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Siqueira MS, Souto LR, Martinez AF, Serrão FV, de Noronha M. Muscle activation, strength, and volume in people with patellofemoral osteoarthritis: a systematic review and meta-analysis. Osteoarthritis Cartilage 2022; 30:935-944. [PMID: 35257862 DOI: 10.1016/j.joca.2022.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE This systematic review investigated whether people with patellofemoral osteoarthritis (PFOA) have muscle strength, volume, and activation around the hip and knee that is different from asymptomatic controls. METHODS Searches were carried out in five electronic databases, with terms related to PFOA, including muscle strength, volume and activation. Only studies with at least one group with symptomatic PFOA and one asymptomatic group were included. The methodological quality of the studies was assessed using the Downs and Black checklist. Certainty of evidence was assessed using the GRADE methodology. Using the random effects model, a meta-analysis was performed when there were at least two studies reporting the same domain. RESULTS Eight studies (250 participants) met the inclusion criteria. Subjects with PFOA had weaker hip abduction (SMD -0.96; 95%CI = -1.34 to -0.57), hip external rotation (-0.55;-1.07 to -0.03), hip extension (-0.72;-1.16 to -0.28), and knee extension (-0.97;-1.41 to -0.53) when compared to asymptomatic controls. People with PFOA also presented with smaller volumes of the gluteus medius, gluteus minimus, tensor fascia lata, vastus medialis (VM), vastus lateralis (VL) and rectus femoris when compared to asymptomatic controls. Also, people with PFOA presented with changes in muscle activation for the VL, VM and gluteus maximus (GMax) when compared to asymptomatic controls. CONCLUSION People with PFOA present with lower strength and volume of the hip and quadriceps muscles and altered muscle activation of the VM, VL and GMax during ascending and descending stairs when compared to asymptomatic controls. However, the certainty of these findings are very low. TRIAL REGISTRATION NUMBER PROSPERO systematic review protocol (ID = CRD42020197776).
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Affiliation(s)
- M S Siqueira
- Department of Physical Therapy, Center of Biological and Health Sciences, Federal University of São Carlos, Washington Luiz Road, km 235, SP310, São Carlos, São Paulo 13565-905, Brazil.
| | - L R Souto
- Department of Physical Therapy, Center of Biological and Health Sciences, Federal University of São Carlos, Washington Luiz Road, km 235, SP310, São Carlos, São Paulo 13565-905, Brazil.
| | - A F Martinez
- Department of Physical Therapy, Center of Biological and Health Sciences, Federal University of São Carlos, Washington Luiz Road, km 235, SP310, São Carlos, São Paulo 13565-905, Brazil.
| | - F V Serrão
- Department of Physical Therapy, Center of Biological and Health Sciences, Federal University of São Carlos, Washington Luiz Road, km 235, SP310, São Carlos, São Paulo 13565-905, Brazil.
| | - M de Noronha
- Rural Department of Allied Health, Rural Health School, La Trobe University, Bendigo, VIC 3660, Australia.
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Shepherd JH, Hyslop T, Fan C, Martinez AF, Parker J, Hoadley K, Hu Z, Li Y, Soloway M, Spears P, Partridge A, Sikov W, Carey LA, Perou CM. Abstract PD9-03: Genomic analysis of the CALGB 40603 (Alliance) neoadjuvant trial in TNBC identifies immune features associated with pathological complete response and event-free survival. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-pd9-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: CALGB (now part of the Alliance for Clinical Trials in Oncology) 40603 was a randomized Phase II study investigating pathological complete response rates (pCR) in triple-negative breast cancer (TNBC) patients receiving neoadjuvant weekly paclitaxel followed by doxorubicin and cyclophosphamide +/- bevacizumab and/or carboplatin for which 5-year event-free survival (EFS) results are now available. This is a valuable resource to characterize clinical and genomic features associated with response and survival. Methods: Clinical parameters and pre-treatment tumor biopsy RNA-sequencing (RNAseq) from 295 TNBC patients were analyzed to identify features associated with pCR and/or EFS. A panel of 689 previously published gene expression signatures were evaluated to provide insights regarding potential associations between clinical endpoints and genomically determined cell types and signaling pathway activities. Additionally, B cell receptor (BCR) and T cell receptor (TCR) sequences were examined, and repertoire abundance, richness, and diversity measures were calculated to investigate correlations with pCR and EFS status. Univariate Mann-Whitney U-Tests were used for continuous variables, and Fisher’s test was used for categorical features, with unadjusted p-values < 0.05 designated as significant. Results: While the addition of bevacizumab and carboplatin each significantly improved pCR rates, neither improved EFS. We examined outcomes according to race and