tbuckley/cabot-search huggingface dataset:
Prevalence-adjusted trends in U.S. healthcare spending on colorectal cancer, 1996-2016.
Authors: Igor Stukalin, Newaz Shubidito Ahmed, Adam Michael Fundytus, Siddharth Singh, Christopher Ma
Journal: Journal of Clinical Oncology (2021)

e18819 Background: Colorectal cancer is rising in prevalence and associated with high healthcare costs. We estimated trends in the US healthcare spending in patients with colorectal cancer between 1996 and 2016. Methods: We used data on national healthcare spending developed by the Institute for Health Metrics and Evaluations for the Disease Expenditure Project. Corresponding US age-specific prevalence of colon cancer was estimated from the Global Burden of Diseases Study. Prevalence-adjusted, temporal trends in the US healthcare spending in patients with colorectal cancer, stratified by age groups ( &lt; 20, 20-44, 45-64, &gt;65) and by type of care (ambulatory, inpatient, emergency department, pharmaceutical prescriptions, nursing care and government administration) were estimated using joinpoint regression, expressed as annual percent change (APC) with 95% confidence intervals. Results: Overall, annual US healthcare spending on colorectal cancer increased from $8.85 billion (95% CI $8.17 billion, $9.53 billion) in 1996 to $10.5 billion (95% CI $9.35 billion, $11.7 billion) in 2016, with total costs increasing by 0.9%/year (95% CI 0.1%, 1.6%). After adjusting for colorectal cancer prevalence, the absolute per capita spending decreased from $8848 to $8427 and there has been no significant change over time (APC 0.3%, 95% CI, -0.2%, 0.8%). However, spending in patients &gt; 65 decreased significantly by 1.3%/year (95% CI -2.2%, -0.5%). Inpatient care was the largest contributor to total colorectal cancer-related expenditures: in 2016, 65.9% (95% CI 59.5%, 71.0%) and 19.7% (95% CI 14.8%, 25.8%) of the total cost were spent on inpatient care and ambulatory care, respectively. Between 1996-2016, increases in the price and intensity of care (defined by the cost per encounter) was the largest positive driver of changing healthcare spending, accounting for $5.02 billion ($2.60, $7.33 billion). Conclusions: After adjusting for rising prevalence, US healthcare spending on colorectal cancer has not changed significantly since 1996, while the per capita cost continues to decrease, primarily in patients &gt; 65 years old. Inpatient care accounts for the majority of colorectal cancer-related expenditures.
Fecal microbiome composition in pancreatic cancer cachexia and response to nutrition support.
Authors: Natalie Moshayedi, Julianne Yang, Venu Lagishetty, Jonathan Jacobs, Veronica Placencio-Hickok, Arsen Osipov, Andrew Eugene Hendifar, Jun Gong
Journal: Journal of Clinical Oncology (2021)

4129 Background: Pancreatic ductal adenocarcinoma (PDAC) carries a poor prognosis with a 5-year survival rate of 10.0%. Previous studies in stool microbiome indicate that microbiome composition has been associated with therapy response and pathogenesis across multiple cancers, and PDAC patients (pts) with higher bacterial diversity have demonstrated greater long-term survival. The fecal microbiome has not previously been characterized for PDAC pts with cancer cachexia or associated interventions. The study addressed the changes in microbiome over the course of treatment and the association between baseline bacterial composition and outcome in PDAC pts with cachexia. Methods: Stool specimens were collected from the PNCX1 trial (NCT02400398), where all pts were given a semi-elemental diet—enzymatically hydrolyzed protein—with enteral tube feeding. Stool samples (n = 29) were collected at time points aligned with enteral feeding and chemotherapy cycles separated by 6 weeks (C1D1, C2D1, and C3D1) and analyzed using 16S v4 sequencing of the microbiome. Microbiome changes from C1D1 to C3D1, weight stability, and overall survival (OS) were measured alongside microbiome characterization. Results: Pts with a complete set of stool samples were analyzed (n = 6) for differences in microbiome composition across treatment cycles. C3D1 samples were significantly associated with both an increased population of Veillonella and Actinomyces and decreased Bacteroides and Butyricicoccus compared to C1D1. Baseline stool microbiome composition was also evaluated to predict weight stability throughout treatment. In patient stool samples (n = 8) at C1D1, greater abundance of Veillonella (p = 0.0006) and reduced Bifidobacterium (p = 2.62E-5) were linked to greater weight stability. Microbiome alpha-diversity was also characterized using Shannon and Chao1 indices, where stable weight was related to reduced species richness (Chao1, p = 0.0194) but not evenness (Shannon, p = 0.1716). C1D1 patient stool samples were then analyzed and compared to OS (n = 16). Although no significant differences in global microbiome composition were noted between OS &lt; 180 days and OS &gt; 180 days, Parasutterella, Tyzzerella, Phascolarctobacterium, and Lachnoclostridium were identified as more prevalent in OS &gt; 180 days despite their relatively low abundance. Conclusions: We are among the first evaluate stool bacteria changes over treatment course in PDAC pts. While Veillonella was associated with weight stability in a cohort of advanced PDAC pts all receiving enteral feeding, several genera were found in abundance in pts with prolonged OS, though this needs further validation. The potential impact of the gut microbiome and enteral feeding on weight stability is provocative given that cachexia is a hallmark of PDAC and an effective strategy to mitigate this process would be transformative.
Active Surveillance as a Management Option for Low-risk Basal Cell Carcinoma
Authors: Eleni Linos, Mary-Margaret Chren
Journal: JAMA Internal Medicine (2021)

