Publications by authors named "Cleary J"

Extracellular vesicles (EVs) have emerged as novel blood-based biomarkers for various pathologies. The development of methods to enrich cell-specific EVs from biofluids has enabled us to monitor difficult-to-access organs, such as the brain, in real time without disrupting their function, thus serving as liquid biopsy. Burgeoning evidence indicates that the contents of neuron-derived EVs (NDEs) in blood reveal dynamic alterations that occur during neurodegenerative pathogenesis, including Alzheimer's disease (AD), reflecting a disease-specific molecular signature.

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Dysregulated epigenetic programs that restrict differentiation, reactivate fetal genes, and confer phenotypic plasticity are critical to colorectal cancer (CRC) development. By screening a small molecule library targeting epigenetic regulators using our dual reporter system, we found that inhibiting histone deacetylase (HDAC) 1/2 promotes CRC differentiation and anti-tumor activity. Comprehensive biochemical, chemical, and genetic experiments revealed that on-target blockade of the HDAC1/2 catalytic domain mediated the differentiated phenotype.

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  • FGFR inhibitors have shown promise in treating FGFR-altered cholangiocarcinoma, but acquired resistance poses a challenge to their effectiveness.
  • The study utilized diverse investigative methods, including DNA analysis and tissue biopsies, to explore resistance mechanisms in a cohort of patients.
  • Results indicated that a significant number of patients with clinical benefits had specific FGFR2 mutations, but polyclonal resistance was influenced by low drug concentrations and specific mutation types affecting drug efficacy.
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The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of rare dominantly inherited neurodegenerative diseases characterized by progressive ataxia. The most common mutation seen across the SCAs is a CAG repeat expansion, causative for SCA1, 2, 3, 6, 7, 12 and 17. We recently identified dysregulation of alternative splicing as a novel, presymptomatic transcriptomic hallmark in mouse models of SCAs 1, 3 and 7.

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Purpose: To develop a 3D distortion-free reduced-FOV diffusion-prepared gradient-echo sequence and demonstrate its application in vivo for diffusion imaging of the spinal cord in healthy volunteers.

Methods: A 3D multi-shot reduced-FOV diffusion-prepared gradient-echo acquisition is achieved using a slice-selective tip-down pulse in the phase-encoding direction in the diffusion preparation, combined with magnitude stabilizers, centric k-space encoding, and 2D phase navigators to correct for intershot phase errors. The accuracy of the ADC values obtained using the proposed approach was evaluated in a diffusion phantom and compared to the tabulated reference ADC values and to the ADC values obtained using a standard spin echo diffusion-weighted single-shot EPI sequence (DW-SS-EPI).

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Purpose: Preclinical studies have identified molecular correlates of sensitivity to ATR inhibition. This translational study was designed to test the ATR inhibitor berzosertib in patients with advanced solid tumors carrying alterations in ATRX, ataxia-telangiectasia-mutated (ATM), genes conferring replication stress (RS), or SDH.

Patients And Methods: Patients were recruited to four cohorts: T1: ATRX-mutant leiomyosarcoma; T2: ATM-mutant solid tumors; T3: solid tumors with mutations in RS-associated genes; and T4: SDH-deficient gastrointestinal stromal tumors (GIST).

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Purpose: We introduce a novel algorithmic approach to design phase I trials for oncology drug combinations.

Methods: Our proposed Toxicity Adaptive Lists Design (TALE) is straightforward to implement, requiring the prespecification of a small number of parameters that define rules governing dose escalation, de-escalation, or reassessment of previously explored dose levels. These rules effectively regulate dose exploration and control the number of toxicities.

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Myotonic dystrophy type 1 (DM1), the leading cause of adult-onset muscular dystrophy, is caused by a CTG repeat expansion. Expression of the repeat causes widespread alternative splicing (AS) defects and downstream pathogenesis, including significant skeletal muscle impacts. The mouse model plays a significant role in therapeutic development.

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Background: Patients with facial nerve palsy often experience lagophthalmos (incomplete eye closure), which can lead to exposure keratitis. The Bionic Lid Implant for Natural Eye Closure (BLINC) is a medical device designed to mimic the more natural blink kinetics than traditional lid loading techniques.

Aims: This study aimed to evaluate potential factors that might influence the design of the BLINC device and willingness of participant to undergo the implant placement surgery.

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  • - The study explores the combination of pembrolizumab (an anti-PD1 therapy) and trebananib (an angiopoietin inhibitor) in patients with metastatic ovarian cancer and microsatellite stable (MSS) colorectal cancer, as both cancers show resistance to PD1 immunotherapy.
  • - Results indicate that the highest tolerated dose of the combination therapy is trebananib at 30 mg/kg weekly plus pembrolizumab at 200 mg every 3 weeks, with a modest overall response rate of 7.3%, including durable responses in three MSS CRC patients.
  • - The successful patients exhibited particular tumor characteristics, such as left-sided CRC and no liver metastases; highlighting the need for further research into how
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Although buprenorphine use has increased dramatically over the past decade, its unique pharmacologic and pharmacokinetic profile often leads to misconceptions about its overall utility and has created a drastic underrepresentation in patients with chronic non-can- cer pain. A common misnomer associated with buprenorphine is because of 'partial agonist' activity, it exhibits a plateauing of typical opioid-related side effects (including respiratory depression, constipation, euphoria, and hypogonadal axis suppression), but additionally it must exhibit a plateauing effect of overall analgesic potential. However, novel downstream molecular and cellular mechanisms offer new insights that help support the clinical potential that buprenorphine's analgesic actions may not have a ceiling, like its side effect profile.

