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Background: Socioeconomically disadvantaged and immigrant cancer survivors account for a significant and growing proportion of the breast cancer population in the US. Research on symptom burden and control among Chinese American (CA) breast cancer survivors (BCS) is scarce. Among all BCS, over 55% report treatment-related symptoms (e.g., fatigue and pain) and psychological stress (e.g., fear of recurrence). In our preliminary cross-sectional study, we found similar rates (~58%) but showed that CA (especially low-acculturated) BCS were particularly likely to report fatigue, pain, and poorer physical functioning relative to non-Hispanic White (NHW) BCS. We understand very little about whether CA and NHW BCS have different ways of managing symptoms, improving quality of life and decreasing risk for functional decline. We therefore propose a study to examine how CA and NHW BCS, two culturally distinct groups with divergent social resources, adapt to breast cancer. Study design: This longitudinal, prospective study will investigate sociocultural influences on individual coping behaviors and how they in turn affect racial differences in inflammation markers, symptom severity, and functional outcomes in breast cancer. This study will enroll 260 CA and 260 NHW female BCS to examine multifactorial pathways to breast cancer survivorship outcomes. The CA cases will be age- and stage-matched to the NHW cases. Utilizing a multilevel biobehavioral framework, we will investigate the dynamics of biological, sociocultural, and behavioral (diet and exercise) influences on symptom severity, physiologic status, and functional outcomes. Participants will complete telephone survey interviews and provide blood samples at baseline and 6- and 12-month follow-up. Pro-inflammatory cytokines (e.g., IL-1β, IL-1a, IL-6, IL8, IL10, TNFα, TNFꞵ, and CRP) and cortisol will be analyzed. In-depth individual interviews with a subset of participants will be conducted to investigate causal factors in order to develop individually and culturally appropriate interventions to improve future clinical care for targeted breast cancer survivor populations. This study is supported by NIH R01CA248413. Eligibility criteria: Eligible participants are CA and NWH women (age >= 18) who are diagnosed with invasive breast cancer (stage I, II, or III), are 1-5 years post diagnosis, and have completed primary treatment (e.g., surgery, radiation, chemotherapy, and/or targeted therapy). Patients currently on adjuvant endocrine therapy are allowed. Specific aims: Aim 1: Examine whether CA BCS’ symptom, functional, and physiologic outcomes (e.g., cytokines and cortisol), and trajectory of these outcomes differ from NHW BCS at baseline, 6- and 12-month follow-up, controlling for covariates. Aim 2: Examine to what extent social resources mediate BCS’ individual behavior (e.g., medical communication, diet, and physical activity) and to what extent such pathways explain outcome differences (Aim1) among BCS. Aim 3: Examine whether race and acculturation moderate the mediational pathways. Statistical methods: Multiple general linear mixed models will be performed to examine racial differences in the trajectory of symptom and biobehavioral outcomes across time, controlling for covariates (Aim 1). To examine mediation and moderation effects (Aims 2 and 3), we will use a cross-lagged path analysis model to simultaneously describe reciprocal relationships, or directional influences, between variables over time. Present accrual and target accrual: A total of 520 participants (260 CA and 260 NHW) will be enrolled at NYU Perlmutter Cancer Center, Columbia University Irving Medical Center, Georgetown University Medical Center, and Texas A&M University community networks. Contact information: Judy Huei-yu Wang, PhD: jw235@gunet.georgetown.edu or 202-687-6306 Maryann Kwa, MD: maryann.kwa@nyulangone.org or 212-731-6364 Citation Format: Maryann Kwa, Marc Schwartz, Katherine D. Crew, Jeanine M. Genkinger, Roger L. Brown, Leena Hilakivi-Clarke, Joanna Kitlinska, Douglas W. Roblin, Michael Antoni, Sylvia Adams, Kathie-Ann Joseph, Lei-Shih Chen, Judy Huei-yu Wang. A longitudinal investigation of sociocultural and behavioral influences on symptom management, biological response, and functioning among Chinese American and White female breast cancer survivors [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT3-14-01. more...

Describe the effect of preoperative hearing on the likelihood of hearing preservation after middle cranial fossa (MCF) approach for resection of vestibular schwannoma (VS) and the effect of hearing preservation on disease-specific quality of life (QOL).Retrospective chart review.Academic tertiary care skull base surgery program.Sixty three adult patients with preoperative word recognition score (WRS) ≥50% who underwent MCF resection of VS between 2017 and 2020.All patients underwent MCF VS resection with attempted hearing preservation.Hearing preservation (postoperative WRS ≥50%), hearing-related Penn Acoustic Neuroma Quality of Life (PANQOL) score.Sixty three patients with mean age 47.4 (±9.6) years and tumor size 11.5 (±0.5) mm were analyzed. Hearing was preserved (+HP) and lost (-HP) in 37 (58.7%) and 26 (41.3%) patients, respectively. Preoperatively, pure tone average audiometry was significantly lower among the +HP group (20.0 dB) versus -HP (31.0 dB, p 0.003). WRS was higher among +HP versus -HP (94% vs. 84%, respectively; p 0.002). Linear regression showed that intra- versus extra-canalicular tumor location, sudden hearing loss history, fundal fluid cap thickness, and tumor size had no relationship to hearing preservation outcomes. When evaluating postoperative QOL data (n = 37) hearing-related PANQOL score differed between +HP and -HP (t35 = 2.458, p = 0.0191) groups.In this cohort of patients undergoing MCF resection of VS, rates of HP were higher for patients with excellent preoperative hearing. Postoperatively, +HP patients reported improved hearing-related PANQOL scores compared to -HP patients. more...

