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Anna Johnson

Publications and source records attributed to Anna Johnson.

14 recordsLinked to original sources
PubMed2026

Understanding randomized controlled trial generalizability through an embedded molecular diagnostics trial.

BACKGROUND: Issues with randomized controlled trial generalizability are well described, but whether these issues result from differences in patient treatment across contexts remains unknown. We studied treatment of patients with high-risk prostate cancer after radical prostatectomy inside and outside a randomized controlled trial evaluating the impact of a genomic classifier on post-radical prostatectomy treatment decision making (Genomics in Michigan Impacting Observation of Radiation [G-MINOR]; ClinicalTrials.gov identifier NCT02783950). METHODS: G-MINOR enrolled 338 patients; propensity score-matched eligible but unenrolled patient cohorts (pretrial and trial contemporary) from the Michigan Urological Surgery Improvement Collaborative (MUSIC), in which the trial was embedded, were compared for rates and time to secondary treatment (adjuvant or salvage therapy) after prostatectomy. RESULTS: Among 338 patients in the G-MINOR cohort, 69 (31 adjuvant, 38 salvage) received secondary treatment compared with 266 (183 adjuvant, 83 salvage) and 104 (60 adjuvant, 44 salvage) in the 1014 contemporary and 338 pretrial-matched MUSIC cohorts. Time to secondary treatment was much shorter in the MUSIC cohort across all comparisons. For example, matching G-MINOR to synchronous MUSIC patients demonstrated 84% vs 74% estimated 2-year treatment-free survival for trial and real-world patients, respectively (P&#x2009;<&#x2009;.001). CONCLUSIONS: Controlling for key clinicopathologic factors, patients in the G-MINOR randomized controlled trial and MUSIC cohorts were treated differently, even after stratifying by genomic risk. These findings suggest that challenges in randomized controlled trial generalizability extend beyond the representativeness of trial participants. Differences in management may also explain why divergent patient outcomes are observed in randomized controlled trials vs real-world settings.

Aged↗
PubMed2025

The functional organization of chromosome territories in single nuclei during zygotic genome activation.

Chromosome territories (CTs) are intricately organized and regulated within the nucleus. Despite remarkable advances in our understanding of genome packaging and gene expression, the interplay among CTs, pairing of parental homologous chromosomes, and genome function during development remains elusive. Here, we employ an Oligopaints-based high-resolution imaging approach to examine variable CT organization in single nuclei during the developmental process of zygotic genome activation. We reveal large-scale chromosome changes with extensive homolog pairing at the whole-chromosome level that decreases locally due to spatial variability in chromosome conformations. In the absence of one homolog copy, the dynamics of CT compaction and RNA polymerase II recruitment are supported by transcriptional changes in haploid embryos. Finally, global inhibition of transcription results in decreased CT opening and no significant impact on CT pairing levels. These findings enhance our understanding of parental genome folding and regulation, which may inform strategies for chromosome-based diseases.

RNA polymerase II↗
PubMed2004

Fibronectin fragments cause release and degradation of collagen-binding molecules from equine explant cultures.

OBJECTIVE: Previous experiments have shown that addition of fragmented fibronectin can induce cartilage chondrolysis. In this study we investigated the fate of the collagen- and cell-binding molecules Cartilage oligomeric matrix protein (COMP) and chondroadherin. DESIGN: Equine articular cartilage explants were stimulated with the C-terminal and the N-terminal heparin-binding fragments of fibronectin respectively, and the conditioned media were analysed by both quantitative (ELISA) and qualitative (mass spectrometry, Western blots) methods. RESULTS: Both COMP and chondroadherin were released in a dose-dependent manner upon stimulation with the Hep II (C-terminal heparin-binding) fragment of fibronectin. The kinetics of release for the two components differed. Moreover, COMP was degraded while no fragments of chondroadherin could be detected. Stimulation with Hep II also induced production of nitric oxide in a dose-dependent manner. We compared effects of the Hep II fragment with that of Hep I (the N-terminal heparin-binding fragment of fibronectin) and found that while Hep I did indeed elicit release of COMP and chondroadherin, the response was less potent, and production of nitric oxide was negligible. The responses to both fragments were elicited within 24h. CONCLUSIONS: We suggest that the events described here may be early, critical stages in cartilage destruction preceding collagen destruction.

Animals↗
PubMed2003

Wetting phase connectivity and irreducible saturation in simple granular media.