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Efficacy of stereotactic body radiotherapy for oligoprogression on PD-1 axis inhibitors in advanced non-small cell lung cancer: A single-center retrospective study.
Authors: Zhen Wang, Jing Li, Han Zhou, Si Li, Xi-xu Zhu
Journal: Journal of Clinical Oncology (2021)

e21065 Background: Immunotherapy has brought considerable benefit for patients with advanced non-small cell lung cancer (NSCLC), while acquired resistance could occur, of which most were oligoprogression. Adding locoregional therapy into the current systematic treatment could significantly improve the survival of oligoprogressed group. One of the conventional locoregional therapy for oligoprogression is stereotactic body radiotherapy (SBRT), however efficacy of combing SBRT to the ongoing PD-1 axis inhibitors was unclear in oligoprogressive NSCLC. Methods: In this study, we retrospectively reviewed data of patients with advanced NSCLC, who received SBRT on oligoprogressive lesions after acquired resistance to PD-1 axis inhibitor (First line or more) in our hospital, between June 2015 and June 2019. Acquired resistance was defined as initial CR/PR (by RECIST) followed by progression/death. Oligo patterns of acquired resistance were defined as progression in ≤ 3 sites of disease. We summarized the locoregional control rate (LR), progression-free survival (PFS) and overall survival (OS) after SBRT. Results: A total of 18 patients were included, 5 females and 13 males. The median age was 63 years (range: 37-82). 10 (55.6%) patients had a PD-L1 expression &gt; 1%, 13 (72.2%) received combination therapy (anti-PD-1+chemo/antivascular), duration of immunotherapy was longer than 24 months in 9 (50%) patients. After acquired resistance, 25 sites of oligoprogressive lesions were identified (11 in brain, 5 in lung, 3 in lymph node, 3 in bone, 2 in adrenal, 1 in liver), the median maximum dimension was 14.8 cm (range, 10 to 79 cm). The SBRT dose were 30-55 Gy/2-6 fx, with the median biological effective dose at 60 Gy (range: 45-124.8). At a median follow-up of 28.5 months (range: 15-60), 12 (48%) lesions achieved complete response, 7 (28%) had a partial response, 4 (16%) remains stable and 2 (8%) developed progressive disease. The 1 and 2 years’ LR were 100% and 77.8% respectively. The median PFS was 10 months (range: 7-18). Among them, 44.4% and 14.8% had a 1 and 2 years of PFS, and 87.5% and 60% achieved 1-year and 2-year survival respectively. Conclusions: We observed that SBRT for oligoprogression can improve disease control and bring survival benefit, suggesting that SBRT could be considered in patients with oligoprogression after required resistance on immunotherapy in NSCLC. Meanwhile, prospective evaluation or stratified analysis with larger sample size was needed to verify its efficacy and safety in specific group.
Using randomized trial data to estimate effects of complex treatment regimens in real-world patients.
Authors: Michael Webster-Clark, Hanna Kelly Sanoff, Jennifer Leigh Lund, Til Sturmer, Daniel Westreich, Alexander P. Keil
Journal: Journal of Clinical Oncology (2021)