Ovarian cancer is an aggressive, heterogeneous disease, burdened with late diagnosis and resistance to chemotherapy. Clinical features of ovarian cancer could be explained by investigating its metabolism, and how the regulation of specific pathways link to individual phenotypes. Ovarian cancer is of particular interest for metabolic research due to its heterogeneous nature, with five distinct subtypes having been identified, each of which may display a unique metabolic signature. To elucidate metabolic differences, constraint-based modeling (CBM) represents a powerful technology, inviting the integration of ‘omics’ data, such as transcriptomics. However, many CBM methods have not prioritised accurate growth rate predictions, and there are very few ovarian cancer genome-scale studies, thus highlighting a niche in disease research. Here, a novel method for constraint-based modeling has been developed, employing the genome-scale model Human1 and flux balance analysis (FBA), enabling the integration ofin vitrogrowth rates, transcriptomics data and media conditions to predict the metabolic behaviour of cells. Using low- and high-grade ovarian cancer as a case study, subtype-specific metabolic differences have been predicted, which have been supported with CRISPR-Cas9 data and an extensive literature review. Metabolic drivers of aggressive phenotypes, as well as pathways responsible for increased proliferation and chemoresistance in low-grade cell lines have been suggested. Experimental gene dependency data has been used to validate fatty acid biosynthesis and the pentose phosphate pathway as essential for low-grade cellular growth, highlighting potential vulnerabilities for this ovarian cancer subtype. more...

Background Approximately half of Crohn’s disease (CD) patients experience recurrence and need for repeat resections, highlighting need for prognostic biomarkers. Presence of epithelioid granuloma on surgical tissue and high Rutgeerts endoscopic score are associated with postoperative CD clinical recurrence. We sought to evaluate presence of epithelioid granuloma at first surgery and Rutgeerts score as a combined risk assessment for CD surgical recurrence. Methods Our study included consented CD patients who underwent initial ileocecal resection and were prospectively followed postoperatively. From 2009 to 2019, 418 CD patients underwent initial ileocecal resection with >4 years of follow-up, including postoperative endoscopic assessment (Rutgeerts score). Results Postoperative CD patients were grouped based on granuloma presence (30.6%; n = 128) or absence (69.4%; n = 290). Endoscopic recurrence (defined as Rutgeerts score ≥i2) was similar between the granuloma (26%) and no granuloma (25%) groups, respectively (P = .82). Patients with granuloma and CD endoscopic recurrence at first postoperative endoscopy had higher number of bowel surgeries compared with all other groups (no granuloma or CD endoscopic recurrence, P = .007; no granuloma but CD endoscopic recurrence present, P = .04; granuloma present and no CD endoscopic recurrence, P = .04). Epithelioid granuloma presence was associated with 1.65 times higher risk of subsequent surgery independently from first postoperative endoscopic recurrence Rutgeerts score. Conclusions Granuloma presence on initial surgical histology is immediately available and identifies high-risk CD patients who may benefit from early postoperative treatment, and these precision intervention trials are warranted. more...

Key Points Patients with AML who received IC were compared with those who received ven to investigate predictors of outcomes.Presence of RUNX1 mutations is associated with better outcomes for ven/aza compared with IC., Visual Abstract, Venetoclax (ven) plus azacitidine (aza) is the standard of care for patients with newly diagnosed acute myeloid leukemia (AML) who are not candidates for intensive chemotherapy (IC). Some patients who are IC candidates instead receive ven/aza. We retrospectively analyzed patients with newly diagnosed AML who received ven/aza (n = 143) or IC (n = 149) to compare outcomes, seek variables that could predict response to 1 therapy or the other, and ascertain whether treatment recommendations could be refined. The response rates were 76.9% for ven/aza and 70.5% for IC. The median overall survival (OS) was 884 days for IC compared with 483 days for ven/aza (P = .0020). A propensity-matched cohort was used to compare outcomes in the setting of equivalent baseline variables, and when matched for age, biological risk, and transplantation, the median OS was 705 days for IC compared with not reached for ven/aza (P = .0667). Variables that favored response to ven/aza over IC included older age, secondary AML, and RUNX1 mutations. AML M5 favored response to IC over ven/aza. In the propensity-matched cohort analyzing OS, older age, adverse risk, and RUNX1 mutations favored ven/aza over IC, whereas intermediate risk favored IC over ven/aza. In conclusion, patients receiving IC have improved OS compared with those receiving ven/aza. However, in a propensity-matched cohort of patients with equivalent baseline factors, there was a trend toward favorable OS for ven/aza. Specific variables, such as RUNX1 mutations, reported here for the first time, can be identified that favor ven/aza or IC, helping to guide treatment decisions for patients who may be eligible candidates for either therapy. more...

Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, different mitigation and management strategies limiting economic and social activities have been implemented across many countries. Despite these strategies, the virus continues to spread and mutate. As a result, vaccinations are now administered to suppress the pandemic. Current COVID-19 epidemic models need to be expanded to account for the change in behaviour of new strains, such as an increased virulence and higher transmission rate. Furthermore, models need to account for an increasingly vaccinated population. We present a network model of COVID-19 transmission accounting for different immunity and vaccination scenarios. We conduct a parameter sensitivity analysis and find the average immunity length after an infection to be one of the most critical parameters that define the spread of the disease. Furthermore, we simulate different vaccination strategies and show that vaccinating highly connected individuals first is the quickest strategy for controlling the disease. more...

In this study an interactive decision aid (DA) for men diagnosed with localized prostate cancer was adapted, extended and pre-tested. The DA's prototype was based on a literature review and other empirically tested DAs. Semi-structured interviews with 12 men (age 65-80) diagnosed with localized prostate cancer were conducted to get feedback on content, usability, and the DA's layout. The interviews were analyzed using thematic analysis and themes were identified using deductive and inductive coding. Participants found the accessibility of the information and the explicit values clarification tool helpful. Four themes were identified: (1) usability and design, (2) content and knowledge, (3) deciding factors of decision-making, and (4) social support. Participants valued receiving extensive and realistic information on surgery/radiation therapy side effects and getting unbiased presentations of treatment options. Following the thematic analysis, the DA was revised and tested in a survey among 11 newly diagnosed prostate cancer patients (age 60-74). The participants valued the DA and found it helpful when making a treatment decision, and all reported that they would recommend it to others making a prostate cancer treatment decision. The DA is currently being tested in a randomized clinical trial (RCT). This is the first DA developed for prostate cancer patients in Iceland and if the results of the RCT show that it is more effective than standard care in assisting newly diagnosed patients with their treatment decision, the DA can be easily translated and adapted to cultures similar to Iceland such as the Nordic countries. more...

