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Fatima K, Javed SO, Saleem A, Marsia S, Zafar R, Noorani K, Kumar S, Ali SM, Ismail I, Hashim I, Ganatra FA. Long-term efficacy of spinal cord stimulation for chronic primary neuropathic pain in the contemporary era: a systematic review and meta-analysis. J Neurosurg Sci 2024; 68:128-139. [PMID: 36943763 DOI: 10.23736/s0390-5616.23.05930-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Spinal cord stimulation (SCS) is a modern neuromodulation technique extensively proven to be an effective modality for treatment of chronic neuropathic pain. It has been mainly studied for complex regional pain syndrome (CRPS) and failed back surgery syndrome (FBSS) and recent data almost uniformly establishes its statistically significant positive therapeutic results. It has also been compared with other available treatment modalities across various studies. However, long term data on maintenance of its efficacious potential remains less explored. Few studies have reported data on long follow-up times (>= 12 months) and have compared its efficacy with other treatment options for chronic pain, respectively. Our study pools and analyzes the available data and compares SCS with other treatment options. It also analyzes the efficacy of SCS in long term management of patients with chronic pain. EVIDENCE ACQUISITION We reviewed all the data available on MEDLINE, Embase and Cochrane CENTRAL using a search strategy designed to fit our pre-set inclusion and exclusion criteria. Both single-arm and double-arm studies were included. The primary outcome was defined as decrease of visual analogue scale (VAS) by >50% at 6, 12 and/or 24 months after SCS. EVIDENCE SYNTHESIS According to the pooled data of double-arm studies, SCS has unanimously proven its superiority over other treatment options at 6 months follow-up; however it fails to prove statistically significant difference in results at longer treatment intervals. Dorsal root ganglion stimulation, a relatively recent technique with the same underlying physiologic mechanisms as SCS, showed far more promising results than SCS. Single-arm studies show around 70% patients experiencing greater than 50% reduction in their VAS scores at 6 and 12 months. CONCLUSIONS SCS is a viable option for management of chronic neuropathic pain secondary to FBSS and CRPS. However, data available for its long term efficacy remains scarce and show no further statistically significant results.
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Alam MJ, Choudhury MR, Haq SA, Islam N, Ahmed S, Shahin A, Ali SM, Mahmood T, Azad AK, Shazzad MN, Rabbani MG. Estimation of 10-Year Fracture Risk with and without Bone Mineral Density in Patients with Rheumatoid Arthritis. Mymensingh Med J 2023; 32:1084-1090. [PMID: 37777905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2023]
Abstract
Rheumatoid arthritis (RA) is the most common inflammatory arthritis affecting 0.5-1.0% of the general population worldwide and although RA is properly considered a disease of the joints, it can cause a variety of extra-articular manifestations. This study was performed to find out any discrepancy in fracture risk estimates with and without bone mineral density (BMD) in rheumatoid arthritis (RA) patients. This observational cross-sectional study was carried out in the Department of Rheumatology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Bangladesh from July 2013 to July 2015. Total 65 consecutive patients with RA fulfilling ACR/EULAR criteria aged 40-90 year were recruited. Ten year fracture risk of these patients was evaluated by the FRAX score with and without BMD and differences were observed. FRAX score without BMD revealed that major fracture risk was low in 58(89.2%) patients, moderate in 7(10.8%) patients but re-estimation with BMD revealed that 55(84.6%) patients remained in low risk group, 8(12.3%) patients in moderate risk group and 2(3.1%) patients went to the high risk group. In case of hip fracture risk without BMD, risk was low in 58(89.2%) patients, high in 7(10.8%) patients; but with BMD, 50(76.9%) patients remained in low risk group but risk of 15(23.1%) patients became high. Almost all the high risk patients (93.3%) were ≥55 years of age. Increasing age, female sex, disease duration and use of steroid were positively correlated with increased FRAX score where as high BMI and high BMD were associated with low FRAX score. But in multivariate analysis it was found that only relation with age was at statistically significant level. Significant numbers of patients with rheumatoid arthritis have high risk of fracture especially hip fracture. The mean of FRAX score increased in both major & hip osteoporotic fracture risk after adding BMD. More than half of the patients above fifty five years or more had high risk of fracture. So, BMD should be done in patients aged more than fifty five.