e18706 Background: Real-world patients often differ from trial participants in prognostic factors such as age, sex, and cancer substage. New methods combine covariate data from real-world patients (the “target population”) with outcome and covariate data from a trial to estimate treatment effects in the target population that take these differences into account. With some assumptions, these methods can also estimate outcomes under treatment regimens not studied in the trial such as “what if we only gave six cycles of chemotherapy?” or “what if patients all perfectly followed a protocol?” Methods: Data from the MOSAIC trial of 5-fluorouracil (5FU) vs oxaliplatin + 5FU (FOLFOX) were combined with covariate data from a target population of stage III colon cancer patients in the US Oncology Network meeting trial eligibility criteria. We used weighting and G-computation to estimate five-year mortality and treatment-related paresthesia risk in the target population for four regimens: treatment with up to 12 cycles of 5FU, if providers used their discretion on dose reductions and delays (5FU-MD); up to 12 cycles of FOLFOX with similar physician discretion (FOLFOX-MD); up to 6 cycles of FOLFOX, with providers perfectly following a strict and specific protocol of dose reductions and delays (6-cycle FOLFOX-P, “P” for “per protocol”); and up to 12 cycles of FOLFOX, following the same strict protocol (12-cycle FOLFOX-P). Results: Tablepresents five-year all-cause mortality and paresthesia risk under each regimen in the stage III target population estimated from the models built in trial participants. Paresthesia risk increased with cumulative oxaliplatin dose. Estimated 5-year mortality was lowest with 12-cycle FOLFOX-P. Conclusions: In a target population of US Oncology Network patients with stage III colon cancer, strict protocols of 12 cycles of FOLFOX were predicted to improve survival compared to strict 6-cycle FOLFOX regimens or less strict 12-cycle FOLFOX and 5FU regimens at the cost of substantial increases in side effects. While estimates of risk differences in 5-year mortality were imprecise, combining trial and real-world data and then using weights and G-computation allowed estimation of benefits and harms of multiple regimens in a clinically relevant patient population.[Table: see text]
Treatment with a long-acting chimeric CSF1 molecule enhances fracture healing of healthy and osteoporotic bones
Authors: Lena Batoon, Susan M. Millard, Liza J. Raggatt, Cheyenne Sandrock, Edmund Pickering, Kyle Williams, Lucas W.H. Sun, Andy C. Wu, Katharine M. Irvine, Peter Pivonka, Vaida Glatt, Martin E. Wullschleger, David A. Hume, Allison R. Pettit
Journal: Biomaterials (2021)
PrEP uptake, persistence, adherence, and effect of retrospective drug level feedback on PrEP adherence among young women in southern Africa: Results from HPTN 082, a randomized controlled trial
Authors: Connie Celum, Sybil Hosek, Mandisa Tsholwana, Sheetal Kassim, Shorai Mukaka, Bonnie J. Dye, Subash Pathak, Nyaradzo Mgodi, Linda-Gail Bekker, Deborah J. Donnell, Ethan Wilson, Krista Yuha, Peter L. Anderson, Yaw Agyei, Heather Noble, Scott M. Rose, Jared M. Baeten, Jessica M. Fogel, Adeola Adeyeye, Lubbe Wiesner, James Rooney, Sinead Delany-Moretlwe
Journal: PLoS Medicine (2021)