The combination of venetoclax (ven) and azacitidine (aza) has resulted in high response rates in the upfront treatment of AML in patients age > 75 and patients unfit for intensive chemotherapy. Given the poor historical outcomes in patients age ≥ 60 treated with induction chemotherapy, ven/aza has become our institutional preference for the initial treatment of non-core binding factor (CBF) AML patients age ≥ 60. The benefit of allogeneic stem cell transplant (SCT) in patients who achieve response to ven/aza is uncertain. We report outcomes of SCT-eligible patients treated at our center. Between 1/2015 and 1/2020, 119 newly diagnosed non-CBF AML patients age ≥ 60 received ven/aza as initial therapy. 21 patients underwent SCT; 31 additional patients were potentially SCT eligible but deferred SCT. Overall survival (OS) was significantly greater among SCT patients (median survival not reached) versus potentially SCT eligible patients not undergoing SCT (median 518 days) (p = 0.01). Our data suggest that ven/aza followed by SCT in newly diagnosed AML patients older than ≥ 60 results in excellent outcomes and likely improves outcomes over maintenance therapy. Ongoing investigation will further refine the optimal timing of and selection of patients for SCT based on prognostic disease features and response assessments. more...

npj Systems biology and applications 8(1), 49 (2022). doi:10.1038/s41540-022-00257-2, Published by Nature Publ. Group, London

Saccharomyces pastorianus is a natural yeast evolved from different hybridization events between the mesophilic S. cerevisiae and the cold-tolerant S. eubayanus. This complex aneuploid hybrid carries multiple copies of the parental alleles alongside specific hybrid genes and encodes for multiple protein isoforms which impart novel phenotypes, such as the strong ability to ferment at low temperature. These characteristics lead to agonistic competition for substrates and a plethora of biochemical activities, resulting in a unique cellular metabolism. Here, we investigated the transcriptional signature of the different orthologous alleles in S. pastorianus during temperature shifts. We identified temperature-dependent media-independent genes and showed that 35% has their regulation dependent on extracellular leucine uptake, suggesting an interplay between leucine metabolism and temperature response. The analysis of the expression of ortholog parental alleles unveiled that the majority of the genes expresses preferentially one parental allele over the other and that S. eubayanus-like alleles are significantly over-represented among the genes involved in the cold acclimatization. The presence of functionally redundant parental alleles may impact on the nature of protein complexes established in the hybrid, where both parental alleles are competing. Our expression data indicate that the majority of the protein complexes investigated in the hybrid are likely to be either exclusively chimeric or unispecific and that the redundancy is discouraged, a scenario that fits well with the gene balance hypothesis. This study offers the first overview of the transcriptional pattern of S. pastorianus and provides a rationalization for its unique industrial traits at the expression level. more...

Summary Serrated epithelial change (SEC) manifests in patients with long-standing inflammatory bowel disease (IBD) and is characterized by disorganized crypt architecture, irregular serrations, and goblet cell–rich epithelium. The serrated nature of SEC is reminiscent of serrated colorectal polyps, which frequently harbor KRAS/BRAF mutations. SEC is, however, not only histologically distinct from sporadic serrated polyps but also associated with colorectal neoplasia. Whether SEC is a precursor to IBD-associated neoplasia remains unclear. To further define the relationship of SEC with serrated colorectal polyps and IBD-associated neoplasia, we performed targeted next-generation sequencing on colorectal specimens to include the following: SEC without dysplasia/neoplasia (n = 10), SEC with separate foci of associated dysplasia/adenocarcinoma from the same patients (n = 17), and uninvolved mucosa (n = 10) from 14 patients. In addition, we molecularly profiled sessile serrated lesion (SSL)–like or serrated lesion, not otherwise specified (SL-NOS), specimens, from 11 patients who also had IBD. This control cohort included SSL-like/SL-NOS without dysplasia/neoplasia (n = 11), SSL-like/SL-NOS with associated low-grade dysplasia (n = 2), and uninvolved mucosa (n = 8). By next-generation sequencing, the most frequently mutated gene in SEC without neoplasia and associated dysplasia/adenocarcinoma from separate foci in the same patients was TP53. Recurrent TP53 mutations were present in 50% of SEC specimens without dysplasia/neoplasia. In addition, alterations in TP53 were detected at a prevalence of 71% in low-grade dysplasia, 83% in high-grade dysplasia, and 100% in adenocarcinoma. Paired sequencing of SEC and associated neoplasia revealed identical TP53 missense mutations for 3 patients. In contrast, 91% of SSL-like/SL-NOS specimens without dysplasia/neoplasia harbored KRAS/BRAF mutations, which were conserved in associated low-grade dysplasia. No genomic alterations were found in uninvolved mucosa from either patients with SEC or patients with SSL-like/SL-NOS. Based on our findings, we conclude SEC is distinct from SSL-like serrated colorectal lesions in patients with IBD and an early precursor to IBD-associated neoplasia that warrants colonoscopic surveillance. more...

Sarcomas include cancer stem cells, but how these cells contribute to local and metastatic relapse is largely unknown. We previously showed the pro-tumor functions of calpain-6 in sarcoma stem cells. Here, we use an osteosarcoma cell model, osteosarcoma tissues and transcriptomic data from human tumors to study gene patterns associated with calpain-6 expression or suppression. Calpain-6 modulates the expression of Hippo pathway genes and stabilizes the hippo effector YAP. It also modulates the vesicular trafficking of β-catenin degradation complexes. Calpain-6 expression is associated with genes of the G2M phase of the cell cycle, supports G2M-related YAP activities and up-regulated genes controlling mitosis in sarcoma stem cells and tissues. In mouse models of bone sarcoma, most tumor cells expressed calpain-6 during the early steps of tumor out-growth. YAP inhibition prevented the neoformation of primary tumors and metastases but had no effect on already developed tumors. It could even accelerate lung metastasis associated with large bone tumors by affecting tumor-associated inflammation in the host tissues. Our results highlight a specific mechanism involving YAP transcriptional activity in cancer stem cells that is crucial during the early steps of tumor and metastasis outgrowth and that could be targeted to prevent sarcoma relapse. more...

