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Introduction: Enhanced recovery after surgery (ERAS) protocols have been implemented to decrease opioid use and decrease patient hospital length of stay (LOS, days). Serratus anterior plane (SAP) blocks anesthetize the T2 through T9 dermatomes of the breast and can be applied intraoperatively. The purpose of this study was to compare postoperative opioid (OME) consumption and LOS between a control group, an ERAS group, and an ERAS/local anesthetic cocktail group in patients who underwent implant-based breast reconstruction. Methods: In this study, 142 women who underwent implant-based breast reconstruction between 2004 and 2020 were divided into Group A (46 patients), a historical cohort; Group B (73 patients), an ERAS/no-block control group; and Group C (23 patients), an ERAS/anesthetic cocktail study group. Primary outcomes of interest were postanesthesia care unit (PACU), inpatient and total hospital OME consumption, and PACU LOS. Results: A significant decrease was observed from Group A to C in PACU LOS (103.3 vs. 80.2 vs. 70.5; p = 0.011), OME use (25.1 vs. 11.4 vs. 5.7; p < 0.0001), and total hospital OME (120.3 vs. 95.2 vs. 35.9; p < 0.05). No difference was observed in inpatient OMEs between the three groups (95.2 vs. 83.8 vs. 30.8; p = 0.212). Despite not reaching statistical significance, Group C consumed an average of 50-60 % less opioids per patient than did Group B in PACU, inpatient, and total hospital OMEs. Conclusion: Local anesthetic blocks are important components of ERAS protocols. Our results demonstrate that a combination regional block with a local anesthetic cocktail in an ERAS protocol can decrease opioid consumption in implant-based breast reconstruction.
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Accurate detection of homologous recombination deficiency (HRD) in cancer patients is paramount in clinical applications, as HRD confers sensitivity to poly (ADP-ribose) polymerase (PARP) inhibitors. With the advances in genome sequencing technology, mutational profiling on a genome-wide scale has become readily accessible, and our knowledge of the genomic consequences of HRD has been greatly expanded and refined. Here, we review the recent advances in HRD detection methods. We examine the copy number and structural alterations that often accompany the genome instability that results from HRD, describe the advantages of mutational signature-based methods that do not rely on specific gene mutations, and review some of the existing algorithms used for HRD detection. We also discuss the choice of sequencing platforms (panel, exome, or whole-genome) and catalog the HRD detection assays used in key PARP inhibitor trials.
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Garrett and Braunstein introduced the concept of the "seat belt sign" in motor vehicle collision (MVC) victims. They defined this as abdominal wall bruising from a lap belt. These signs of trauma are not uncommon. However, "seat belt syndrome," a pattern of musculoskeletal and internal organ injuries resulting from deceleration forces exerted by the safety device is rarely seen. Here, we illustrate a case of traumatic closed rupture of the rectus abdominis muscle secondary to seat belt injury. This potential injury is important to recognize and our case will illustrate the need for careful imaging review and clinical assessment to identify associated intra-abdominal injuries.
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The emergence of large language models (LLMs) has sparked considerable interest in their potential application in psychological research, mainly as a model of the human psyche or as a general text-analysis tool. However, the trend of using LLMs without sufficient attention to their limitations and risks, which we rhetorically refer to as "GPTology", can be detrimental given the easy access to models such as ChatGPT. Beyond existing general guidelines, we investigate the current limitations, ethical implications, and potential of LLMs specifically for psychological research, and show their concrete impact in various empirical studies. Our results highlight the importance of recognizing global psychological diversity, cautioning against treating LLMs (especially in zero-shot settings) as universal solutions for text analysis, and developing transparent, open methods to address LLMs' opaque nature for reliable, reproducible, and robust inference from AI-generated data. Acknowledging LLMs' utility for task automation, such as text annotation, or to expand our understanding of human psychology, we argue for diversifying human samples and expanding psychology's methodological toolbox to promote an inclusive, generalizable science, countering homogenization, and over-reliance on LLMs.