Background Pre-exposure prophylaxis (PrEP) is highly effective and an important prevention tool for African adolescent girls and young women (AGYW), but adherence and persistence are challenging. PrEP adherence support strategies for African AGYW were studied in an implementation study. Methods and findings HIV Prevention Trials Network (HPTN) 082 was conducted in Cape Town, Johannesburg (South Africa) and Harare (Zimbabwe) from October 2016 to October 2018 to evaluate PrEP uptake, persistence, and the effect of drug level feedback on adherence. Sexually active HIV–negative women ages 16–25 were offered PrEP and followed for 12 months; women who accepted PrEP were randomized to standard adherence support (counseling, 2-way SMS, and adherence clubs) or enhanced adherence support with adherence feedback from intracellular tenofovir-diphosphate (TFV-DP) levels in dried blood spots (DBS). PrEP uptake, persistence through 12 months (no PrEP hold or missed visits), and adherence were assessed. The primary outcome was high adherence (TFV-DP ≥700 fmol/punch) at 6 months, compared by study arm. Of 451 women enrolled, median age was 21 years, and 39% had curable sexually transmitted infections (STIs). Most (95%) started PrEP, of whom 55% had uninterrupted PrEP refills through 12 months. Of those with DBS, 84% had detectable TFV-DP levels at month 3, 57% at month 6, and 31% at month 12. At 6 months, 36/179 (21%) of AGYW in the enhanced arm had high adherence and 40/184 (22%) in the standard adherence support arm (adjusted odds ratio [OR] of 0.92; 95% confidence interval [CI] 0.55, 1.34; p = 0.76). Four women acquired HIV (incidence 1.0/100 person-years), with low or undetectable TFV-DP levels at or prior to seroconversion, and none of whom had tenofovir or emtricitabine resistance mutations. The study had limited power to detect a modest effect of drug level feedback on adherence, and there was limited awareness of PrEP at the time the study was conducted. Conclusions In this study, PrEP initiation was high, over half of study participants persisted with PrEP through month 12, and the majority of young African women had detectable TFV-DP levels through month 6 with one-fifth having high adherence. Drug level feedback in the first 3 months of PrEP use did not increase the proportion with high adherence at month 6. HIV incidence was 1% in this cohort with 39% prevalence of curable STIs and moderate PrEP adherence. Strategies to support PrEP use and less adherence-dependent formulations are needed for this population. Trial registration ClinicalTrials.gov NCT02732730 .
Factors associated with open access publishing costs in oncology journals.
Authors: Alex Koong, Ulysses Gardner, Jason C. Burton, Caleb Stewart, Petria Thompson, Clifton Dave Fuller, Ethan B. Ludmir, Michael Kevin Rooney
Journal: Journal of Clinical Oncology (2021)

11032 Background: The open access (OA) publishing model represents an exciting opportunity to facilitate dissemination of scientific information to global audiences. In contrast to many traditional models, which require readers to pay subscription fees or rely upon institutional subscriptions for article access, the OA model grants free access to all consumers. However, OA publication is often associated with significant article processing charges (APCs) for authors, which may thus serve as a barrier to publication. In this investigation, we aimed to identify journal-level factors associated with OA publication costs in oncology journals. Methods: We identified oncology journals using the SCImago Journal &amp; Country Rank database. All journals under the “Oncology” category that offer an OA publishing option with APC data openly available were included. For all journals, we searched journal websites and tabulated journal characteristics, including APC amount (USD), OA model (hybrid vs full), journal 2-year impact factor (IF), H-index, number of citable documents, primary treatment modality (surgery, radiation, medical, non-specific), treatment site (e.g. breast, etc), and continent of origin. Pearson correlation was used to evaluate univariate linear relationships between variables; for variables with significant correlation, we generated a multiple regression model to identify journal characteristics independently associated with OA APC amount. Results: Of 367 oncology journals screened, 266 met final inclusion criteria. The median APC was 2810 USD (range 0 – 5200). On univariate linear correlation regression testing, journals with the full OA model (p &lt; 0.001), higher journal IF (p &lt; 0.001), higher H-index (p &lt; 0.001), greater number of published articles (p &lt; 0.001), and those from North America or Europe (p &lt; 0.001) tended to have higher OA publishing costs. When these co-variates were analyzed in a multiple regression model, only full OA status (p &lt; 0.001), higher IF (p &lt; 0.001), and North American or European origin (p &lt; 0.001) persisted as independently associated with greater OA APC. Conclusions: Large APCs may serve as a barrier to OA publication and therefore create or exacerbate disparities among scientific investigators seeking to share their research. In this investigation, we find that OA publication costs are greater in oncology journals that utilize the hybrid OA model, have higher IF, and are based in North America or Europe. These findings may inform targeted action to help the oncology community fully appreciate the benefits of open science.
miR-130b and miR-128a are essential lineage-specific codrivers of t(4;11) MLL-AF4 acute leukemia
Authors: Camille Malouf, Eric T. B. Antunes, Michael O’Dwyer, Hélène Jakobczyk, Franziska Sahm, Sophie-Luise Landua, Richard A. Anderson, Abdenour Soufi, Christina Halsey, Katrin Ottersbach
Journal: Blood (2021)
Therapies to prevent post-infarction remodelling: From repair to regeneration
Authors: Paolo Contessotto, Abhay Pandit
Journal: Biomaterials (2021)

