Sample Selection Bias Due to Differential Mortality: A Supplementary Measure of Old-Age Poverty.

Traditional "head count" measures of poverty at advanced older ages understate the risk of falling into poverty because of survivorship bias due to the income-mortality gradient, which indicates that people in poverty have higher mortality rates than people with higher income. Survivorship bias is a form of sample selection bias. This paper presents a supplementary measure for poverty at older ages, based on an adaption of a model for correcting survivorship bias in rate of return data for mutual funds. Using U.S. longitudinal data from the Health and Retirement Study (HRS) for 1996 and 2002-2012 for the same cohort, we develop a new estimate of poverty at older ages that suggests that traditional cross-sectional measures understate the risk of falling into poverty by roughly a quarter. This finding has important implications for social programs that relate to the causes and consequences of the selectivity bias.

Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort.

The drivers of critical coronavirus disease 2019 (COVID-19) remain unknown. Given major confounding factors such as age and comorbidities, true mediators of this condition have remained elusive. We used a multi-omics analysis combined with artificial intelligence in a young patient cohort where major comorbidities were excluded at the onset. The cohort included 47 "critical" (in the intensive care unit under mechanical ventilation) and 25 "non-critical" (in a non-critical care ward) patients with COVID-19 and 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cell proteomics, cytokine profiling, and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing, and structural causal modeling were used. Patients with critical COVID-19 were characterized by exacerbated inflammation, perturbed lymphoid and myeloid compartments, increased coagulation, and viral cell biology. Among differentially expressed genes, we observed up-regulation of the metalloprotease ADAM9. This gene signature was validated in a second independent cohort of 81 critical and 73 recovered patients with COVID-19 and was further confirmed at the transcriptional and protein level and by proteolytic activity. Ex vivo ADAM9 inhibition decreased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, cohort of individuals with COVID-19, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. We further identified ADAM9 as a driver of disease severity and a candidate therapeutic target.

Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia.

B-cell receptor (BCR) signaling is crucial for the pathophysiology of most mature B-cell lymphomas/leukemias and has emerged as a therapeutic target whose effectiveness remains limited by the occurrence of mutations. Therefore, deciphering the cellular program activated downstream this pathway has become of paramount importance for the development of innovative therapies. Using an original ex vivo model of BCR-induced proliferation of chronic lymphocytic leukemia cells, we generated 108 temporal transcriptional and proteomic profiles from 1 h up to 4 days after BCR activation. This dataset revealed a structured temporal response composed of 13,065 transcripts and 4027 proteins, comprising a leukemic proliferative signature consisting of 430 genes and 374 proteins. Mathematical modeling of this complex cellular response further highlighted a transcriptional network driven by 14 early genes linked to proteins involved in cell proliferation. This group includes expected genes (EGR1/2, NF-kB) and genes involved in NF-kB signaling modulation (TANK, ROHF) and immune evasion (KMO, IL4I1) that have not yet been associated with leukemic cells proliferation. Our study unveils the BCR-activated proliferative genetic program in primary leukemic cells. This approach combining temporal measurements with modeling allows identifying new putative targets for innovative therapy of lymphoid malignancies and also cancers dependent on ligand-receptor interactions.

Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics.

Sample preparation is a key step in proteomics workflows. Tube-gel (TG) is a fast and repeatable sample preparation method that consists in the instantaneous trapping of the sample in a polyacrylamide gel matrix. It takes advantage of in-gel sample preparations by allowing the use of high concentrations of sodium-dodecyl sulfate but avoids the time-consuming step of electrophoresis. Therefore, TG limits the sample handling and is thus particularly suitable for high-throughput quantitative proteomics when large sample numbers have to be processed, as it is often the case in biomarker research and clinical proteomics projects.

Nutritional status at diagnosis of cancer in children and adolescents in Guatemala and its relationship to socioeconomic disadvantage: A retrospective cohort study.