no differences were seen for either pCR rate or EFS. 131 features, including high proliferation and multiple interferon signatures were significantly associated with pCR, but not with EFS. Alternatively, 69 features, including clinical factors for T stage and node status, were prognostic for EFS, but not significantly associated with pCR. Nevertheless, pCR itself was the strongest predictor of EFS, and was the only feature significantly associated with EFS after adjusting for multiple comparisons (Benjamini-Hochberg False Discovery Rate = 6.7e-3). In total, 52 genomic features were significantly correlated with both pCR and EFS, 44 of which were features of the immune microenvironment. Immune associated features included signatures of T cells, B cells and NK cells, immune checkpoint pathways (PD-1, PD-L1, CTLA4), and antigen presentation (dendritic cells, MHC-I, MHC-II). In particular, low BCR evenness, which is a measure of uniformity of unique BCR sequence abundance, was strongly associated with both pCR and EFS, suggesting that an antigen-specific adaptive immune response with clonally selected B cells is occurring in patients that have improved response and survival. Furthermore, a multivariate Cox Proportional Hazards model assessing BCR evenness along with age, T stage, N stage, grade and pCR found BCR evenness to be an independent prognostic feature for EFS in TNBC. Conclusions: Evidence of distinct predictors of pCR and EFS in TNBC patients treated with neoadjuvant chemotherapy suggests that, while pCR is still the strongest prognostic feature, high expression of many immune related gene expression signatures in pretreatment tumor samples are promising biomarkers of improved EFS. In addition to the important role of T cells in an anti-tumor response, these data show high IgG expression and evidence of B cell clonal selection associates with improved response and survival, supporting an important role for B cells in the adaptive response that portends a long-term benefit of chemotherapy in TNBC. Support: U10CA180821, U10CA180882, U24CA196171, P50-CA58223, Genentech, and The Breast Cancer Research Foundation. https://acknowledgments.alliancefound.org; ClinicalTrials.gov Identifier: NCT00861705
Citation Format: Jonathan H Shepherd, Terry Hyslop, Cheng Fan, Aranzazu Fernandez Martinez, Joel Parker, Katherine Hoadley, Zhiyuan Hu, Yun Li, Matthew Soloway, Patricia Spears, Ann Partridge, William Sikov, Lisa A Carey, Charles M Perou. Genomic analysis of the CALGB 40603 (Alliance) neoadjuvant trial in TNBC identifies immune features associated with pathological complete response and event-free survival [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD9-03.
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Affiliation(s)
| | | | - Cheng Fan
- 1University of North Carolina, Chapel Hill, NC
| | | | - Joel Parker
- 1University of North Carolina, Chapel Hill, NC
| | | | - Zhiyuan Hu
- 1University of North Carolina, Chapel Hill, NC
| | - Yun Li
- 1University of North Carolina, Chapel Hill, NC
| | | | | | | | - William Sikov
- 4Warren Alpert Medical School of Brown University, Providence, RI
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Vélez JI, Chandrasekharappa SC, Henao E, Martinez AF, Harper U, Jones M, Solomon BD, Lopez L, Garcia G, Aguirre-Acevedo DC, Acosta-Baena N, Correa JC, Lopera-Gómez CM, Jaramillo-Elorza MC, Rivera D, Kosik KS, Schork NJ, Swanson JM, Lopera F, Arcos-Burgos M. Pooling/bootstrap-based GWAS (pbGWAS) identifies new loci modifying the age of onset in PSEN1 p.Glu280Ala Alzheimer's disease. Mol Psychiatry 2013; 18:568-75. [PMID: 22710270 PMCID: PMC3596442 DOI: 10.1038/mp.2012.81] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The literature on GWAS (genome-wide association studies) data suggests that very large sample sizes (for example, 50,000 cases and 50,000 controls) may be required to detect significant associations of genomic regions for complex disorders such as Alzheimer's disease (AD). Because of the challenges of obtaining such large cohorts, we describe here a novel sequential strategy that combines pooling of DNA and bootstrapping (pbGWAS) in order to significantly increase the statistical power and exponentially reduce expenses. We applied this method to a very homogeneous sample of patients belonging to a unique and clinically well-characterized multigenerational pedigree with one of the most severe forms of early onset AD, carrying the PSEN1 p.Glu280Ala mutation (often referred to as E280A mutation), which originated as a consequence of a founder effect. In this cohort, we identified novel loci genome-wide significantly associated as modifiers of the age of onset of AD (CD44, rs187116, P=1.29 × 10⁻¹²; NPHP1, rs10173717, P=1.74 × 10⁻¹²; CADPS2, rs3757536, P=1.54 × 10⁻¹⁰; GREM2, rs12129547, P=1.69 × 10⁻¹³, among others) as well as other loci known to be associated with AD. Regions identified by pbGWAS were confirmed by subsequent individual genotyping. The pbGWAS methodology and the genes it targeted could provide important insights in determining the genetic causes of AD and other complex conditions.