Poor translatability of animal disease models has hampered the development of new inflammatory bowel disorder (IBD) therapeutics. We describe a preclinical, ex vivo system using freshly obtained and well-characterized human colorectal tissue from patients with ulcerative colitis (UC) and healthy control (HC) participants to test potential therapeutics for efficacy and target engagement, using the JAK/STAT inhibitor tofacitinib (TOFA) as a model therapeutic. Colorectal biopsies from HC participants and patients with UC were cultured and stimulated with multiple mitogens ± TOFA. Soluble biomarkers were detected using a 29-analyte multiplex ELISA. Target engagement in CD3(+)CD4(+) and CD3(+)CD8(+) T-cells was determined by flow cytometry in peripheral blood mononuclear cells (PBMCs) and isolated mucosal mononuclear cells (MMCs) following the activation of STAT1/3 phosphorylation. Data were analyzed using linear mixed-effects modeling, t test, and analysis of variance. Biomarker selection was performed using penalized and Bayesian logistic regression modeling, with results visualized using uniform manifold approximation and projection. Under baseline conditions, 27 of 29 biomarkers from patients with UC were increased versus HC participants. Explant stimulation increased biomarker release magnitude, expanding the dynamic range for efficacy and target engagement studies. Logistic regression analyses identified the most representative UC baseline and stimulated biomarkers. TOFA inhibited biomarkers dependent on JAK/STAT signaling. STAT1/3 phosphorylation in T-cells revealed compartmental differences between PBMCs and MMCs. Immunogen stimulation increases biomarker release in similar patterns for HC participants and patients with UC, while enhancing the dynamic range for pharmacological effects. This work demonstrates the power of ex vivo human colorectal tissue as preclinical tools for evaluating target engagement and downstream effects of new IBD therapeutic agents. NEW & NOTEWORTHY Using colorectal biopsy material from healthy volunteers and patients with clinically defined IBD supports translational research by informing the evaluation of therapeutic efficacy and target engagement for the development of new therapeutic entities. Combining experimental readouts from intact and dissociated tissue enhances our understanding of the tissue-resident immune system that contribute to disease pathology. Bayesian logistic regression modeling is an effective tool for predicting ex vivo explant biomarker release patterns. more...

New fecal microbiota for cancer patients The composition of the gut microbiome influences the response of cancer patients to immunotherapies. Baruch et al. and Davar et al. report first-in-human clinical trials to test whether fecal microbiota transplantation (FMT) can affect how metastatic melanoma patients respond to anti–PD-1 immunotherapy (see the Perspective by Woelk and Snyder). Both studies observed evidence of clinical benefit in a subset of treated patients. This included increased abundance of taxa previously shown to be associated with response to anti–PD-1, increased CD8 + T cell activation, and decreased frequency of interleukin-8–expressing myeloid cells, which are involved in immunosuppression. These studies provide proof-of-concept evidence for the ability of FMT to affect immunotherapy response in cancer patients. Science , this issue p. 602 , p. 595 ; see also p. 573 more...

Widely-used response criteria, conditional upon count recovery, were developed for acute myeloid leukemia (AML) in the context of intensive chemotherapy (IC). Extending these definitions to continuously-administered venetoclax-based therapies might underestimate responses. Best practices for venetoclax-based therapies mandate interruption after an end-of-cycle 1 bone marrow biopsy shows morphologic remission with cytopenias. We analyzed 435 patients with newly-diagnosed AML and follow-up response assessments. Of the 101 who responded to venetoclax + azacitidine, overall survival for patients whose response was upgraded due to count recovery during a 14-day post-disease assessment period, from complete remission (CR) with incomplete recovery of blood counts to CR, was not different compared to patients who did not need the 14-day period for count recovery. These results were distinct from 138 IC patients. Although sample sizes for the comparison groups were small, and conclusions are exploratory and must be verified, these findings support consideration of new response criteria for venetoclax-based regimens. more...

Background Immunoglobulin G subclass 4 (IgG4) is hypothesized to play an immunomodulatory role, downregulating humoral immune responses. The role of this anti-inflammatory molecule in inflammatory bowel disease (IBD) has not been fully characterized. We sought to define alterations in serum IgG4 in patients with IBD and their association with multiyear disease severity. Methods We analyzed metadata derived from curated electronic health records from consented patients with IBD prospectively followed at a tertiary center over a 10-year time period. Patients with IBD with IgG4 serum levels available formed the study population. Demographics and multiyear clinical data were collected and analyzed. We stratified patients with IBD with low, normal, or high serum IgG4 levels. Results We found IgG4 characterized in 1193 patients with IBD and low IgG4 levels in 233 patients (20%) and elevated IgG4 levels in 61 patients (5%). An IgG4 deficiency did not significantly correlate with other antibody deficiencies. In a multiple Poisson regression analysis, low IgG4 was associated with more years on biologic agents (P = 0.002) and steroids (P = 0.049) and more hospital admissions (P < 0.001), clinic visits (P = 0.010), outpatient antibiotic prescriptions (P < 0.001), and CD-related surgeries (P = 0.011) during the study period after controlling for certain confounders. Elevated IgG4 was only associated with primary sclerosing cholangitis (P = 0.011). A cohort of patients with IgG4-deficient severe IBD received intravenous Ig replacement therapy, which benefited and was continued in 10 out of 11 individuals. Conclusions An IgG4 subclass deficiency, distinct from other antibody deficiencies, occurred commonly in a referral IBD population and was associated with multiple markers of disease severity. This is the first association of IgG4 subclass deficiency with an inflammatory disease process. Further work is needed to define the mechanistic role of IgG4 deficiency in this severe IBD subgroup. more...

