Factors associated with participation in a walking intervention for veterans who smoke and have chronic pain.

This analysis was part of the Pain and Smoking Study (PASS), a randomized trial of a cognitive behavioral intervention (CBI) for Veterans with chronic pain who smoke. The objective of this study was to examine factors associated with participation in the walking component of the intervention. Demographics and clinical characteristics were obtained at baseline. Completion of two or more CBI counseling sessions was required to be included in analyses. Average daily step counts obtained via pedometer in the prior week were recorded in up to three telephone counseling sessions. Participants were then categorized as "sedentary" (≤ 4999 daily steps) or "not sedentary" (≥ 5000 daily steps). Multivariable logistic regression was used to model variance in activity categorization. Overall, 91.0% of participants were men, 70.5% were white, mean age was 58.4 years, mean BMI was 28.6, median pack years was 20.5, and 43.8% were depressed. Veterans reported moderate pain intensity (4.9/10) and pain interference (5.4/10). Pain locations included: lower extremity (67.4%), back (53.4%) and upper extremity (28.1%). Median daily steps were 2491 [IQR: 1720-3550] (sedentary) (n = 65), 7307 [IQR: 5952-8533] (not sedentary) (n = 24), and 3196 [IQR: 2237-5067] (overall) (n = 89). Veterans with older age (odds ratio (OR): 1.10, 95% confidence interval (CI): 1.04, 1.17) and presence of LE pain (OR: 5.98, 95% CI: 1.82, 19.65) had increased odds of being "sedentary." Integrated smoking cessation and chronic pain self-management interventions that include a walking component may need to consider the impact of age and pain location on participation.Trial registration: The trial is registered at www.ClinicalTrials.gov (NCT02971137). First posted on November 22, 2016.

A Systems Approach for Assessing Low Back Pain Care Quality in Veterans Health Administration Chiropractic Visits: A Cross-Sectional Analysis.

OBJECTIVE: The purpose of this study was to explore a systemwide process for assessing components of low back pain (LBP) care quality in Veterans Health Administration (VHA) chiropractic visits using electronic health record (EHR) data. METHODS: We performed a cross-sectional quality improvement project. We randomly sampled 1000 on-station VHA chiropractic initial visits occurring from October 1, 2017, to September 30, 2018, for patients with no such visits within the prior 12 months. Characteristics of LBP visits were extracted from VHA national EHR data via structured data queries and manual chart review. We developed quality indicators for history and/or examination and treatment procedures using previously published literature and calculated frequencies of visits meeting these indicators. Visits meeting our history and/or examination and treatment indicators were classified as "high-quality" visits. We performed a regression analysis to assess associations between demographic/clinical characteristics and visits meeting our quality criteria. RESULTS: There were 592 LBP visits identified. Medical history, physical examination, and neurologic examination were documented in 76%, 77%, and 63% of all LBP visits, respectively. Recommended treatments, such as any manipulation, disease-specific education/advice, and therapeutic exercise, occurred in 75%, 69%, and 40% of chronic visits (n = 383), respectively. In acute/subacute visits (n = 37), any manipulation (92%), manual soft tissue therapy (57%), and disease-specific advice/education (54%) occurred most frequently. Female patients and those with a neck pain comorbid diagnosis were significantly less likely to have a "high-quality" visit, while other regression associations were non-significant. CONCLUSION: This study explored a systemwide process for assessing components of care quality in VHA chiropractic visits for LBP. These results produced a potential framework for uniform assessment of care quality in VHA chiropractic visits for LBP and highlight potential areas for improvements in LBP care quality assessments.

Ribosomal protein RPL26 is the principal target of UFMylation.

Ubiquitin fold modifier 1 (UFM1) is a small, metazoan-specific, ubiquitin-like protein modifier that is essential for embryonic development. Although loss-of-function mutations in UFM1 conjugation are linked to endoplasmic reticulum (ER) stress, neither the biological function nor the relevant cellular targets of this protein modifier are known. Here, we show that a largely uncharacterized ribosomal protein, RPL26, is the principal target of UFM1 conjugation. RPL26 UFMylation and de-UFMylation is catalyzed by enzyme complexes tethered to the cytoplasmic surface of the ER and UFMylated RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes. Biochemical analysis and structural modeling establish that UFMylated RPL26 and the UFMylation machinery are in close proximity to the SEC61 translocon, suggesting that this modification plays a direct role in cotranslational protein translocation into the ER. These data suggest that UFMylation is a ribosomal modification specialized to facilitate metazoan-specific protein biogenesis at the ER.