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Background: Atrial fibrillation (AF) is the most common arrhythmia reported worldwide. There is significant heterogeneity in AF care pathways for a patient seen in the emergency room, impacting access to guideline-driven therapies. Objectives: The purpose of this study was to compare the difference in AF outcomes between those treated with an organized treatment pathway vs routine-care approach. Methods: The emergency room to electrophysiology service study (ER2EP) is a multicenter, prospective observational registry (NCT04476524) enrolling patients with AF from sites where a pathway for management of AF was put in place compared to sites where a pathway was not in place within the same health system and the same physicians providing services at all sites. Multivariable regression modeling was performed to identify predictors of clinical outcomes. Beta coefficient or odds ratio was reported as appropriate. Results: A total of 500 patients (ER2EP group, n = 250; control group, n = 250) were included in the study. The mean age was 73.4 ± 12.9 years, and 52.2% were males. There was a statistically significant difference in primary endpoint [time to ablation (56 ± 50.9 days vs 183.3 ± 109.5 days; P < 0.001), time to anticoagulation initiation (2.1 ± 1.6 days vs 19.7 ± 35 days, P < 0.001), antiarrhythmic drug initiation (4.8 ± 7.1 days vs 24.7 ± 44.4 days, P < 0.001) compared to the control group, respectively. As such, this resulted in reduced length of stay in the ER2EP group compared to the control group (2.4 ± 1.4 days vs 3.23 ± 2.5 days, P = 0.002). Conclusions: This study provides evidence that having an organized pathway from the emergency department for AF patients involving electrophysiology services can improve early access to definitive therapies and clinical outcomes.
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BACKGROUND: Traditional constraints specify that 700 cc of liver should be spared a hepatotoxic dose when delivering liver-directed radiotherapy to reduce the risk of inducing liver failure. We investigated the role of single-photon emission computed tomography (SPECT) to identify and preferentially avoid functional liver during liver-directed radiation treatment planning in patients with preserved liver function but limited functional liver volume after receiving prior hepatotoxic chemotherapy or surgical resection. METHODS: This phase I trial with a 3 + 3 design evaluated the safety of liver-directed radiotherapy using escalating functional liver radiation dose constraints in patients with liver metastases. Dose-limiting toxicities were assessed 6-8 weeks and 6 months after completing radiotherapy. RESULTS: All 12 patients had colorectal liver metastases and received prior hepatotoxic chemotherapy; 8 patients underwent prior liver resection. Median computed tomography anatomical nontumor liver volume was 1584 cc (range = 764-2699 cc). Median SPECT functional liver volume was 1117 cc (range = 570-1928 cc). Median nontarget computed tomography and SPECT liver volumes below the volumetric dose constraint were 997 cc (range = 544-1576 cc) and 684 cc (range = 429-1244 cc), respectively. The prescription dose was 67.5-75 Gy in 15 fractions or 75-100 Gy in 25 fractions. No dose-limiting toxicities were observed during follow-up. One-year in-field control was 57%. One-year overall survival was 73%. CONCLUSION: Liver-directed radiotherapy can be safely delivered to high doses when incorporating functional SPECT into the radiation treatment planning process, which may enable sparing of lower volumes of liver than traditionally accepted in patients with preserved liver function. TRIAL REGISTRATION: NCT02626312.
Subject(s)
Colorectal Neoplasms , Liver Neoplasms , Liver , Radiotherapy, Image-Guided , Tomography, Emission-Computed, Single-Photon , Humans , Male , Female , Liver Neoplasms/secondary , Liver Neoplasms/radiotherapy , Liver Neoplasms/diagnostic imaging , Middle Aged , Aged , Liver/diagnostic imaging , Liver/radiation effects , Radiotherapy, Image-Guided/methods , Colorectal Neoplasms/radiotherapy , Colorectal Neoplasms/pathology , Colorectal Neoplasms/diagnostic imaging , Organ Size , Radiotherapy Dosage , Tomography, X-Ray Computed , Radiotherapy Planning, Computer-Assisted/methods , AdultABSTRACT
This paper argues that a range of current AI systems have learned how to deceive humans. We define deception as the systematic inducement of false beliefs in the pursuit of some outcome other than the truth. We first survey empirical examples of AI deception, discussing both special-use AI systems (including Meta's CICERO) and general-purpose AI systems (including large language models). Next, we detail several risks from AI deception, such as fraud, election tampering, and losing control of AI. Finally, we outline several potential solutions: first, regulatory frameworks should subject AI systems that are capable of deception to robust risk-assessment requirements; second, policymakers should implement bot-or-not laws; and finally, policymakers should prioritize the funding of relevant research, including tools to detect AI deception and to make AI systems less deceptive. Policymakers, researchers, and the broader public should work proactively to prevent AI deception from destabilizing the shared foundations of our society.