We present drainage simulations that allow trapping of wetting phase in a simple but nontrivial granular medium, a dense random packing of equal spheres. The basis for the simulations is a network model derived directly from the known locations and dimensions of pore space features. This provides a means of evaluating the morphology of trapped wetting phase. The possible morphologies depend on the assumed connectivity of the wetting phase. At one extreme, we assume that the entire wetting phase except for pendular rings is connected. At the opposite extreme, we illustrate a low level of connectivity by assuming that pendular rings are trapped as soon as the pores surrounding them are drained; any wetting phase not yet drained from pore throats connecting these pores is also assumed to be trapped. Finally we consider a set of criteria involving larger neighborhoods within the network, which allows trapping in individual pores. Irreducible wetting phase saturations obtained in the latter case agree with experimental data. The numbers of pendular rings and liquid bridges are also consistent with observations. Because the agreement does not involve adjustable parameters, we conclude that a relatively simple, local evaluation of trapping criteria can yield physically representative wetting phase configurations.

Journal Article↗
PubMed2003

Mutated VH genes and preferential VH3-21 use define new subsets of mantle cell lymphoma.

Mantle cell lymphoma (MCL) is believed to originate from a naive B cell. However, we recently demonstrated that a subset of MCL displayed mutated V(H) genes. We also reported restricted use of certain V(H) genes. To assess the prognostic impact of these new findings, we performed V(H) gene analysis of 110 patients, revealing that 18 (16%) patients had mutated and 92 (84%) patients had unmutated V(H) genes. Because the mutation rate was low in the mutated group (2.2%-6.7%), further investigation of the germline V(H) gene in T cells from 5 patients with mutated V(H) genes was carried out; results showed that the unrearranged V(H) gene was identical to the published sequence. These data confirm that the base pair substitutions within the rearranged V(H) genes represent hypermutations, and indicate germinal center exposure. However, V(H) gene mutation status did not correlate with prognosis because there was no difference in clinical outcome between the unmutated and mutated groups. The most frequently used V(H) genes were V(H)3-21 (21 patients) and V(H)4-34 (19 patients). A novel finding was that V(H)3-21(+) MCL almost exclusively expressed lambda light chains and displayed highly restricted use of the V(lambda)3-19 gene. V(H)3-21(+) patients had longer median survival than the remaining patients (53 vs 34 months; P =.03), but they tended to be younger at diagnosis. The combined use of V(H)3-21/V(lambda)3-19 suggests a possible role for antigen(s) in the pathogenesis of these tumors and indicates that V(H)3-21(+) patients constitute a new MCL entity.

Adult↗
PubMed2003

Chronic lymphocytic leukemias utilizing the VH3-21 gene display highly restricted Vlambda2-14 gene use and homologous CDR3s: implicating recognition of a common antigen epitope.

The immunoglobulin variable heavy chain (IgVH) gene mutation status is an important prognostic factor in chronic lymphocytic leukemia (CLL), since cases with mutated VH genes show significantly longer survival than unmutated cases. Recently, we reported a preferential use of the VH3-21 gene in mutated CLL and showed that mutated VH3-21 cases had an inferior overall survival compared with other mutated CLL. In order to further characterize this subset, we performed VH gene analysis in 265 CLL cases and identified 31 VH3-21 cases (11.7%); 21 cases had mutated and 10 cases unmutated VH genes. Regardless of VH gene mutation status, a poor overall survival was found in the VH3-21 cases with a median survival of 83 months. These survival data confirm that VH3-21 cases do not fit into the general prognostic grouping of mutated and unmutated CLL. A large fraction of VH3-21 cases also demonstrated unique features with shorter lengths of the third complementarity determining region (CDR3) and CDR3s with highly homologous amino acid sequences. Furthermore, the VH3-21 cases showed a striking dominance of lambda light chain expression, and analysis of the Iglambda gene rearrangements revealed highly restricted use of the Vlambda2-14/Jlambda3 genes in the majority of cases. Taken together, our new findings strengthen the suggestion that VH3-21-using cases comprise a new CLL entity, irrespective of VH gene mutation status, and implicate that a common antigen epitope, perhaps of pathogenic significance, is recognized by the highly homologous VH3-21/Vlambda2-14 Ig molecules expressed in individual tumors.

Amino Acid Sequence↗
PubMed2003

Primary treatment with autologous stem cell transplantation in mantle cell lymphoma: outcome related to remission pretransplant.