A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast.

BACKGROUND: CRISPR/Cas9-mediated transcriptional interference (CRISPRi) enables programmable gene knock-down, yielding loss-of-function phenotypes for nearly any gene. Effective, inducible CRISPRi has been demonstrated in budding yeast, and genome-scale guide libraries enable systematic, genome-wide genetic analysis. RESULTS: We present a comprehensive yeast CRISPRi library, based on empirical design rules, containing 10 distinct guides for most genes. Competitive growth after pooled transformation revealed strong fitness defects for most essential genes, verifying that the library provides comprehensive genome coverage. We used the relative growth defects caused by different guides targeting essential genes to further refine yeast CRISPRi design rules. In order to obtain more accurate and robust guide abundance measurements in pooled screens, we link guides with random nucleotide barcodes and carry out linear amplification by in vitro transcription. CONCLUSIONS: Taken together, we demonstrate a broadly useful platform for comprehensive, high-precision CRISPRi screening in yeast.

Non-pharmacological Interventions for Muscle Cramps and Pain in Patients With Cirrhosis: A Systematic Review.

Despite the high prevalence of pain and challenges associated with traditional pharmacological pain management in patients with cirrhosis, little is known about the safety and effectiveness of non-pharmacological management of pain in this patient population. A systematic literature search of published studies was conducted in nine databases from inception through January 11, 2023, including any clinical trial, cohort, or case-control study of non-pharmacological pain interventions in adult patients with cirrhosis. Studies using nutritional supplements were included. The primary and secondary outcomes for this review were pain/analgesic effect and safety, respectively. Two reviewers independently performed data extraction and risk of bias assessment. Of the 4,087 studies initially screened, 11 studies representing 340 patients ultimately met inclusion criteria, including seven observational and four randomized controlled trials. Five studies reported muscle cramp severity, four reported muscle cramp frequency, and two reported non-cramp pain. Oral zinc sulfate, L-carnitine, and taurine were reported to decrease cramp frequency. Oral vitamin E, oral zinc sulfate, L-carnitine, taurine, and pickle juice decreased cramp severity. Curcumin supplementation, resistance training, and stretching and walking programs improved non-cramp pain. Mild adverse events were reported in four studies. The risk of bias was moderate to high for all studies, largely due to missing data, study design, and a lack of blinding of participants. Numerous nutritional and non-pharmacological interventions have been reported to be safe and effective for the treatment of pain and painful muscle cramps in patients with cirrhosis. However, further research is needed to better determine the efficacy, safety, and optimal frequency and dosage of interventions.

Attitudes, beliefs, and recommendations for persistent low back pain patients: cross-sectional surveys of students and faculty at a chiropractic college.

BACKGROUND: While the use of chiropractic care for persistent low back pain (PLBP) is prevalent, chiropractors' attitudes and beliefs related to PLBP patients are not fully understood. The purpose of this study was to assess the attitudes, beliefs and activity/work recommendations of students and faculty at a chiropractic college regarding PLBP patients. METHODS: The Health Care Providers Pain and Impairment Relationship Scale (HC-PAIRS) and clinical vignettes were requested to be completed by chiropractic students and faculty at Parker University in April 2018. Higher HC-PAIRS scores indicate stronger beliefs that PLBP justifies disability and limitation of activities. Activity and work recommendations from clinical vignettes were rated as "adequate", "neutral", or "inadequate", as defined in previous literature. Descriptive statistics, independent t-tests, and logistic regression were used to analyze results. RESULTS: Student and faculty response rates were 63.6% and 25.9%, respectively. Faculty mean HC-PAIRS scores (3.66 [SD:0.88]) were significantly lower than students' (4.41 [SD:0.71]). The percentage of faculty providing "adequate" activity (62.1%) and work (41.0%) recommendations was significantly greater than the percentage of students (activity: 33.9%, work: 21.2%) (p < 0.05). Higher HC-PAIRS scores in students were associated with decreased odds of providing "adequate" activity and work recommendations. CONCLUSIONS: Student and faculty attitudes and beliefs, and students' activity/work recommendations were found to be dissimilar to those from similar studies and less congruent with CPG recommendations. Lower HC-PAIRS scores increased the odds of students providing "adequate" activity and work recommendations to patients with PLBP. Results from this study may help guide future research and training opportunities.