BACKGROUND: At least 80% of children with cancer live in low- and middle-income countries where the prevalence of malnutrition and socioeconomic disadvantage is high. We examined the relationship between nutritional status (NS), assessed by arm anthropometry, and socioeconomic status (SES) in children diagnosed with cancer at Unidad Nacional de Oncologia Pediatrica (UNOP) in Guatemala over a three-year period. METHOD: Patients aged 0 to 18 years of age diagnosed between January 2015 and December 2017 were included. NS was evaluated by mid-upper arm circumference, triceps skin fold thickness, and serum albumin level, and subjects were classified as adequately nourished, moderately depleted, and severely depleted nutritionally. SES was measured by a 15-item instrument developed at UNOP. RESULTS: Of 1365 patients diagnosed in the study period, 1060 (78%) fulfilled the eligibility criteria. Only 6% of patients were classified as medium to high, the remainder as medium-low to extremely low SES. Almost 47% were severely depleted at diagnosis, 19% moderately depleted, and 34% adequately nourished. SES was shown to be a determinant of NS; with progressively lower SES, the probability of a decline in NS increased by a factor of 1.04 points (P < 0.0001). Leukemia and lymphoma were also important predictors of nutritional depletion with odds ratios of 6.08 (95% CI, 1.74-28.28; P = 0.008) for leukemias and 4.83 (95% CI, 1.33-23.03; P = 0.03) for lymphomas. CONCLUSION: Both low SES and a diagnosis of leukemia or lymphoma are strong predictors of poor NS at diagnosis in children with cancer in Guatemala.

Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma.

The prognosis of patients with relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL) remains unsatisfactory and, despite major advances in genomic studies, the biological mechanisms underlying chemoresistance are still poorly understood. We conducted for the first time a large-scale differential multi-omics investigation on DLBCL patient's samples in order to identify new biomarkers that could early identify patients at risk of R/R disease and to identify new targets that could determine chemorefractoriness. We compared a well-characterized cohort of R/R versus chemosensitive DLBCL patients by combining label-free quantitative proteomics and targeted RNA sequencing performed on the same tissues samples. The cross-section of both data levels allowed extracting a sub-list of 22 transcripts/proteins pairs whose expression levels significantly differed between the two groups of patients. In particular, we identified significant targets related to tumor metabolism (Hexokinase 3), microenvironment (IDO1, CXCL13), cancer cells proliferation, migration and invasion (S100 proteins) or BCR signaling pathway (CD79B). Overall, this study revealed several extremely promising biomarker candidates related to DLBCL chemorefractoriness and highlighted some new potential therapeutic drug targets. The complete datasets have been made publically available and should constitute a valuable resource for the future research.

Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes.

Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors). To clarify the function of Trm112 in archaea, we have characterized functionally and structurally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies. Interestingly, among the identified enzymes, some are functionally orthologous to eukaryotic Trm112 partners, emphasizing again the similarity between eukaryotic and archaeal translation machineries. Other partners display some similarities with bacterial methyltransferases, suggesting that Trm112 is a general partner for methyltransferases in all living organisms.

Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics.

Sample preparation for quantitative proteomics is a crucial step to ensure the repeatability and the accuracy of the results. However, there is no universal method compatible with the wide variety of protein extraction buffers currently used. We have recently demonstrated the compatibility of tube-gel with SDS-based buffers and its efficiency for label-free quantitative proteomics by comparing it to stacking gel and liquid digestion. Here, we investigated the compatibility of tube-gel with alternatives to SDS-based buffers allowing notably the extraction of proteins in various pH conditions. We also explored the use of photopolymerization to extend the number of possibilities, as it is compatible with a wide range of pH and is non-oxidative. To achieve this goal, we compared six extraction buffers in combination with two polymerization conditions to further optimize the tube-gel protocol and evaluate its versatility. Identification and quantitative results demonstrated the compatibility of tube-gel with all tested conditions by overall raising quite comparable results. In conclusion, tube-gel is a versatile and simple sample preparation method for large-scale quantitative proteomics applications. Complete datasets are available via ProteomeXchange with identifier PXD008656.

EB1-binding-myomegalin protein complex promotes centrosomal microtubules functions.