OBJECTIVES: The aim of the first Nordic mantle cell lymphoma (MCL) protocol was to study the clinical significance of an augmented CHOP induction chemotherapy followed by high-dose chemotherapy and autologous stem cell transplantation (ASCT) and to examine the prognostic significance of stem cell contamination rates in newly diagnosed patients with MCL. PATIENTS AND METHODS: Forty-one newly diagnosed patients below 66 yr were enrolled and given three series of an augmented CHOP regimen. Responders underwent stem cell mobilization with a fourth course of CHOP, stem cell harvest and ASCT. Stem cell purging was optional in the protocol and followed the routine of each participating centre. The number of tumour cells in the reinfused autografts was estimated by flow cytometry or quantitative PCR. RESULTS: Induction therapy led to complete remission (CR) in 11 of 41 patients (27%), partial remission (PR) in 20 of 41 patients (49%) and no response in nine patients (22%), whereas one patient was not evaluable. Twenty-seven of the 31 responders underwent ASCT and 24 achieved or maintained a CR. The overall and failure-free 4-yr survival on intention-to-treat basis were 51% and 15%, respectively. Among the transplanted patients, a significantly increased failure-free (P<0.03) and overall survival (P=0.03) was noted among patients transplanted in CR compared with PR, respectively. By contrast, reinfusion of highly variable numbers of tumour cells with the autografts (range 0.71-80 x 10(6) tumour cells), did not affect outcome. CONCLUSION: In MCL, an important strategy to improve the outcome will be to intensify the induction chemotherapy.

Adult↗
PubMed2002

Polymorphism in the P2X7 receptor gene and survival in chronic lymphocytic leukaemia.

BACKGROUND: The P2X7 receptor is a ligand-gated cation channel that mediates ATP-induced apoptotic death in haemopoietic and chronic lymphocytic leukaemia (CLL) cells. We aimed to investigate the clinical effect of a single nucleotide polymorphism in the P2X7 receptor gene (1513A-->C) and correlate findings with the immunoglobulin heavy chain variable (V(H)) gene mutation status, a prognostic marker in CLL. METHODS: We investigated tumour DNA in 170 patients with CLL using PCR-RFLP analysis with HhaI restriction enzyme cleavage to screen for the polymorphism in the P2X7 receptor gene. The VH gene mutation status was assessed in 165 patients by PCR amplification and nucleotide sequencing. We correlated the findings of the P2X7 receptor genotype with the V(H) gene mutation data and overall survival and screened for the P2X7 receptor polymorphism in 200 healthy controls. FINDINGS: Of the 170 patients, 35 (21%) were heterozygous and one (1%) homozygous for the 1513C allele; whereas 134 (79%) had the 1513A/A genotype of the P2X7 receptor gene. Overall survival was significantly longer for patients with CLL heterozygous for the 1513C allele than those with the 1513A/A genotype. Median survival for heterozygous patients was 104 months (range 33-467) and 72 months (1-190) for homozygous patients (p=0.009). Of the 165 patients with CLL in whom we assessed the V(H) gene mutation status, the V(H) genes were mutated in 71 (43%) patients and unmutated in 94; 18 (25%) of the 71 patients with mutated genes had 1513C allele compared with 17 (18%) of 94 who had unmutated genes. In patients with mutated VH genes, those with CLL who were 1513C positive had 53 months' longer median survival than did those with the 1513A/A genotype (151 vs 98 months, p=0.011). INTERPRETATION: The P2X7 polymorphism could affect clinical outcome in CLL, especially in patients with mutated V(H) genes. Studies are necessary to elucidate the biological role of the P2X7 polymorphism in CLL in vivo.

Adult↗
PubMed2002

AUA as a translation initiation site in vitro for the human transcription factor Sp3.

Sp3 is a bifunctional transcription factor that has been reported to stimulate or repress the transcription of numerous genes. Although the size of Sp3 mRNA is 4.0 kb, the size of the known Sp3 cDNA sequence is 3.6 kb. Thus, Sp3 functional studies have been performed with an artificially introduced start codon, and thus an aminoterminus that differs from the wild-type. Ideally, full-length cDNA expression vectors with the appropriate start codon should be utilized for these studies. Using 5'rapid amplification of cDNA ends, a full-length Sp3 cDNA clone was generated and the sequence verified in nine cell lines. No AUG initiation codon was present. However, stop codons were present in all three frames 5' to the known coding sequence. In vitro translation of this full-length cDNA clone produced the expected three isoforms-one at 100 kDa and two in the mid 60 kDa range. Electrophoretic mobility shift assays showed that the protein products had the ability to bind to the Sp1/3 consensus sequence. In vitro studies, using our Sp3 clone and site directed mutagenesis, identified the translation initiation site for the larger isoform as AUA. AUA has not been previously described as an endogenous initiation codon in eukaryotes.