Do infographics 'spin' the findings of health and medical research?

OBJECTIVE: To compare the prevalence of 'spin', and specific reporting strategies for spin, between infographics, abstracts and full texts of randomised controlled trials (RCTs) reporting non-significant findings in the field of health and medicine and to assess factors associated with the presence of spin. DESIGN: Cross-sectional observational study. DATA SOURCE: Publications in top quintile health and medical journals from August 2018 to October 2020 (Journal Citation Reports database). ELIGIBILITY CRITERIA: Infographics, abstracts and full texts of RCTs with non-significant results for a primary outcome. MAIN OUTCOMES AND MEASURES: Presence of spin (any spin and spin in the results and conclusions of infographics, abstracts and full texts). EXPOSURES: Conflicts of interest, industry sponsorship, trial registration, journal impact factor, spin in the abstract, spin in the full text. RESULTS: 119 studies from 40 journals were included. One-third (33%) of infographics contained spin. Infographics were not more likely to contain any spin than abstracts (33% vs 26%, OR 1.4; 95% CI 0.8 to 2.4) or full texts (33% vs 26%, OR 1.4; 95% CI 0.8 to 2.4). Higher journal impact factor was associated with slightly lower odds of spin in infographics and full texts, but not abstracts. Infographics, but not abstracts or full texts, were less likely to contain spin if the trial was prospectively registered. No other significant associations were found. CONCLUSIONS: Nearly one-third of infographics spin the findings of RCTs with non-significant results for a primary outcome, but the prevalence of spin is not higher than in abstracts and full texts. Given the increasing popularity of infographics to disseminate research findings, there is an urgent need to improve the reporting of research in infographics.

A scoping review to explore the use of the Health Care Providers' Pain and Impairment Relationship Scale.

OBJECTIVES: Patients' interactions with health care providers influence back pain-related outcomes. The Health Care Providers' Pain and Impairment Relationship Scale (HC-PAIRS) is an instrument that assesses providers' attitudes and beliefs about patients with persistent back pain, with lower scores implying that persistent pain does not indicate disability or limitation of activities. This scoping review aims to explore the extent of research involving the HC-PAIRS. LITERATURE SURVEY: PubMed, Embase, and PEDro databases were searched from inception to April 2022. METHODS: Extracted HC-PAIRS scores were standardized to 15-item scores and categorized by profession, student or professional status, and pre/post-educational intervention to evaluate scores. Psychometric properties and educational interventions of the HC-PAIRS were described. RESULTS: After screening, 51 studies representing 10,416 participants were included. Student and professional scores were investigated in 24 and 29 studies, respectively. Twenty-one studies included educational interventions, with heterogenous follow-up. Psychometric properties of the HC-PAIRS were assessed in 10 studies and demonstrated acceptable reliability and validity. The overall baseline mean score among all participants was 55.34 (95% CI: 53.54-57.14) (students: 56.54 [56.54-60.87]; professionals: 51.67 [49.08-54.27]). Nurses (61.99 [55.66-68.31]) and non-health care professionals (65.30 [57.33-73.28]) had the highest overall baseline mean scores, whereas chiropractors (51.69 [33.73-69.66]), MDs/PAs (52.64 [47.27-58.00]), physical therapists (53.42 [50.67-56.17]), and exercise professionals (57.36 [49.39-65.33]) had lower scores. CONCLUSIONS: The HC-PAIRS has been used across many disciplines in both students and professionals and demonstrated acceptable reliability and validity. Professionals commonly treating back pain had lower HC-PAIRS scores. Future research could benefit from standardization of interventions and timing of follow-up assessments.

Education can reassure people with rotator cuff-related shoulder pain: a 3-arm, randomised, online experiment.