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Improvements in single-cell whole-genome sequencing (scWGS) assays have enabled detailed characterization of somatic copy number alterations (CNAs) at the single-cell level. Yet, current computational methods are mostly designed for detecting chromosome-scale changes in cancer samples with low sequencing coverage. Here, we introduce HiScanner (High-resolution Single-Cell Allelic copy Number callER), which combines read depth, B-allele frequency, and haplotype phasing to identify CNAs with high resolution. In simulated data, HiScanner consistently outperforms state-of-the-art methods across various CNA types and sizes. When applied to high-coverage scWGS data from human brain cells, HiScanner shows a superior ability to detect smaller CNAs, uncovering distinct CNA patterns between neurons and oligodendrocytes. For 179 cells we sequenced from longitudinal meningioma samples, integration of CNAs with point mutations revealed evolutionary trajectories of tumor cells. These findings show that HiScanner enables accurate characterization of frequency, clonality, and distribution of CNAs at the single-cell level in both non-neoplastic and neoplastic cells.
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Insertion of active retroelements-L1s, Alus, and SVAs-can disrupt proper genome function and lead to various disorders including cancer. However, the role of de novo retroelements (DNRTs) in birth defects and childhood cancers has not been well characterized due to the lack of adequate data and efficient computational tools. Here, we examine whole-genome sequencing data of 3,244 trios from 12 birth defect and childhood cancer cohorts in the Gabriella Miller Kids First Pediatric Research Program. Using an improved version of our tool xTea (x-Transposable element analyzer) that incorporates a deep-learning module, we identified 162 DNRTs, as well as 2 pseudogene insertions. Several variants are likely to be causal, such as a de novo Alu insertion that led to the ablation of a whole exon in the NF1 gene in a proband with brain tumor. We observe a high de novo SVA insertion burden in both high-intolerance loss-of-function genes and exons as well as more frequent de novo Alu insertions of paternal origin. We also identify potential mosaic DNRTs from embryonic stages. Our study reveals the important roles of DNRTs in causing birth defects and predisposition to childhood cancers.
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Persistent postsurgical pain (PPSP) is one of the most bothersome and disabling long-term complications after inguinal hernia repair surgery. Understanding perioperative risk factors that contribute to PPSP can help identify high-risk patients and develop risk-mitigation approaches. The objective of this study was to systematically review and meta-analyze risk factors that contribute to PPSP after inguinal hernia repair. The literature search resulted in 303 papers included in this review, 140 of which were used for meta-analyses. Our results suggest that younger age, female sex, preoperative pain, recurrent hernia, postoperative complications, and postoperative pain are associated with a higher risk of PPSP. Laparoscopic techniques reduce the PPSP occurrence compared to anterior techniques such as Lichtenstein repair, and tissue-suture techniques such as Shouldice repair. The use of fibrin glue for mesh fixation was consistently associated with lower PPSP rates compared to tacks, staples, and sutures. Considerable variability was observed with PPSP assessment and reporting methodology in terms of study design, follow-up timing, clarity of pain definition, as well as pain intensity or interference threshold. High or moderate risk of bias in at least one domain was noted in >75% of studies. These may limit the generalizability of our results. Future studies should assess and report comprehensive preoperative and perioperative risk factors for PPSP adjusted for confounding factors, and develop risk-prediction models to drive stratified PPSP-mitigation trials and personalized clinical decision-making. PERSPECTIVE: This systematic review and meta-analysis summarizes the current evidence on risk factors for persistent pain after inguinal hernia repair. The findings can help identify patients at risk and test personalized risk-mitigation approaches to prevent pain. PROSPERO REGISTRATION: htttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=154663.