Animals↗
PubMed2002

Somatically mutated Ig V(H)3-21 genes characterize a new subset of chronic lymphocytic leukemia.

Recent studies on the immunoglobulin variable heavy chain (IgV(H)) genes have revealed that B-cell chronic lymphocytic leukemia (B-CLL) consists of at least 2 clinical entities with either somatically mutated or unmutated V(H) genes. We have analyzed the V(H) gene mutation status and V(H) gene usage in 119 B-CLL cases and correlated them to overall survival. A novel finding was the preferential use of the V(H)3-21 gene in mutated cases, whereas biased V(H)1-69 gene usage was found in unmutated cases as previously reported. Interestingly, the subset of mutated cases using the V(H)3-21 gene displayed distinctive genotypic/phenotypic characteristics with shorter average length of the complementarity determining region 3 and clonal expression of lambda light chains. In addition, this mutated subset showed significantly shorter survival than other mutated cases and a similar clinical course to unmutated cases. We therefore suggest that B-CLL cases with mutated V(H)3-21 genes may constitute an additional entity of B-CLL.

Aged↗
PubMed2002

Somatic hypermutation and V(H) gene usage in mantle cell lymphoma.

Mantle cell lymphoma (MCL) is considered to derive from naïve, pregerminal center (GC) CD5+ B-cells. However, the cell of origin has been questioned in recent studies that showed somatic hypermutations in the immunoglobulin (Ig) variable heavy chain (V(H)) genes in subsets of MCL. To clarify this issue, we analyzed the IgV(H) genes for the presence of somatic hypermutations in 51 MCL cases. Twenty percent of the MCL cases displayed somatically mutated V(H) genes (defined as >2% mutated), whereas 80% showed unmutated V(H) genes. This finding suggests that MCL is a genetically heterogeneous disease, with the majority of cases originating from unmutated pre-GC B-cells and a subset deriving from more mature B-cells which have been exposed to the GC environment and have undergone somatic hypermutation. A biased V(H) gene usage has been demonstrated in several B-cell malignancies; however, this has not yet been investigated in MCL, although V(H)4-34 overusage has been indicated by small studies. Interestingly, we found a restricted usage of three individual V(H) genes in our MCL material; V(H)4-34 (22%), V(H)3-21 (16%) and V(H)5-51 (12%). This novel finding of preferential V(H) gene usage in half of the MCL cases may suggest an antigen driven process occurring in B-cells expressing specific VH genes, thus implicating that Ig specificity could be involved in mantle cell lymphoma development.

Adult↗
PubMedDate not supplied

Five-year changes in North Carolina outpatient cardiac rehabilitation.

PURPOSE: The purpose of this study was to describe cardiac rehabilitation programming, barriers to participation, and reasons for dropout in North Carolina from a program director's perspective and to compare those results with those of a similar statewide survey conducted 5 years earlier. METHODS: In 1999 and 2004, a survey was mailed to all North Carolina program directors of outpatient cardiac rehabilitation programs. The response rate was 85% (61/72) in 1999 and 79% (61/77) in 2004. RESULTS: More than 85% of North Carolinians older than 40 years lived within a 15-mile buffer of an outpatient cardiac rehabilitation program in 2004. Most programs were staffed with personnel trained in nursing, exercise physiology, and nutrition in 1999 and 2004. Women and African Americans remained disproportionately underrepresented as participants in the program for both years. In 2004, approximately one third of cardiac rehabilitation programs reported having a referral to rehabilitation on the hospital discharge plan for myocardial infarction and coronary artery bypass surgery. In 1999 and 2004, the most frequently reported barrier to participation remained financial, followed by lack of interest or motivation and workplace conflicts. Work conflicts, lack of interest, and comorbidities were the most frequently reported reasons for dropping out from cardiac rehabilitation programs in both 1999 and 2004. CONCLUSIONS: Increasing participation in cardiac rehabilitation programs by addressing barriers at multiple levels may facilitate greater patient participation. This statewide survey could be used in other states as a surveillance tool, to track changes in rehabilitation over time from a program director's perspective.

Ambulatory Care Facilities↗