ABSTRACT: We aimed to investigate the immediate effect of best practice education (with and without pain science messages) and structure-focused education on reassurance among people with rotator cuff-related shoulder pain. We conducted a 3-arm, parallel-group, randomised experiment. People with rotator cuff-related shoulder pain were randomised (1:1:1) to (1) best practice education (highlights that most shoulder pain is not serious or a good indicator of tissue damage and recommends simple self-management strategies); (2) best practice education plus pain science messages (which attempt to improve understanding of pain); and (3) structure-focused education (highlighting that structural changes are responsible for pain and should be targeted with treatment). Coprimary outcomes were self-reported reassurance that no serious condition is causing their pain and continuing with daily activities is safe. Secondary outcomes measured management intentions, credibility and relevance of the education, and similarity to previous education. Two thousand two hundred thirty-seven participants were randomised and provided primary outcome data. Best practice education increased reassurance that no serious condition is causing their pain (estimated mean effect 0.5 on a 0-10 scale, 95% confidence interval [CI] 0.2-0.7) and continuing with daily activities is safe (0.6, 95% CI 0.3-0.8) compared with structure-focused education . Adding pain science messages to best practice education slightly increased both measures of reassurance (0.2, 95% CI 0.0-0.4). Clinicians treating patients with rotator cuff-related shoulder pain should highlight that most shoulder pain is not serious or a good indicator of tissue damage and recommend simple self-management strategies. The benefit of adding pain science messages is small.

A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants.

Plants often generate secondary metabolites as defense mechanisms against parasites. Although some fungi may potentially overcome the barrier presented by antimicrobial compounds, only a limited number of examples and molecular mechanisms of resistance have been reported. Here, we found an Aglaia plant-parasitizing fungus that overcomes the toxicity of rocaglates, which are translation inhibitors synthesized by the plant, through an amino acid substitution in a eukaryotic translation initiation factor (eIF). De novo transcriptome assembly revealed that the fungus belongs to the Ophiocordyceps genus and that its eIF4A, a molecular target of rocaglates, harbors an amino acid substitution critical for rocaglate binding. Ribosome profiling harnessing a cucumber-infecting fungus, Colletotrichum orbiculare, demonstrated that the translational inhibitory effects of rocaglates were largely attenuated by the mutation found in the Aglaia parasite. The engineered C. orbiculare showed a survival advantage on cucumber plants with rocaglates. Our study exemplifies a plant-fungus tug-of-war centered on secondary metabolites produced by host plants.

Although plants may seem like passive creatures, they are in fact engaged in a constant battle against the parasitic fungi that attack them. To combat these fungal foes, plants produce small molecules that act like chemical weapons and kill the parasite. However, the fungi sometimes fight back, often by developing enzymes that can break down the deadly chemicals into harmless products. One class of anti-fungal molecules that has drawn great interest is rocaglates, as they show promise as treatments for cancer and COVID-19. Rocaglates are produced by plants in the Aglaia family and work by targeting the fungal molecule eIF4A which is fundamental for synthesizing proteins. Since proteins perform most of the chemistry necessary for life, one might think that rocaglates could ward off any fungus. But Chen et al. discovered there is in fact a species of fungi that can evade this powerful defense mechanism. After seeing this new-found fungal species successfully growing on Aglaia plants, Chen et al. set out to find how it is able to protect itself from rocoglates. Genetic analysis of the fungus revealed that its eIF4A contained a single mutation that 'blocked' rocaglates from interacting with it. Chen et al. confirmed this effect by engineering a second fungal species (which infects cucumber plants) so that its elF4A protein contained the mutation found in the new fungus. Fungi with the mutated eIF4A thrived on cucumber leaves treated with a chemical derived from rocaglates, whereas fungi with the non-mutated version were less successful. These results shed new light on the constant 'arms race' between plants and their fungal parasites, with each side evolving more sophisticated ways to overcome the other's defenses. Chen et al. hope that identifying the new rocaglate-resistant eIF4A mutation will help guide the development and use of any therapies based on rocaglates. Further work investigating how often the mutation occurs in humans will also be important for determining how effective these therapies will be.

Codon optimality modulates protein output by tuning translation initiation.

The impact of synonymous codon choice on protein output has important implications for understanding endogenous gene expression and design of synthetic mRNAs. Previously, we used a neural network model to design a series of synonymous fluorescent reporters whose protein output in yeast spanned a seven-fold range corresponding to their predicted translation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability, but rather, that an active mechanism further decreases the number of proteins made per mRNA. We combine simulations and careful experiments on fluorescent reporters to argue that translation initiation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen to discover factors modulating the output from non-optimal transcripts, we identify a set of translation initiation factors including multiple subunits of eIF3 whose depletion restored protein output of a non-optimal reporter. Our results show that codon usage can directly limit protein production, across the full range of endogenous variability in codon usage, by limiting translation initiation.

