to significant problems with airway patency, voice production, and swallowing. Conflict in the literature exists regarding the most suitable way to manage this injury. CASE REPORT: We present the case of a 29-year-old Caucasian man who sustained a displaced fracture of the thyroid cartilage due to blunt trauma. He reported no swallowing, breathing, or voice problems after 1 year, and his recovery can be attributed to the early recognition and proper management of his condition. CONCLUSION: This case illustrates the importance of ensuring a high level of suspicion for laryngeal fracture in the acute trauma patient. Early identification of this injury allows early intervention that not only protects the airway but also improves long-term voice and airway outcomes.