Subject(s)
Hernia, Inguinal , Herniorrhaphy , Pain, Postoperative , Humans , Hernia, Inguinal/surgery , Pain, Postoperative/etiology , Herniorrhaphy/adverse effects , Risk Factors , Chronic Pain/etiologyABSTRACT
Short-cationic alpha-helical antimicrobial peptides (SCHAMPs) are promising candidates to combat the growing global threat of antimicrobial resistance. They are short-sequenced, selective against bacteria, and have rapid action by destroying membranes. A full understanding of their mechanism of action will provide key information to design more potent and selective SCHAMPs. Molecular Dynamics (MD) simulations are invaluable tools that provide detailed insights into the peptide-membrane interaction at the atomic- and meso-scale level. We use atomistic and coarse-grained MD to look into the exact steps that four promising SCHAMPs-BP100, Decoralin, Neurokinin-1, and Temporin L-take when they interact with membranes. Following experimental set-ups, we explored the effects of SCHAMPs on anionic membranes and vesicles at multiple peptide concentrations. Our results showed all four peptides shared similar binding steps, initially binding to the membrane through electrostatic interactions and then flipping on their axes, dehydrating, and inserting their hydrophobic moieties into the membrane core. At higher concentrations, fully alpha-helical peptides induced membrane budding and protrusions. Our results suggest the carpet mode of action is fit for the description of SCHAMPs lysis activity and discuss the importance of large hydrophobic residues in SCHAMPs design and activity.
Subject(s)
Antimicrobial Cationic Peptides , Molecular Dynamics Simulation , Antimicrobial Cationic Peptides/chemistry , Antimicrobial Cationic Peptides/pharmacology , Antimicrobial Peptides/chemistry , Antimicrobial Peptides/pharmacology , Hydrophobic and Hydrophilic Interactions , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Static ElectricityABSTRACT
OBJECTIVE: To create a data-driven definition of post-COVID conditions (PCC) by directly measure changes in symptomatology before and after a first COVID episode. MATERIALS AND METHODS: Retrospective cohort study using Optum® de-identified Electronic Health Record (EHR) dataset from the United States of persons of any age April 2020-September 2021. For each person with COVID (ICD-10-CM U07.1 "COVID-19" or positive test result), we selected up to 3 comparators. The final COVID symptom score was computed as the sum of new diagnoses weighted by each diagnosis' ratio of incidence in COVID group relative to comparator group. For the subset of COVID cases diagnosed in September 2021, we compared the incidence of PCC using our data-driven definition with ICD-10-CM code U09.9 "Post-COVID Conditions", first available in the US October 2021. RESULTS: The final cohort contained 588,611 people with COVID, with mean age of 48 years and 38% male. Our definition identified 20% of persons developed PCC in follow-up. PCC incidence increased with age: (7.8% of persons aged 0-17, 17.3% aged 18-64, and 33.3% aged 65+) and did not change over time (20.0% among persons diagnosed with COVID in 2020 versus 20.3% in 2021). For cases diagnosed in September 2021, our definition identified 19.0% with PCC in follow-up as compared to 2.9% with U09.9 code in follow-up. CONCLUSION: Symptom and U09.9 code-based definitions alone captured different populations. Maximal capture may consider a combined approach, particularly before the availability and routine utilization of specific ICD-10 codes and with the lack consensus-based definitions on the syndrome.
Subject(s)
COVID-19 , Humans , Male , United States/epidemiology , Middle Aged , Female , COVID-19/epidemiology , Electronic Health Records , Post-Acute COVID-19 Syndrome , Retrospective Studies , International Classification of DiseasesABSTRACT
Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons. Correlation of mutations with single-nucleus RNA profiles and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed across the genome similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These stark differences suggest an assortment of active mutagenic processes in oligodendrocytes and neurons.
Subject(s)
Aging , Brain , Neurons , Oligodendroglia , Humans , Aging/genetics , Aging/pathology , Chromatin/genetics , Chromatin/metabolism , Mutation , Neurons/metabolism , Neurons/pathology , Oligodendroglia/metabolism , Oligodendroglia/pathology , Single-Cell Gene Expression Analysis , Whole Genome Sequencing , Brain/metabolism , Brain/pathology , Polymorphism, Single Nucleotide , INDEL Mutation , Biological Specimen Banks , Oligodendrocyte Precursor Cells/metabolism , Oligodendrocyte Precursor Cells/pathologyABSTRACT
In all terrestrial vertebrates, the parathyroid glands are critical regulators of calcium homeostasis and the sole source of parathyroid hormone (PTH). Hyperparathyroidism and hypoparathyroidism are clinically important disorders affecting multiple organs. However, our knowledge regarding regulatory mechanisms governing the parathyroids has remained limited. Here, we present the comprehensive maps of the chromatin landscape of the human parathyroid glands, identifying active regulatory elements and chromatin interactions. These data allow us to define regulatory circuits and previously unidentified genes that play crucial roles in parathyroid biology. We experimentally validate candidate parathyroid-specific enhancers and demonstrate their integration with GWAS SNPs for parathyroid-related diseases and traits. For instance, we observe reduced activity of a parathyroid-specific enhancer of the Calcium Sensing Receptor gene, which contains a risk allele associated with higher PTH levels compared to the wildtype allele. Our datasets provide a valuable resource for unraveling the mechanisms governing parathyroid gland regulation in health and disease.