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Affiliation(s)
- J I Vélez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - S C Chandrasekharappa
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - E Henao
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - A F Martinez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - U Harper
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Jones
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - B D Solomon
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - L Lopez
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - G Garcia
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - D C Aguirre-Acevedo
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - N Acosta-Baena
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - J C Correa
- Escuela de Estadística, Universidad Nacional de Colombia, Sede Medellín, Medellín, Colombia
| | - C M Lopera-Gómez
- Escuela de Estadística, Universidad Nacional de Colombia, Sede Medellín, Medellín, Colombia
| | - M C Jaramillo-Elorza
- Escuela de Estadística, Universidad Nacional de Colombia, Sede Medellín, Medellín, Colombia
| | - D Rivera
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - K S Kosik
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - N J Schork
- Department of Biostatistics and Bioinformatics, The Scripps Research Institute, La Jolla, CA, USA
| | - J M Swanson
- Department of Psychiatry, Florida International University, Miami, FL, USA,Child Development Center, University of California at Irvine, Irvine, CA, USA
| | - F Lopera
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - M Arcos-Burgos
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA,Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia,Translational Genomics Group, Department of Translational Medicine, John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, The Australian National University, Canberra, ACT, Australia,Translational Genomics Group, ANU College of Medicine, Biology & Environment, John Curtin School of Medical Research, The Australian National University, Building 131 Garran Road, Canberra, ACT 0200, Australia. E-mail:
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Womble DD, Dong X, Wu RP, Luckow VA, Martinez AF, Rownd RH. IncFII plasmid incompatibility product and its target are both RNA transcripts. J Bacteriol 1984; 160:28-35. [PMID: 6207169 PMCID: PMC214676 DOI: 10.1128/jb.160.1.28-35.1984] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The region of DNA coding for incompatibility (inc) and copy number control (cop) of the IncFII plasmid NR1 is transcribed in both the rightward and leftward directions. The rightward transcripts serve as mRNA for the repA1 protein, which is required for replication. A small, 91-base leftward transcript is synthesized from the opposite DNA strand and is complementary to a portion of the rightward mRNA near its 5' end. A 262-base-pair Sau3A restriction fragment that encodes the small leftward transcript, but does not include the rightward transcription promoters, was cloned into the vector pBR322 or pUC8. The same fragment was cloned from an Inc- mutant of NR1 that does not make the small leftward transcript. Transcription through the cloned fragments in these derivatives was under control of the tetracycline resistance gene in pBR322 or the lac promoter-operator in pUC8. In one orientation of the inserted DNA, a hybrid transcript containing rightward NR1 RNA sequences was synthesized. In the other orientation, a hybrid transcript containing leftward NR1 RNA sequences was synthesized. These plasmids were used to vary the intracellular levels of the rightward or leftward NR1 RNA transcripts and to test their effects in trans on various coresident derivatives of NR1. An excess of rightward NR1 RNA in trans stimulated expression of the essential repA1 gene and caused an increase in the copy number of a coresident NR1 plasmid. An excess of leftward NR1 RNA in trans inhibited the expression of the repA1 gene and lowered the coresident NR1 copy number, thereby causing incompatibility. A pBR322 derivative with no transcription through the cloned NR1 DNA had no effect in trans. These results suggest that the small leftward transcript is the incompatibility inhibitor of NR1 and that its target is the complementary portion of the rightward mRNA.
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