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Sasmal PK, Sahoo A, Mishra TS, Das Poddar KK, Ali SM, Singh PK, Kumar P. Feasibility and outcomes of Desarda vs Lichtenstein hernioplasty by local anesthesia for inguinal hernia: a noninferiority randomized clinical trial. Hernia 2023; 27:1155-1163. [PMID: 37452974 DOI: 10.1007/s10029-023-02837-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
INTRODUCTION The Desarda autologous tissue repair is comparable to the Lichtenstein hernioplasty for inguinal hernia regarding recurrence, chronic groin pain, and return to work activities. This study was designed to establish the outcomes of Desarda's repair versus Lichtenstein's hernioplasty concerning post-operative recovery to normal gait and its feasibility under local anesthesia (LA). MATERIALS AND METHODS This study was a single-center, prospective, double-blinded, non-inferiority, randomized trial. Patients undergoing open hernia repair for primary inguinal hernia were included. Patients were randomly assigned and followed up for 2 years. The primary endpoint was the time to return to normal gait post-surgery with comfort (non-inferiority margin fixed as 0.5 days). The secondary outcomes studied were post-operative pain score, the time required to return to work (all previously performed activities), and surgical-site occurrences (SSO). RESULTS One hundred ten eligible patients were randomly assigned [56 patients (50.9%) in the Desarda group and 54 patients (49.1%) in the Lichtenstein group]. All the procedures were safely performed under LA. The median (interquartile range) time for resuming gait post-surgery with comfort was 5 days in the Desarda vs 4 days in Lichtenstein's arm (P = 0.16), thereby failing to demonstrate non-inferiority of Desarda against Lichtenstein hernioplasty. However, there were no significant differences in days to return to work, SSO, chronic groin pain, and recurrence within two years of surgery. CONCLUSIONS AND RELEVANCE This study could not demonstrate the non-inferiority of the Desarda repair versus Lichtenstein hernioplasty regarding the time taken to return to normal gait. Comparing the days to return to work, pain score, SSO, and chronic groin pain, including recurrence rate, Desarda repair faired equally with Lichtenstein hernioplasty, thereby highlighting its feasibility and efficacy under LA. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT03512366.
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Williams LA, Whisenant MS, Mendoza TR, Peek AE, Malveaux D, Griffin DK, Ponce DA, Granwehr BP, Sheshadri A, Hutcheson KA, Ali SM, Peterson SK, Heymach JV, Cleeland CS, Subbiah IM. Measuring symptom burden in patients with cancer during a pandemic: the MD Anderson symptom inventory for COVID-19 (MDASI-COVID). J Patient Rep Outcomes 2023; 7:48. [PMID: 37237077 PMCID: PMC10215036 DOI: 10.1186/s41687-023-00591-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Symptom expression in SARS-CoV-2 infection (COVID-19) may affect patients already symptomatic with cancer. Patient-reported outcomes (PROs) can describe symptom burden during the acute and postacute stages of COVID-19 and support risk stratification for levels of care. At the start of the COVID-19 pandemic, our purpose was to rapidly develop, launch through an electronic patient portal, and provide initial validation for a PRO measure of COVID-19 symptom burden in patients with cancer. METHODS We conducted a CDC/WHO web-based scan for COVID-19 symptoms and a relevance review of symptoms by an expert panel of clinicians treating cancer patients with COVID-19 to create a provisional MD Anderson Symptom Inventory for COVID-19 (MDASI-COVID). English-speaking adults with cancer who tested positive for