Subject(s)
Calcium , Parathyroid Glands , Animals , Humans , Calcium/metabolism , Parathyroid Glands/metabolism , Parathyroid Hormone/genetics , Parathyroid Hormone/metabolism , Chromatin/genetics , Epigenesis, GeneticABSTRACT
Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
Subject(s)
Music , Neoplasms , Humans , Neoplasms/genetics , Mutation , Carcinogenesis/genetics , INDEL MutationABSTRACT
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
Subject(s)
Aneuploidy , Humans , Female , Breast Neoplasms/genetics , Breast Neoplasms/pathology , DNA Copy Number Variations , Neoplasms/genetics , Neoplasms/pathology , Translocation, Genetic , Evolution, Molecular , Cell Proliferation/genetics , Receptors, Notch/genetics , Receptors, Notch/metabolism , Organ Specificity/genetics , Epithelial Cells/metabolism , Epithelial Cells/pathologyABSTRACT
Purpose: Recurrent or new primary breast cancer requiring comprehensive regional nodal irradiation after prior radiation therapy (RT) to the supraclavicular area and upper axilla is challenging due to cumulative brachial plexus (BP) dose tolerance. We assessed BP dose sparing achieved with pencil beam scanning proton therapy (PBS-PT) and photon volumetric modulated arc therapy (VMAT). Methods and Materials: In an institutional review board-approved planning study, all patients with ipsilateral recurrent breast cancer treated with PBS-PT re-RT (PBT1) with at least partial BP overlap from prior photon RT were identified. Comparative VMAT plans (XRT1) using matched BP dose constraints were developed. A second pair of proton (PBT2) and VMAT (XRT2) plans using standardized target volumes were created, applying uniform prescription dose of 50.4 per 1.8 Gy and a maximum BP constraint <25 Gy. Incidence of brachial plexopathy was also assessed. Results: Ten consecutive patients were identified. Median time between RT courses was 48 months (15-276). Median first, second, and cumulative RT doses were 50.4 Gy (range, 42.6-60.0), 50.4 Gy relative biologic effectiveness (RBE) (45.0-64.4), and 102.4 Gy (RBE) (95.0-120.0), respectively. Median follow-up was 15 months (5-33) and 18 months for living patients (11-33) Mean BP max was 37.5 Gy (RBE) for PBT1 and 36.9 Gy for XRT1. Target volume coverage of V85% (volume receiving 85% of prescription dose), V90%, and V95% were numerically lower for XRT1 versus PBT1. Similarly, axilla I-III and supraclavicular area coverage were significantly higher for PBT2 than XRT2 at dose levels of V55%, V65%, V75%, V85%, and V95%. Only axilla I V55% did not reach significance (P = .06) favoring PBS-PT. Two patients with high cumulative BPmax (95.2 Gy [RBE], 101.6 Gy [RBE]) developed brachial plexopathy symptoms with ulnar nerve distribution neuropathy without pain or weakness (1 of 2 had symptom resolution after 6 months without intervention). Conclusions: PBS-PT improved BP sparing and target volume coverage versus VMAT. For patients requiring comprehensive re-RT for high-risk, nonmetastatic breast cancer recurrence with BP overlap and reasonable expectation for prolonged life expectancy, PBT may be the preferred treatment modality.