Plasmid and Sequencing Library Preparation for CRISPRi Barcoded Expression Reporter Sequencing (CiBER-seq) in Saccharomyces cerevisiae.

Genetic networks regulate nearly all biological processes, including cellular differentiation, homeostasis, and immune responses. Determining the precise role of each gene within a regulatory network can explain its overall, integrated function, and pinpoint mechanisms underlying misregulation in disease states. Transcriptional reporter assays are a useful tool for dissecting these genetic networks, because they link a molecular process to a measurable readout, such as the expression of a fluorescent protein. Here, we introduce a new technique that uses expressed RNA barcodes as reporters, to measure transcriptional changes induced by CRISPRi-mediated genetic perturbation across a diverse, genome-wide library of guide RNAs. We describe an exemplary reporter based on the promoter that drives His4 expression in these guidelines, which can be used as a framework to interrogate other expression phenotypes. In this workflow, a library of plasmids is assembled, encoding a CRISPRi guide RNA (gRNA) along with one or more transcriptional reporters that drive expression of guide-specific nucleotide barcode sequences. For example, when interrogating regulation of the budding yeast HIS4 promoter normalized against a control housekeeping promoter that drives Pgk1 expression, this plasmid library contains a gRNA expression cassette, a HIS4 reporter driving expression of one gRNA-specific nucleotide barcode, and a PGK1 reporter driving expression of a second, gRNA-specific barcode. Long-read sequencing is used to determine which gRNA is associated with these nucleotide barcodes. The plasmid library is then transformed into yeast cells, where each cell receives one plasmid, and experiences a genetic perturbation driven by the guide on that plasmid. The expressed RNA barcodes are extracted in bulk and quantified using high-throughput sequencing, thereby measuring the effect of their corresponding gRNA on barcoded reporter expression. In the case of the HIS4 reporter described above, guides disrupting translation elongation will increase expression of the associated HIS4 barcode specifically, without changing expression of the PGK1 control barcode. It is further possible to quantify plasmid abundance by DNA sequencing, as an additional approach to normalize for differences in plasmid abundance within the population of cells. This protocol outlines the steps to prepare barcode reporter CRISPRi plasmid libraries, link guides to barcodes with long-read sequencing, and measure expression changes through barcode RNA and DNA sequencing. This method is ideal for probing transcriptional or post-transcriptional regulation, as it measures the effects of a genetic perturbation by directly quantifying reporter RNA abundance, rather than relying on indirect growth or fluorescence readouts. Graphic abstract.

CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes.

To realize the promise of CRISPR-Cas9-based genetics, approaches are needed to quantify a specific, molecular phenotype across genome-wide libraries of genetic perturbations. We addressed this challenge by profiling transcriptional, translational, and posttranslational reporters using CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). Our barcoding approach allowed us to connect an entire library of guides to their individual phenotypic consequences using pooled sequencing. CiBER-seq profiling fully recapitulated the integrated stress response (ISR) pathway in yeast. Genetic perturbations causing uncharged transfer RNA (tRNA) accumulation activated ISR reporter transcription. Notably, tRNA insufficiency also activated the reporter, independent of the uncharged tRNA sensor. By uncovering alternate triggers for ISR activation, we illustrate how precise, comprehensive CiBER-seq profiling provides a powerful and broadly applicable tool for dissecting genetic networks.

Success Rate and Complications of Sharp Recanalization for Treatment of Central Venous Occlusions.

PURPOSE: To evaluate success and safety of needle (sharp) recanalization as a method to re-establish access in patients with chronic central venous occlusions. MATERIALS AND METHODS: Thirty-nine consecutive patients who underwent this procedure were retrospectively reviewed to establish success rate and associated complications. In all cases, a 21- or 22-gauge needle was used to restore connection between two chronically occluded segments after conventional wire and catheter techniques had failed. The needle was guided toward a target placed through a separate access by fluoroscopic guidance. When successful, the procedure was completed by placing a catheter, ballooning the segment, and/or stenting. RESULTS: The procedure was successful in 37 of the 39 patients (95%). The vast majority of the treated lesions were in the SVC and/or right innominate vein. Occlusions ranged in length between 10 and 110 mm, and the average length of occluded venous segment was 40 mm in the treated group. There were four minor (SIR classification B) complications involving pain management after the procedure. There were two major (SIR classification D) complications both of which involved hemorrhage into the pericardium treated with covered stents (5.1%). CONCLUSIONS: Sharp recanalization is a viable procedure for patients who have exhausted standard wire and catheter techniques. The operator performing this procedure should be familiar with potential complications so that they can be addressed urgently if needed.