Myocardial infarction is the first cause of worldwide mortality, with an increasing incidence also reported in developing countries. Over the past decades, preclinical research and clinical trials continually tested the efficacy of cellular and acellular-based treatments. However, none of them resulted in a drug or device currently used in combination with either percutaneous coronary intervention or coronary artery bypass graft. Inflammatory, proliferation and remodelling phases follow the ischaemic event in the myocardial tissue. Only recently, single-cell sequencing analyses provided insights into the specific cell populations which determine the final fibrotic deposition in the affected region. In this review, ischaemia, inflammation, fibrosis, angiogenesis, cellular stress and fundamental cellular and molecular components are evaluated as therapeutic targets. Given the emerging evidence of biomaterial-based systems, the increasing use of injectable hydrogels/scaffolds and epicardial patches is reported both as acellular and cellularised/functionalised treatments. Since several variables influence the outcome of any experimented treatment, we return to the pathological basis with an unbiased view towards any specific process or cellular component. Thus, by evaluating the benefits and limitations of the approaches based on these targets, the reader can weigh the rationale of each of the strategies that reached the clinical trials stage. As recent studies focused on the relevance of the extracellular matrix in modulating ischaemic remodelling and enhancing myocardial regeneration, we aim to portray current trends in the field with this review. Finally, approaches towards feasible translational studies that are as yet unexplored are also suggested.
A comprehensive Memorial Sloan Kettering Cancer Center real-world data model: Core clinical data elements.
Authors: Neil J. Shah, Nadia Bahadur, Lauren Esposito, Andrew Niederhausern, Chelsea Nichols, Anjali Pillai, Fenil Gandhi, Laura Barton, Kimberly Chan, Latasha Estrada, Joshua Goldberg, Grace Capreol, Bernard H. Bochner, Marisa Kollmeier, Hikmat A. Al-Ahmadie, Samantha Brown, Jasme Lee, Jonathan E. Rosenberg, John Philip, Theodora Bakker
Journal: Journal of Clinical Oncology (2021)

e18755 Background: The 2016 21 st Century Cures Act supports the use of Real-World Data (RWD) for regulatory decision/approval. Due to technological advances, a vast amount of health-related data are now available, but most are not standardized nor readily useable for research. Also, currently available standardized RWD models are not applicable across cancer types or oncology specialties (surgery, medical oncology, radiation oncology, pathology, radiology, etc.). To address these deficiencies Memorial Sloan Kettering Cancer Center (MSKCC) built a comprehensive, pan-cancer, pan-specialty RWD model. Methods: The Core Clinical Data Element (CCDE) data model incorporates aspects of existing academic and biopharma data models, including PRISSMM framework, ASCO’s mCODE, and NAACCR tumor registry model. The data model encompasses 11 domains that are critical to the understanding of the patient’s cancer journey, including: demographic, comorbidities, diagnosis, pathology, imaging, genomics, cancer surgeries, radiation oncology treatments, medical oncology treatments, cancer status/progression, and additional health information. To align with current standards, we are using ICD-10, ICDO3, CTACE V5.0, HL7, SNOMED and LOINC code sets. Further, this adaptable model allows for 5-10 disease specific elements to accommodate for disease heterogenicity and capture the differences among cancer types. Results: The CCDE database includes 1,126 of total data elements. MSKCC has 52,704 patients with MSK-IMPACT (Next-Generation sequencing platform with 505 genes panel) testing of which, we have identified 1,132 bladder cancer patients with at-least one year of cancer care follow-up for the initial curation cohort. Patients were identified as having an OncoTree bladder tumor type code that is assigned by a pathologist who attests the diagnosis by reviewing results from clinical tests on tumor specimens. To the date, 641 patients including 46,415 curated forms have been curated (Table). Conclusions: The comprehensive MSKCC’s CCDE data model standardizes the common and critical pan-cancer and pan-specialty elements for RWD. The dataset resulting from this curation efforts will provide robust structured and unified genomic and phenomic data across tumor types for future research enabling greater collaboration across various cancer types as well as oncology specialties.[Table: see text]