Cells contain intracellular compartments, including membrane-bound organelles and the nucleus, and are surrounded by a plasma membrane. Proteins are localised to one or more of these cellular compartments; the correct localisation of proteins is crucial for their correct processing and function. Moreover, proteins and the cellular processes they partake in are regulated by relocalisation in response to various cellular stimuli. High-throughput ‘omics experiments result in a list of proteins or genes of interest; one way in which their functional role can be understood is through the knowledge of their subcellular localisation, as deduced through statistical enrichment for Gene Ontology Cellular Component (GOCC) annotations or similar. We have designed a bioinformatics tool, named SubcellulaRVis, that compellingly visualises the results of GOCC enrichment for quick interpretation of the localisation of a group of proteins (rather than single proteins). We demonstrate that SubcellulaRVis precisely describes the subcellular localisation of gene lists whose locations have been previously ascertained. SubcellulaRVis can be accessed via the web (http://phenome.manchester.ac.uk/subcellular/) or as a stand-alone app (https://github.com/JoWatson2011/subcellularvis). SubcellulaRVis will be useful for experimental biologists with limited bioinformatics expertise who want to analyse data related to protein (re)localisation and location-specific modules within the intracellular protein network. more...

IntroductionThe Cervical Dystonia Patient Registry for Observation of OnabotulinumtoxinA Efficacy (CD PROBE) study (ClinicalTrials.gov identifier: NCT00836017), a multicenter, prospective, observational registry, was designed to identify real-world practices and outcomes for patients with cervical dystonia (CD) treated with onabotulinumtoxinA (onabotA). This secondary analysis from CD PROBE aims to determine the impact of presentation subtype on onabotA utilization and CD severity.Materials and MethodsThe study cohort includes those who completed all 3 treatments, 4 office visits, and had data recorded for all assessments. Patient outcomes were assessed with the Cervical Dystonia Impact Profile (CDIP-58), Toronto Western Spasmodic Torticollis Rating Scale (TWSTRS), and determination of CD severity. Treatment interval, dose, and adverse events (AEs) were also recorded. Data were stratified according to prior exposure to botulinum toxins (BoNTs) and analyzed with descriptive statistics.ResultsTorticollis was the most common presentation subtype in the study cohort (N = 350); the proportion of patients with torticollis was highest in those with severe disease. At each treatment, between 40.7 and 65.2% of those categorized as severe shifted to moderate or mild severity after treatment. Sustained improvements in CDIP-58 and TWSTRS were observed regardless of prior exposure to BoNTs. Dosing of onabotA generally increased from injection 1 to injection 3 and tended to be lower for patients naïve to BoNT. Median time interval between injections for the study cohort was 94.0 to 97.5 days. The most common AEs (dysphagia, muscular weakness) and injection intervals were similar between naïve vs. non-naïve patients; there were no serious treatment-related AEs.ConclusionsThis secondary cohort analysis from CD PROBE demonstrates that three repeat treatments with onabotA at intervals consistent with labeling attenuated disease severity and neck pain, resulting in sustained improvements in physician- and patient-reported outcomes. No new safety signals were identified. more...

Serum protein reflects albumin and globulin levels, both of which can be altered in inflammatory bowel disease (IBD). The implications of a high globulin fraction in IBD are unknown. We hypothesized that a high globulin fraction may function independently of albumin as a biomarker of disease severity in IBD patients over a multiyear period.This was an observational study from a prospective IBD registry of a tertiary care center. High globulin fraction was defined as an elevated globulin level4 g/dL. Data collected included patient demographics, medication exposures, quality-of-life scores, disease activity, emergency department visits, telephone calls, hospitalizations, and IBD-related surgeries over a 4-year period. Comparisons between patients with a high globulin fraction and those without were performed using Pearson's chi-squared, Student's and Mann-Whitney tests. Multivariate analyses were used to assess the relationship between high globulin fraction and healthcare utilization.A total of 1767 IBD patients with a 4-year follow up were included: 53.5% female, mean age 48.4±15.1 years, and 65.4% with Crohn's disease. Of these patients, 446 (25.2%) presented with elevated globulin fraction. Patients with a high globulin fraction were more likely to be hospitalized during the study period. This result remained significant after multivariate analysis for both Crohn's disease patients and those with ulcerative colitis.A high globulin fraction is independently associated with greater disease severity and healthcare utilization in IBD patients, and may function as a routinely available biomarker of a more severe future disease trajectory. more...

Background Women with inflammatory bowel diseases (IBDs), such as Crohn’s disease or ulcerative colitis, face several disease-specific concerns related to their reproductive health decisions. This study explored the reproductive health decision-making experiences and preferences of women with IBD to discover ways to improve this aspect of comprehensive care. Methods We recruited women ages 18–44 years with IBD to participate in individual, semistructured interviews exploring their experiences and attitudes toward parenthood, pregnancy, contraception, and family planning care. Two independent coders performed analysis using an inductive and deductive coding approach and identified key themes. Results Twenty-one women with IBD participated in interviews (average age 24.7 ± 5.9 years, range 18–43 years; average age of diagnosis 14.1 ± 2.0 years). We identified 4 key themes: (1) Nulliparous women who do not currently desire pregnancy appear to lack reproductive health knowledge; (2) Women with IBD lack clarity regarding the role IBD plays in contraceptive choice; (3) Related to pregnancy, women are concerned about the heredity of IBD, antepartum disease activity, and the safety of their current medications; (4) Women with IBD typically default to their reproductive health provider for reproductive health care and counseling, but they expect their gastroenterologist to initiate relevant reproductive health discussions with them and to provide information in the context of their disease. Conclusions Women have concerns about the effects of IBD on pregnancy, parenthood, and contraceptive choice; however, many have had limited or no discussion with their gastroenterologist about the topic. more...

SummaryReceptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we revealed FGFR signalling partners proximal to recycling endosomes (REs) by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphopeptide enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncovered that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the REs, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve celllar signalling. more...

Receptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we reveal FGFR signalling partners proximal to recycling endosomes by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphorylated peptides enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncover that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the recycling endosomes, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve cellular signalling. more...