COVID-19 participated in the psychometric testing phase. Patients completed longitudinal assessments of the MDASI-COVID and the EuroQOL 5 Dimensions 5 Levels (EQ-5D-5L) utility index and visual analog scale, which were presented through an electronic health record patient portal. To test the validity of the MDASI-COVID to distinguish between known groups of patients, we hypothesized that patients hospitalized, including having a hospitalization extended, for COVID-19 versus those not hospitalized would experience higher symptom burden. Correlation of mean symptom severity and interference scores with relevant EQ-5D-5L scores tested concurrent validity. The reliability of the MDASI-COVID was evaluated by calculating Cronbach alpha coefficients and test-retest reliability was evaluated by calculating Pearson correlation coefficients between the initial assessment and a second assessment no more than 14 days later. RESULTS The web-based scan found 31 COVID-19-related symptoms; rankings of a 14-clinician expert panel reduced this list to 11 COVID-specific items to be added to the core MDASI. Time from literature scan start in March 2020 to instrument launch in May 2020 was 2 months. Psychometric analysis established the MDASI-COVID's reliability, known-group validity, and concurrent validity. CONCLUSIONS We were able to rapidly develop and electronically launch a PRO measure of COVID-19 symptom burden in patients with cancer. Additional research is needed to confirm the content domain and predictive validity of the MDASI-COVID and define the symptom burden trajectory of COVID-19.
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Anjaneyan P, Kuttippurath J, Hareesh Kumar PV, Ali SM, Raman M. Spatio-temporal changes of winter and spring phytoplankton blooms in Arabian sea during the period 1997-2020. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117435. [PMID: 36746044 DOI: 10.1016/j.jenvman.2023.117435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Arabian Sea (AS) experiences Chlorophyll-a (Chl-a) blooms during winter and early spring (November-March) mainly due to the changes induced by seasonally reversing monsoon winds and associated processes. The seasonal blooms exhibit distinct regional patterns in their onset, duration, intensity and peak period. Recent changes in ocean dynamics and plankton composition have inflicted adverse effects in the distribution of Chl-a concentration in AS. Here, we analyse the long-term spatio-temporal changes in winter and early spring bloom events during the period 1997-2020, and evaluate the role of sea surface temperature (SST), mixed layer depth (MLD), sea surface salinity, winds, mesoscale eddies and surface currents on these bloom occurrences. We observe a significant reduction in these blooms, which started in the early 2000s and intensified in the last decade (2010-2020), with a notable drop in the adjacent gulfs (Gulf of Aden: 1.38 ± 0.7 × 10-5 mg m-3 yr-1, Gulf of Oman: 4.71 ± 1.35 × 10-6 mg m-3 yr-1) and West coast of India (-6.71 ± 2.85 × 10-6 mg m-3 yr-1). The MLD and ocean temperature are the major factors that govern bloom in Gulf of Oman and open waters. Conversely, the coastal upwelling and eddies drive blooms in Gulf of Aden. The winter cooling trigger the bloom in the northern Indian west coast, but the inter-basin exchange of surface waters through the West Indian Coastal Current inhibits its southward spread. This study, therefore, reveals unique processes that initiate and control the winter and early spring blooms in different regions of AS. The ongoing warming of AS could contribute to further decline in these seasonal blooms, which would be a great concern for regional marine productivity and associated regional food security.