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Background: Historically, there has been limited evidence and no clear consensus suggesting best practices for perioperative buprenorphine management (PBM). Previously published PBM strategies included a wide variation in dosing, complexity, and clinical decision making points. Importantly, there are limited published algorithms reporting corresponding patient outcomes data.

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Purpose: Transcriptional profiling of pancreatic cancers has defined two main transcriptional subtypes: classical and basal. Initial data suggest shorter survival for patients with basal tumors and differing treatment sensitivity to FOLFIRINOX and gemcitabine plus nab-paclitaxel by transcriptional subtype.

Experimental Design: We examined 8,743 patients with RNA sequencing from pancreatic cancers performed at Caris Life Sciences.

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Spinocerebellar ataxias (SCAs) are a genetically heterogenous group of devastating neurodegenerative conditions for which clinical care currently focuses on managing symptoms. Across these diseases there is an unmet need for therapies that address underlying disease mechanisms. We utilised the shared CAG repeat expansion mutation causative for a large subgroup of SCAs, to develop a novel disease-gene independent and mechanism agnostic small molecule screening approach to identify compounds with therapeutic potential across multiple SCAs.

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Myotonic dystrophy type 1 (DM1) is a heterogeneous multisystemic disease caused by a CTG repeat expansion in DMPK. Transcription of the expanded allele produces toxic CUG repeat RNA that sequesters the MBNL family of alternative splicing (AS) regulators into ribonuclear foci, leading to pathogenic mis-splicing. To identify genetic modifiers of toxic CUG RNA levels and the spliceopathy, we performed a genome-scale siRNA screen using an established HeLa DM1 repeat-selective screening platform.

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Preclinical studies suggest that simultaneous HER2/VEGF blockade may have cooperative effects in gastroesophageal adenocarcinomas. In a single-arm investigator initiated clinical trial for patients with untreated advanced HER2+ gastroesophageal adenocarcinoma, bevacizumab was added to standard of care capecitabine, oxaliplatin, and trastuzumab in 36 patients (NCT01191697). Primary endpoint was objective response rate and secondary endpoints included safety, duration of response, progression free survival, and overall survival.

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  • * A study of 216 adults with TBM utilized brain MRI and clinical data, applying machine learning models to predict disease progression, achieving 60% balanced accuracy in prognosis across six categories.
  • * The model successfully identified TBM-related brain lesions in both HIV-positive and negative patients and accurately tracked disease changes in 80% of cases, showcasing potential for improved patient outcomes through timely clinical intervention.
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Biliary tract cancers (BTCs) are a group of deadly malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we present the integrative analysis of 63 BTC cell lines via multi-omics clustering and genome- scale CRISPR screens, providing a platform to illuminate BTC biology and inform therapeutic development. We identify dependencies broadly enriched in BTC compared to other cancers as well as dependencies selective to the anatomic subtypes.

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  • The gene IDH1 often changes in many cancers, leading to a harmful substance that messes with the body's natural defenses.
  • Tumors with this change often keep immune cells out, but blocking the mutant IDH1 can help the body's immune system attack the cancer.
  • The study shows that the mutant IDH1 silences certain genes that would usually help the immune system work, but stopping this mutation can help reactivate those genes and boost immunity against tumors.
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  • The study investigates the effects of blocking IL1β in combination with PD1 blockade and chemotherapy on myeloid immunosuppression and T-cell responses in patients with advanced pancreatic cancer.
  • Results showed a slight increase in activated CD8+ T cells and a reduction in myeloid-derived suppressor cells (MDSCs) in the blood of trial patients compared to those receiving standard chemotherapy.
  • However, changes in the tumor microenvironment were minimal, suggesting that larger studies are needed to fully understand the impacts of these treatments on tumor immunity.
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Purpose Of Review: Squamous cell carcinoma of the anus (SCCA) is an HPV-associated malignancy that has limited treatment options. Immunotherapy has expanded these options and here we review current and emerging immunotherapeutic approaches.

Recent Findings: Multiple studies of single-agent anti-PD1/PD-L1 immunotherapy have demonstrated a modest response rate of approximately 10% to 15%.

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  • - This study evaluated the safety and effectiveness of Debio 1347, a new oral drug targeting FGFR fusions in patients with advanced solid tumors, focusing on its ability to produce objective responses and other outcomes in different cancer types.
  • - A total of 63 patients participated, with only a 5% objective response rate, leading to the trial's early termination due to lower-than-expected effectiveness, despite manageable side effects like hyperphosphatemia and stomatitis.
  • - The findings suggest that while the drug has some tolerance, its lack of significant efficacy means it should not undergo further testing for FGFR fusion tumors; the study also provided insight into the characteristics of FGFR fusions in solid tumors.
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  • The document outlines updated guidelines from ASCO on incorporating palliative care into cancer treatment, aiming to enhance care for patients diagnosed with cancer.
  • An Expert Panel reviewed relevant literature from 2015-2023, focusing on improving quality of life, patient satisfaction, and addressing psychological and physical symptoms.
  • Recommendations include early involvement of specialized palliative care for patients with advanced cancer and support for caregivers to alleviate distress and improve overall well-being.
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Daptomycin use for gram-positive infections has increased. This cost minimization analysis aimed to determine cost and/or time savings of daptomycin over vancomycin. The estimated hospital cost savings was US$166.

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