High-throughput ‘omics methods result in lists of differentially regulated or expressed genes or proteins, whose function is generally studied through statistical methods such as enrichment analyses. One aspect of protein regulation is subcellular localization, which is crucial for their correct processing and function and can change in response to various cellular stimuli. Enrichment of proteins for subcellular compartments is often based on Gene Ontology Cellular Compartment annotations. Results of enrichment are typically visualized using bar-charts, however enrichment analyses can result in a long list of significant annotations which are highly specific, preventing researchers from gaining a broad understanding of the subcellular compartments their proteins of interest may be located in. Schematic visualization of known subcellular locations has become increasingly available for single proteins via the UniProt and COMPARTMENTS platforms. However, it is not currently available for a list of proteins (e.g. from the same experiment) or for visualizing the results of enrichment analyses.To generate an easy-to-interpret visualization of protein subcellular localization after enrichment we developed the SubcellulaRVis web app, which visualizes the enrichment of subcellular locations of gene lists in an easy and impactful manner. SubcellulaRVis projects the results of enrichment analysis on a graphical representation of a eukaryotic cell. Implemented as a web app and an R package, this tool is user-friendly, provides exportable results in different formats, and can be used for gene lists derived from multiple organisms.Here, we show the power of SubcellulaRVis to assign proteins to the correct subcellular compartment using gene list enriched in previously published spatial proteomics datasets. We envision SubcellulaRVis will be useful for cell biologists with limited bioinformatics expertise wanting to perform precise and quick enrichment analysis and immediate visualization of gene lists.Author SummaryCells contain intracellular compartments, such as membrane-bound organelles and the nucleus, and are surrounded by a plasma membrane. Proteins can be found in different cellular compartments; depending on the subcellular compartment they are localized to, they can be differentially regulated or perform location-specific functions. High-throughput ‘omics experiments result in a list of proteins or genes of interest; one way in which their functional role can be understood is through their subcellular localization, as deduced through statistical enrichment for Gene Ontology Cellular Component (GOCC) annotations or similar. We have designed a bioinformatic tool, named SubcellulaRVis, that compellingly visualizes the results of protein localization after enrichment and simplifies the results for a quick interpretation. We demonstrate that SubcellulaRVis precisely describes the subcellular localization of gene lists whose locations have been previously ascertained in publications. SubcellulaRVis can be accessed via the web or as a stand-alone app. SubcellulaRVis will be useful for experimental biologists with limited bioinformatics expertise analyzing data related to cellular signalling, protein (re)localization and regulation, and location-specific functional modules within the cell. more...

Plants acclimate their photosynthetic capacity (Pmax) in response to changing environmental conditions. In Arabidopsis thaliana, photosynthetic acclimation to cold requires the accumulation of the organic acid fumarate, catalysed by a cytosolically localized fumarase, FUM2. However, the role of this accumulation is currently unknown. Here, we use an integrated experimental and modelling approach to examine the role of FUM2 and fumarate across the physiological temperature range. We have studied three genotypes: Col-0; a fum2 mutant in a Col-0 background; and C24, an accession with reduced FUM2 expression. While low temperature causes an increase in Pmax in the Col-0 plants, this parameter decreases following exposure of plants to 30 °C for 7 d. Plants in which fumarate accumulation is partially (C24) or completely (fum2) abolished show a reduced acclimation of Pmax across the physiological temperature range (i.e. Pmax changes less in response to changing temperature). To understand the role of fumarate accumulation, we have adapted a reliability engineering technique, Failure Mode and Effect Analysis (FMEA), to formalize a rigorous approach for ranking metabolites according to the potential risk that they pose to the metabolic system. FMEA identifies fumarate as a low-risk metabolite, while its precursor, malate, is shown to be high risk and liable to cause system instability. We propose that the role of FUM2 is to provide a fail-safe in order to control malate concentration, maintaining system stability in a changing environment. We suggest that FMEA is a technique that is not only useful in understanding plant metabolism but can also be used to study reliability in other systems and synthetic pathways. more...

Background Peripheral blood eosinophilia (PBE) is a biomarker of an aggressive multiyear natural history in adults with inflammatory bowel diseases (IBDs). Additionally, PBE at diagnosis is associated with higher disease activity in pediatric-onset IBD. We sought to determine if PBE can function as a biomarker of long-term disease severity in pediatric-onset IBD patients who are followed into adulthood. Methods We analyzed a consented, prospective, natural history IBD registry at an adult tertiary center from 2009 to 2018. Prevalence of PBE was evaluated in both pediatric- and adult-onset IBD patients. Demographics, clinical characteristics, and health care utilization data were compared in patients with and without PBE. Results Among 2800 adult IBD patients, 23.4% had pediatric-onset disease. PBE was found in 34% of the pediatric-onset patients compared with 26.8% of the adult-onset IBD patients (P < 0.001). In the pediatric-onset IBD cohort, PBE was associated with higher rates of allergies (P < 0.0001), but not of asthma, allergic rhinitis, or primary sclerosing cholangitis. In the adult IBD patients with pediatric-onset disease, PBE was associated with higher rates of C-reactive protein elevation (P < 0.0001), erythrocyte sedimentation rate elevation (P < 0.0001), higher health care utilization, and higher average health care charges per year (P < 0.00001). Conclusions Peripheral blood eosinophilia was more prevalent in adult IBD patients with pediatric-onset compared with adult-onset disease. Among all IBD patients with long-term follow-up, PBE defined a subgroup with more severe illness. These data suggest that PBE may be a biomarker for a high-risk subgroup with high cost trajectory and long-term severity in pediatric-onset IBD that persists into adulthood. more...