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Alsuwaidi HN, Ahmed AI, Alkorbi HA, Ali SM, Altarawneh LN, Uddin SI, Roueentan SR, Alhitmi AA, Djouhri L, Chivese T. Association Between Metabolic Syndrome and Decline in Cognitive Function: A Cross-Sectional Study. Diabetes Metab Syndr Obes 2023; 16:849-859. [PMID: 36974329 PMCID: PMC10039709 DOI: 10.2147/dmso.s393282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/04/2023] [Indexed: 03/29/2023] Open
Abstract
AIM We investigated whether metabolic syndrome (MetS) is associated with a decline in cognitive function in a cohort of middle-aged and elderly individuals without known cognitive dysfunction diseases in Qatar. METHODS We conducted a cross-sectional study on randomly selected participants aged 40-80 years from the Qatar Biobank, with data on cognitive tests and MetS components. Participants with a history of dementia, stroke, or mental disorders were excluded. MetS was diagnosed using the NCEP-ATP III criteria and cognitive performance was assessed using the Cambridge Neuropsychological Test Automated Battery (CANTAB). Two cognitive function domains were assessed. These are speed of reaction, measured using the Reaction Time (RT), and short-term visual memory, measured using the Paired Associate Learning (PAL) test. Multivariable logistic regression models were used to determine associations between MetS and poor speed of reaction and poor memory performance. RESULTS The mean age of the participants included was 49.8 years (SD 6.7). Of these, 51.9% were females and 88.0% were of Qatari nationality. Most of the 1000 participants had MetS (n=302) or 1-2 MetS components (n=523), whereas only 170 had no MetS components. There was a strong association between MetS and poor memory performance (OR 1.76, 95% CI 1.04-2.96, P=0.034), but a weaker association with poor speed of reaction (OR 1.5, 95% CI 0.89-2.50, P=0.125). CONCLUSION In middle-aged and elderly individuals, MetS was strongly associated with diminished short-term visual memory, psychomotor coordination and motor speed.
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Talha KA, Patwary MI, Alam ZN, Ali SM, Ahmed S, Nafee A, Selina F, Khan MH, Shusmita FR, Avi SG, Rahman MN. Case-Control Study to Evaluate Zinc Deficiency as a Risk Factor for Oxygen Requirement in Patients with COVID-19. Mymensingh Med J 2022; 31:216-222. [PMID: 34999705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Zinc is one of the important trace elements of blood. It helps in maturation of immune system in our body. In the past studies originate the relationship between viral disease and serum zinc deficiency. This was a multicenter case-control study to measure the serum zinc level of COVID-19 patients with different respiratory supports and to evaluate the Odds Ratio (OR) and Relative risk (RR) of zinc deficiency for oxygen requirement for COVID-19 patients. Study places were COVID-19 unit of three tertiary hospitals of Sylhet, a Northern district of Bangladesh. There were 30 controls and 90 cases in this study. The mean zinc level of cases (53-38mcg/dl) was significantly (p=0.000072) lower than the level of controls (73-23mcg/dl). The mean zinc level of the COVID-19 patients required oxygen (49-33mcg/dl) was significantly (p=0.0054) lower than the patients were not treated by oxygen therapy (64-51mcg/dl). The RR of getting affected by COVID-19 was 1-91 for the low zinc level people. Among the COVID-19 affected participants the lower zinc level people had a RR of 1-93 to receive oxygen supplementation. Lower zinc level people are more likely to be affected by COVID-19 in comparison to the normal zinc level people. Among the COVID-19 patients the lower zinc level people had nearly double (RR 1-93) risk of becoming hypoxic and eventually prone for oxygen support.