Characterization of diverse homoserine lactone synthases in Escherichia coli.

Quorum sensing networks have been identified in over one hundred bacterial species to date. A subset of these networks regulate group behaviors, such as bioluminescence, virulence, and biofilm formation, by sending and receiving small molecules called homoserine lactones (HSLs). Bioengineers have incorporated quorum sensing pathways into genetic circuits to connect logical operations. However, the development of higher-order genetic circuitry is inhibited by crosstalk, in which one quorum sensing network responds to HSLs produced by a different network. Here, we report the construction and characterization of a library of ten synthases including some that are expected to produce HSLs that are incompatible with the Lux pathway, and therefore show no crosstalk. We demonstrated their function in a common lab chassis, Escherichia coli BL21, and in two contexts, liquid and solid agar cultures, using decoupled Sender and Receiver pathways. We observed weak or strong stimulation of a Lux receiver by longer-chain or shorter-chain HSL-generating Senders, respectively. We also considered the under-investigated risk of unintentional release of incompletely deactivated HSLs in biological waste. We found that HSL-enriched media treated with bleach were still bioactive, while autoclaving deactivates LuxR induction. This work represents the most extensive comparison of quorum signaling synthases to date and greatly expands the bacterial signaling toolkit while recommending practices for disposal based on empirical, quantitative evidence.

Can the natural diversity of quorum-sensing advance synthetic biology?

Quorum-sensing networks enable bacteria to sense and respond to chemical signals produced by neighboring bacteria. They are widespread: over 100 morphologically and genetically distinct species of eubacteria are known to use quorum sensing to control gene expression. This diversity suggests the potential to use natural protein variants to engineer parallel, input-specific, cell-cell communication pathways. However, only three distinct signaling pathways, Lux, Las, and Rhl, have been adapted for and broadly used in engineered systems. The paucity of unique quorum-sensing systems and their propensity for crosstalk limits the usefulness of our current quorum-sensing toolkit. This review discusses the need for more signaling pathways, roadblocks to using multiple pathways in parallel, and strategies for expanding the quorum-sensing toolbox for synthetic biology.

Corrigendum: Can the Natural Diversity of Quorum-Sensing Advance Synthetic Biology?

[This corrects the article on p. 30 in vol. 3, PMID: 25806368.].

An Efficient Method for Electroporation of Small Interfering RNAs into ENCODE Project Tier 1 GM12878 and K562 Cell Lines.

The Encyclopedia of DNA Elements (ENCODE) Project aims to identify all functional sequence elements in the human genome sequence by use of high-throughput DNA/cDNA sequencing approaches. To aid the standardization, comparison, and integration of data sets produced from different technologies and platforms, the ENCODE Consortium selected several standard human cell lines to be used by the ENCODE Projects. The Tier 1 ENCODE cell lines include GM12878, K562, and H1 human embryonic stem cell lines. GM12878 is a lymphoblastoid cell line, transformed with the Epstein-Barr virus, that was selected by the International HapMap Project for whole genome and transcriptome sequencing by use of the Illumina platform. K562 is an immortalized myelogenous leukemia cell line. The GM12878 cell line is attractive for the ENCODE Projects, as it offers potential synergy with the International HapMap Project. Despite the vast amount of sequencing data available on the GM12878 cell line through the ENCODE Project, including transcriptome, chromatin immunoprecipitation-sequencing for histone marks, and transcription factors, no small interfering siRNA-mediated knockdown studies have been performed in the GM12878 cell line, as cationic lipid-mediated transfection methods are inefficient for lymphoid cell lines. Here, we present an efficient and reproducible method for transfection of a variety of siRNAs into the GM12878 and K562 cell lines, which subsequently results in targeted protein depletion.