Background Given the rising prevalence of diabetes mellitus (DM) and the limited data on its effect on the course of inflammatory bowel disease (IBD), we characterized multiyear patterns of disease severity in a cohort of IBD patients with coexistent DM. Methods Data of consented IBD patients followed prospectively in a natural history registry at a tertiary center between 2009 and 2017 were analyzed. Patients with ≥3 years of clinical follow-up were included. Patients identified with a diagnosis of DM were compared with 400 consecutive IBD controls without a diagnosis of DM, no laboratory evidence of hyperglycemia, and no history of antihyperglycemic treatment. Results Out of 2810 IBD patients, 141 (5%) had DM (IBD DM; 44% ulcerative colitis, 56% Crohn’s disease, 48.2% female). IBD DM had higher use of 5-aminosalicylic acid (5ASA) agents (P = 0.04), narcotics (P < 0.001), and antibiotics (P = 0.007) but not immunomodulators and/or biologics compared with IBD controls. When analyzing biomarkers of severity, IBD DM demonstrated higher frequencies of elevated C-reactive protein (CRP; P = 0.006), elevated erythrocyte sedimentation rate (ESR; P = 0.001), eosinophilia (P = 0.004), monocytosis (P = 0.02), and hypoalbuminemia (P = 0.001). IBD DM had worse quality of life (mean Short Inflammatory Bowel Disease Questionnaire; P < 0.001). IBD DM had increased health care utilization compared with controls (emergency room usage P = 0.008, hospitalizations P < 0.001, gastroenterology clinic visits P < 0.001, and median annual charges P < 0.001). Among IBD DM patients, the use of immunomodulators and/or biologics was not associated with further complications as measured by antibiotic use or hospitalizations. Conclusions This study of a large IBD cohort suggests that DM in IBD may be associated with increased disease severity and that there may be room for increasing use of highly effective immunomodulator and/or biologic agents in this group. more...

Light response curves (LRCs) describe how the rate of photosynthesis varies as a function of light. They provide information on the maximum photosynthetic capacity, quantum yield, light compensation point and leaf radiation use efficiency of leaves. Light response curves are widely used to capture photosynthetic phenotypes in response to changing environmental conditions. However, models describing these are predominantly empirical and do not attempt to explain behaviour at a mechanistic level. Here, we use modelling to understand the metabolic changes required for photosynthetic acclimation to changing environmental conditions. Using a simple kinetic model, we predicted LRCs across the physiological temperature range of Arabidopsis thaliana and confirm these using experimental data. We use our validated metabolic model to make novel predictions about the metabolic changes of temperature acclimation. We demonstrate that NADPH utilization are enhanced in warm-acclimated plants, whereas both NADPH and CO2 utilization is enhanced in cold-acclimated plants. We demonstrate how different metabolic acclimation strategies may lead to the same photosynthetic response across environmental change. We further identify that certain metabolic acclimation strategies, such as NADPH utilization, are only triggered when plants are moved beyond a threshold high or low temperature. Electronic supplementary material The online version of this article (10.1007/s11120-019-00681-2) contains supplementary material, which is available to authorized users. more...

Desbuquois dysplasia type 1 (DBQD1) is a chondrodysplasia caused by mutations in CANT1 gene encoding an ER/Golgi calcium activated nucleotidase 1 that hydrolyses UDP. Here, using Cant1 knock-in and knock-out mice recapitulating DBQD1 phenotype, we report that CANT1 plays a crucial role in cartilage proteoglycan synthesis and in endochondral ossification. Specifically, the glycosaminoglycan synthesis was decreased in chondrocytes from Cant1 knock-out mice and their hydrodynamic size was reduced, whilst the sulfation was increased and the overall proteoglycan secretion was delayed. Interestingly, knock-out chondrocytes had dilated ER cisternae suggesting delayed protein secretion and cellular stress; however, no canonical ER stress response was detected using microarray analysis, Xbp1 splicing and protein levels of BiP and ATF4. The observed proteoglycan defects caused deregulated chondrocyte proliferation and maturation in the growth plate resulting in the reduced skeletal growth. In conclusion, the pathogenic mechanism of DBQD1 comprises deregulated chondrocyte performance due to defective intracellular proteoglycan synthesis and altered proteoglycan properties in the extracellular matrix., Highlights • Desbuquois dysplasia type 1 (DBQD1) is a recessive skeletal dysplasia caused by mutations in CANT1 gene, a Calcium activated nucleotidase of the ER/Golgi. • The Cant1 knock-out mouse recapitulates human DBQD1. • Cant1 is critical for different steps of proteoglycan biosynthesis including glycosaminoglycan chain synthesis, length and sulfation. • The intracellular GAG synthesis defects cause delayed proteoglycan secretion with ER enlargement. • In Cant1 knock-out chondrocytes ER enlargement is not linked to canonical ER stress. • The proteoglycan defects cause deregulated chondrocyte proliferation and maturation in the growth plate resulting in reduced skeletal growth. more...

Single agents have demonstrated activity in relapsed and refractory (R/R) peripheral T-cell lymphoma (PTCL). Their benefit relative to combination chemotherapy remains undefined. Patients with histologically confirmed PTCL were enrolled in the Comprehensive Oncology Measures for Peripheral T-cell Lymphoma Treatment (COMPLETE) registry. Eligibility criteria included those with R/R disease who had received one prior systemic therapy and were given either a single agent or combination chemotherapy as first retreatment. Treatment results for those with R/R disease who received single agents were compared to those who received combination chemotherapy. The primary endpoint was best response to retreatment. Fifty-seven patients met eligibility criteria. At first retreatment, 46% (26/57) received combination therapy and 54.5% (31/57) received single agents. At median follow up of 2 years, a trend was seen towards increased complete response rate for single agents versus combination therapy (41% vs 19%; P = .02). There was also increased median overall survival (38.9 vs 17.1 months; P = .02) and progression-free survival (11.2 vs 6.7 months; P = .02). More patients receiving single agents received hematopoietic stem-cell transplantation (25.8% vs 7.7%, P = .07). Adverse events of grade 3 or 4 occurred more frequently in those receiving combination therapy, although this was not statistically significant. The data confirm the unmet need for better treatment in R/R PTCL. Despite a small sample, the analysis shows greater response and survival in those treated with single agents as first retreatment in R/R setting, while maintaining the ability to achieve transplantation. Large, randomized trials are needed to identify the best strategy. more...