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Hassan L, Ali SM, Iqbal W, Baig S, Viney K, Hadi H. Automated detection and reduction of stigma in online discussions about TB. Int J Tuberc Lung Dis 2021; 25:869-870. [PMID: 34615587 DOI: 10.5588/ijtld.21.0270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Talha KA, Patwary MI, Bari ZJ, Rahman AS, Alam ZN, Ali SM, Selina F, Nath UD. Evaluating the Respiratory Support Pattern and Relationship with Initial Oxygen Saturation of the COVID Isolation Unit Patients in Sylhet. Mymensingh Med J 2021; 30:1139-1145. [PMID: 34605488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
COVID-19 is the devastating pandemic of the century predominantly fatal due to its respiratory failure nature. Severe and critical patients need oxygen supplementation in different forms. This cross-sectional study was conducted in four tertiary hospitals of Sylhet, Bangladesh from November 2020 to March 2021. All the patients admitted in the COVID-19 isolation units and fulfill the selection criterion were enrolled in this study. The primary objective of this study was to evaluate different types of respiratory supports and its relationship with initial oxygen saturation (SpO₂). Total 481 patients were enrolled. There was a male predominance (65.00%) in the participants. Highest number of participants was from 61-70 years age group. Number of ventilated patients were significantly high (p<0.001) in the COVID-19 patient group. The initial SpO₂ and hospital staying period of COVID-19 positive and negative group did not show any significant difference but these two parameters showed significant difference among died and survived group (p<0.001). Nearly one fourth patients (24.94%) of total patients were treated in ICU with high flow nasal cannula (HFNC), non-invasive ventilation (NIV) and mechanical ventilation. Among the ICU admitted patients nearly one-fourth (24.16%) patients were treated with mechanical ventilation. Mortality rate was 62.00% for ventilated patients, 70.60% for NIV patients and 15.80% for the HFNC patients.
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Sokol ES, Feng YX, Jin DX, Basudan A, Lee AV, Atkinson JM, Chen J, Stephens PJ, Frampton GM, Gupta PB, Ross JS, Chung JH, Oesterreich S, Ali SM, Hartmaier RJ. Loss of function of NF1 is a mechanism of acquired resistance to endocrine therapy in lobular breast cancer. Ann Oncol 2020; 30:115-123. [PMID: 30423024 PMCID: PMC6336006 DOI: 10.1093/annonc/mdy497] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Background Invasive lobular carcinoma (ILC) as a disease entity distinct from invasive ductal carcinoma (IDC) has merited focused studies of the genomic landscape, but those to date are largely limited to the assessment of early-stage cancers. Given that genomic alterations develop as acquired resistance to endocrine therapy, studies on refractory ILC are needed. Patients and methods Tissue from 336 primary-enriched, breast-biopsied ILC and 485 estrogen receptor (ER)-positive IDC and metastatic biopsy specimens from 180 ILC and 191 ER-positive IDC patients was assayed with hybrid-capture-based comprehensive genomic profiling for short variant, indel, copy number variants, and rearrangements in up to 395 cancer-related genes. Results Whereas ESR1 alterations are enriched in the metastases of both ILC and IDC compared with breast specimens, NF1 alterations are enriched only in ILC metastases (mILC). NF1 alterations are predominantly under loss of heterozygosity (11/14, 79%), are mutually exclusive with ESR1 mutations [odds ratio = 0.24, P < 0.027] and are frequently polyclonal in ctDNA assays. Assessment of paired specimens shows that NF1 alterations arise in the setting of acquired resistance. An in vitro model of CDH1 mutated ER-positive breast cancer demonstrates that NF1 knockdown confers a growth advantage in the presence of 4-hydroxy tamoxifen. Our study further identified a significant increase in tumor mutational burden (TMB) in mILCs relative to breast ILCs or metastatic IDCs (8.9% >20 mutations/mb; P < 0.001). Most TMB-high mILCs harbor an APOBEC trinucleotide signature (14/16; 88%). Conclusions This study identifies alteration of NF1 as enriched specifically in mILC. Mutual exclusivity with ESR1 alterations, polyclonality in relapsed ctDNA, and de novo acquisition suggest a role for NF1 loss in endocrine therapy resistance. Since NF1 loss leads to RAS/RAF kinase activation, patients may benefit from a matched inhibitor. Moreover, for an independent subset of mILC, TMB was elevated relative to breast ILC, suggesting possible benefit from immune checkpoint inhibitors.