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INTRODUCTION/BACKGROUND: Immune checkpoint inhibitors (ICIs) have limited efficacy in prostate cancer (PCa). Better biomarkers are needed to predict responses to ICIs. We sought to demonstrate that a panel-based mutational signature identifies mismatch repair (MMR) deficient (MMRd) PCa and is a biomarker of response to pembrolizumab. PATIENTS AND METHODS: Clinico-genomic data was obtained for 2664 patients with PCa sequenced at Dana-Farber Cancer Institute (DFCI) and Memorial Sloan Kettering (MSK). Clinical outcomes were collected for patients with metastatic castration-resistant PCa (mCRPC) treated with pembrolizumab at DFCI. SigMA was used to characterize tumors as MMRd or MMR proficient (MMRp). The concordance between MMRd with microsatellite instability (MSI-H) was assessed. Radiographic progression-free survival (rPFS) and overall survival (OS) were collected for patients treated with pembrolizumab. Event-time distributions were estimated using Kaplan-Meier methodology. RESULTS: Across both cohorts, 100% (DFCI: 12/12; MSK: 43/43) of MSI-H tumors were MMRd. However, 14% (2/14) and 9.1% (6/66) of MMRd tumors in the DFCI and MSK cohorts respectively were microsatellite stable (MSS), and 26% (17/66) were MSI-indeterminate in the MSK cohort. Among patients treated with pembrolizumab, those with MMRd (n = 5) versus MMRp (n = 14) mCRPC experienced markedly improved rPFS (HR = 0.088, 95% CI: 0.011-0.70; P = .0064) and OS (HR = 0.11, 95% CI: 0.014-0.80; P = .010) from start of treatment. Four patients with MMRd experienced remissions of >= 2.5 years. CONCLUSION: SigMA detects additional cases of MMRd as compared to MSI testing in PCa and identifies patients likely to experience durable response to pembrolizumab.
Subject(s)
Brain Neoplasms , Colorectal Neoplasms , Neoplastic Syndromes, Hereditary , Prostatic Neoplasms, Castration-Resistant , Male , Humans , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/genetics , Antibodies, Monoclonal, Humanized/therapeutic use , Neoplastic Syndromes, Hereditary/chemically induced , Neoplastic Syndromes, Hereditary/drug therapyABSTRACT
Despite the overall efficacy of immune checkpoint blockade (ICB) for mismatch repair deficiency (MMRD) across tumor types, a sizable fraction of patients with MMRD still do not respond to ICB. We performed mutational signature analysis of panel sequencing data (n = 95) from MMRD cases treated with ICB. We discover that T>C-rich single base substitution (SBS) signatures-SBS26 and SBS54 from the COSMIC Mutational Signatures catalog-identify MMRD patients with significantly shorter overall survival. Tumors with a high burden of SBS26 show over-expression and enriched mutations of genes involved in double-strand break repair and other DNA repair pathways. They also display chromosomal instability (CIN), likely related to replication fork instability, leading to copy number losses that trigger immune evasion. SBS54 is associated with transcriptional activity and not with CIN, defining a distinct subtype. Consistently, cancer cell lines with a high burden of SBS26 and SBS54 are sensitive to treatments targeting pathways related to their proposed etiology. Together, our analysis offers an explanation for the heterogeneous responses to ICB among MMRD patients and supports an SBS signature-based predictor as a prognostic biomarker for differential ICB response.
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We test whether large language models (LLMs) can be used to simulate human participants in social-science studies. To do this, we ran replications of 14 studies from the Many Labs 2 replication project with OpenAI's text-davinci-003 model, colloquially known as GPT-3.5. Based on our pre-registered analyses, we find that among the eight studies we could analyse, our GPT sample replicated 37.5% of the original results and 37.5% of the Many Labs 2 results. However, we were unable to analyse the remaining six studies due to an unexpected phenomenon we call the "correct answer" effect. Different runs of GPT-3.5 answered nuanced questions probing political orientation, economic preference, judgement, and moral philosophy with zero or near-zero variation in responses: with the supposedly "correct answer." In one exploratory follow-up study, we found that a "correct answer" was robust to changing the demographic details that precede the prompt. In another, we found that most but not all "correct answers" were robust to changing the order of answer choices. One of our most striking findings occurred in our replication of the Moral Foundations Theory survey results, where we found GPT-3.5 identifying as a political conservative in 99.6% of the cases, and as a liberal in 99.3% of the cases in the reverse-order condition. However, both self-reported 'GPT conservatives' and 'GPT liberals' showed right-leaning moral foundations. Our results cast doubts on the validity of using LLMs as a general replacement for human participants in the social sciences. Our results also raise concerns that a hypothetical AI-led future may be subject to a diminished diversity of thought.