Pancreatic cancer is a lethal disease in part because tumor cells exist in distinct transcriptional phenotypes (e.g. basal and classical states), each with a selective ability to evade current chemotherapy regimens. Two major mechanisms have been suggested for treatment evasion: 1) intrinsic resistance of certain phenotypes to particular chemotherapy regimens and 2) plasticity of treatment sensitive phenotypes to adopt more resistant phenotypes. However, the relative contribution of these mechanisms to treatment resistance is still poorly understood. Whereas previous work has described the redistribution of tumor cell states under selective treatment pressure, there is no direct evidence that tumor cells exhibit phenotypic plasticity at steady state or with treatment. By leveraging technological advancements in single-cell methods, lineage tracing and functional genomics, we have now shown direct evidence of phenotypic state switching in human pancreatic cancer cell lines. By performing single-cell RNA-seq on 5 barcoded PDAC cell lines over a steady state timecourse and under chemotherapy selective pressure (>600k cells total), we identify unique plasticity phenotypes within these cell lines and infer regulators of these plastic states. We validate the role of several of these regulators using bulk phenotypic CRISPRi screens in these cell lines. We next perform CRISPRi perturbations along with lineage tracing and single-cell multiomics (>300k cells) to dissect the regulatory relationships that underlie these cell states. We identify several novel epithelial and mesenchymal biasing factors, including those with unique roles in the most plastic clones. Collectively, we nominate several regulators that bias PDAC cell states thus posing a paradigm whereby perturbations may be used to homogenize tumor populations towards treatment-sensitive phenotypes. We believe this approach combined with current chemotherapy regimens could benefit pancreatic cancer patients by targeting residual, resistant tumor cells in the localized and metastatic disease settings to improve patient survival. Citation Format: Arnav Mehta, Lynn Bi, Aziz Al'Khafaji, Martin Jankowiak, Milan Parikh, Mehrtash Babadi, Alex Bloemendal, Marc Schwartz, Glen Munson, Joeseph Chan, Cassandra Burdziak, Elisa Donnard, Ryan Park, Chen Lu, Philippe Rigollet, Andrew Aguirre, Vidya Subramanian, Ray Jones, Eric S. Lander, David T. Ting, Dana Pe'er, Nir Hacohen. Quantifying and dissecting pancreatic cancer cell phenotypic plasticity using lineage tracing, single-cell multiomics and CRISPR perturbations reveals novel regulators of plastic states [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B016. more...

Osteocytes are mechanosensitive cells that control bone remodeling in response to mechanical loading. To date, specific signaling pathways modulated by mechanical loading in osteocytes are not well understood. Yes associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), the main effectors of the Hippo pathway, are reported to play a role in mechanotransduction and during osteoblastogenesis. Here, we hypothesized that YAP/TAZ signaling mediates osteocyte mechanosensing to target genes of the bone remodeling process. We aimed to investigate the contribution of YAP/TAZ in modulating the gene expression in an osteocyte-like cell line MLO-Y4. We developed a 3D osteocyte compression culture model from an MLO-Y4 osteocyte cell line embedded in concentrated collagen hydrogel. 3D-mechanical loading led to the increased expression of mechanosensitive genes and a subset of chemokines, including M-csf, Cxcl1, Cxcl2, Cxcl3, Cxcl9, and Cxcl10. The transcription regulators YAP and TAZ translocated to the nucleus and upregulated their target genes and proteins. RNAseq analysis revealed that YAP/TAZ knockdown mediated the regulation of several genes including osteocyte dendrite formation. Use of YAP/TAZ knockdown partially blunted the increase in M-csf and Cxcl3 levels in response to MLO-Y4 compression. These findings demonstrate that YAP/TAZ signaling is required for osteocyte-like cell mechano-transduction, regulates the gene expression profiles and controls chemokine expression. more...

Cancer health disparities remain a significant problem in the USA, compounded by lack of access to care, language barriers and systemic biases in health care. These disparities are particularly evident in areas such as genetics/genomics. For example, Latinas at high risk for hereditary breast and ovarian cancer (HBOC) have extremely low rates of genetic counseling/testing. Long-standing barriers and inequities in access to services such as genetic counseling and testing require innovative solutions. One solution can involve training community outreach and education professionals (CORE-Ps) to bridge the gap between underserved communities and genetic specialists. We sought to develop and pilot test a training program for English-Spanish bilingual CORE-Ps to reduce disparities in access to and uptake of genetic services among Latino populations. Guided by Adult Learning Theory and with input from multiple stakeholders, we developed ÁRBOLES Familiares (Family Trees), an in-person and online training program for bilingual CORE-Ps to facilitate identification, referral, and navigation of Latinas to genetic counseling/testing. We conducted a pilot test of 24 CORE-Ps recruited from across the United States and assessed knowledge, genetic literacy, and self-efficacy at baseline and follow-up. At follow-up, participants in the pilot with complete baseline and follow-up data (N = 15) demonstrated significant improvements in HBOC knowledge, genetic literacy, self-efficacy and reports of fewer barriers to identify/navigate Latinas (ps.05). Qualitative assessment identified ways to improve the training curriculum. Pilot results suggest ÁRBOLES is a promising approach for training CORE-Ps to identify and refer high-risk Latinas to genetic services. Next steps involve further refinement of ÁRBOLES, development of an online toolkit, and adaptation for virtual delivery.Latinas at high risk for hereditary breast and ovarian cancer (HBOC) have low rates of genetic counseling and testing. Latinas may not have ready access to services like genetic counseling and testing, which need special solutions. One solution can involve training community health workers to bridge the gap between Latinas and genetic specialists. We developed an online and in person training program (ÁRBOLES Familiares or Family Trees) for English-Spanish bilingual community health workers that teaches them how to help Latinas get access to genetic services. We tested this program with a small group of community health workers. After the program, their HBOC knowledge, genetic literacy, and confidence to help Latinas get access to genetic services had improved. Trainees also made suggestions to improve the program, which will be used to help future trainees expand their knowledge and skills to work with Latinas at risk of HBOC. more...