Control of microtubule dynamics underlies several fundamental processes such as cell polarity, cell division, and cell motility. To gain insights into the mechanisms that control microtubule dynamics during cell motility, we investigated the interactome of the microtubule plus-end-binding protein end-binding 1 (EB1). Via molecular mapping and cross-linking mass spectrometry we identified and characterized a large complex associating a specific isoform of myomegalin termed "SMYLE" (for short myomegalin-like EB1 binding protein), the PKA scaffolding protein AKAP9, and the pericentrosomal protein CDK5RAP2. SMYLE was associated through an evolutionarily conserved N-terminal domain with AKAP9, which in turn was anchored at the centrosome via CDK5RAP2. SMYLE connected the pericentrosomal complex to the microtubule-nucleating complex (γ-TuRC) via Galectin-3-binding protein. SMYLE associated with nascent centrosomal microtubules to promote microtubule assembly and acetylation. Disruption of SMYLE interaction with EB1 or AKAP9 prevented microtubule nucleation and their stabilization at the leading edge of migrating cells. In addition, SMYLE depletion led to defective astral microtubules and abnormal orientation of the mitotic spindle and triggered G1 cell-cycle arrest, which might be due to defective centrosome integrity. As a consequence, SMYLE loss of function had a profound impact on tumor cell motility and proliferation, suggesting that SMYLE might be an important player in tumor progression.

Cross-Continuum Tool Is Associated with Reduced Utilization and Cost for Frequent High-Need Users.

INTRODUCTION: High-need, high-cost (HNHC) patients can over-use acute care services, a pattern of behavior associated with many poor outcomes that disproportionately contributes to increased U.S. healthcare cost. Our objective was to reduce healthcare cost and improve outcomes by optimizing the system of care. We targeted HNHC patients and identified root causes of frequent healthcare utilization. We developed a cross-continuum intervention process and a succinct tool called a Complex Care Map (CCM)© that addresses fragmentation in the system and links providers to a comprehensive individualized analysis of the patient story and causes for frequent access to health services. METHODS: Using a pre-/post-test design in which each subject served as his/her own historical control, this quality improvement project focused on determining if the interdisciplinary intervention called CCM© had an impact on healthcare utilization and costs for HNHC patients. We conducted the analysis between November 2012 and December 2015 at Mercy Health Saint Mary's, a Midwestern urban hospital with greater than 80,000 annual emergency department (ED) visits. All referred patients with three or more hospital visits (ED or inpatient [IP]) in the 12 months prior to initiation of a CCM© (n=339) were included in the study. Individualized CCMs© were created and made available in the electronic medical record (EMR) to all healthcare providers. We compared utilization, cost, social, and healthcare access variables from the EMR and cost-accounting system for 12 months before and after CCMs© implementation. We used both descriptive and limited inferential statistics. RESULTS: ED mean visits decreased 43% (p<0.001), inpatient mean admissions decreased 44% (p<0.001), outpatient mean visits decreased 17% (p<0.001), computed tomography mean scans decreased 62% (p<0.001), and OBS/IP length of stay mean days decreased 41% (p<0.001). Gross charges decreased 45% (p<0.001), direct expenses decreased 47% (p<0.001), contribution margin improved by 11% (p=0.002), and operating margin improved by 73% (p<0.001). Patients with housing increased 14% (p<0.001), those with primary care increased 15% (p<0.001), and those with insurance increased 16% (p<0.001). CONCLUSION: Individualized CCMs© for a select group of patients are associated with decreased healthcare system overutilization and cost of care.

Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics.

Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label-free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG-prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841).

Employer Reactions to the Affordable Care Act.

Although the implementation of parts of the Affordable Care Act (ACA) was delayed until 2015, many firms had already made changes to their health insurance plans and their business practices. This article reports results from a survey administered to western Michigan firms in October 2013 requesting information on any changes they made in response to ACA. The authors found that although 89% of employers planned to offer health insurance in 2014, that number dropped to 66% in 2015. The main ways organizations were controlling health costs were by changing prescription coverage, passing on the costs to employees through higher copays and premiums and offering more high-deductible health plans with health savings accounts. Employers also were altering business practices by decreasing future hiring and decreasing the hours of part-time workers. The authors find that many of these changes were due to the uncertainty firms were facing during the ACA implementation process.