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El-Missiry MA, Othman AI, Amer MA, Sedki M, Ali SM, El-Sherbiny IM. Nanoformulated ellagic acid ameliorates pentylenetetrazol-induced experimental epileptic seizures by modulating oxidative stress, inflammatory cytokines and apoptosis in the brains of male mice. Metab Brain Dis 2020; 35:385-399. [PMID: 31728888 DOI: 10.1007/s11011-019-00502-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022]
Abstract
The present study evaluated the neuroprotective and antiepileptic efficacy of ellagic acid (EA) encapsulated in calcium-alginate nanoparticles (Ca2+-ALG NPs) in pentylenetetrazol (PTZ)-induced seizures in male mice. EA was encapsulated in ALG NPs using a nanospray drying method followed by ionotropic crosslinking with Ca2+. Characterization of the developed Ca2+-crosslinked EA-ALG NPs showed spherical, high stability NPs; successful loading of EA within crosslinked ALG NPs; and sustained release of EA. Male Swiss albino mice were divided into ten groups as follows; Group I- (control), Group II (50 mg EA /kg) - (EA), Group III polyethylene glycol (PEG), Group IV EA NPs (50 mg/kg) - (EA NP), Group (50 mg/kg alginate) V void V NPs - (void NPs), Group VI: (37.5 PTZ mg/kg) -(PTZ), Group VII: PTZ and EA - (PTZ-EA). Group VIII: animals received PTZ and PEG concurrently (PTZ-PEG). Group IX; animals received PTZ and void NPs concurrently - (PTZ-void). Group X: animals received PTZ and EA NPs concurrently (PTZ-EA NPs). PTZ was used to induce experimental epilepsy. Ca2+-ALG NPs prevented seizures throughout the experimental period and had a more prominent effect than free EA did. Ca2+-ALG NPs prevented increased glutamate, decreased GABA concentrations and ameliorated increased amyloid-β and homocysteine levels in the serum and brain. Ca2+-EA-ALG NPs were superior to free EA in improving increased IL-6 and TNF-α. Ca2+-ALG NPs ameliorated PTZ-induced oxidative stress, as evidenced by decreased 4HNE levels and enhanced GSH, GR and GPx levels in the brain. These changes were accompanied by amelioration of apoptosis and its regulating proteins, including Cytochrome C, P53, Bax, Bcl2 and caspase-3 and caspase-9, and protected against DNA damage. Histological examination of the hippocampus confirmed that the neuroprotective effect of Ca2+-EA-ALG NPs was superior and more effective than that of free EA.
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Hartmaier RJ, Trabucco SE, Priedigkeit N, Chung JH, Parachoniak CA, Vanden Borre P, Morley S, Rosenzweig M, Gay LM, Goldberg ME, Suh J, Ali SM, Ross J, Leyland-Jones B, Young B, Williams C, Park B, Tsai M, Haley B, Peguero J, Callahan RD, Sachelarie I, Cho J, Atkinson JM, Bahreini A, Nagle AM, Puhalla SL, Watters RJ, Erdogan-Yildirim Z, Cao L, Oesterreich S, Mathew A, Lucas PC, Davidson NE, Brufsky AM, Frampton GM, Stephens PJ, Chmielecki J, Lee AV. Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer. Ann Oncol 2019; 29:872-880. [PMID: 29360925 PMCID: PMC5913625 DOI: 10.1093/annonc/mdy025] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer. Patients and methods To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots. Results We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations. Conclusions Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.
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Schrock AB, Ouyang C, Sandhu J, Sokol E, Jin D, Ross JS, Miller VA, Lim D, Amanam I, Chao J, Catenacci D, Cho M, Braiteh F, Klempner SJ, Ali SM, Fakih M. Tumor mutational burden is predictive of response to immune checkpoint inhibitors in MSI-high metastatic colorectal cancer. Ann Oncol 2019; 30:1096-1103. [PMID: 31038663 DOI: 10.1093/annonc/mdz134] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Microsatellite instability (MSI) is a biomarker for response to immune checkpoint inhibitors (ICPIs). PD-1 inhibitors in metastatic colorectal carcinoma (mCRC) with MSI-high (MSI-H) have demonstrated a high disease control rate and favorable progression-free survival (PFS); however, reported response rates to pembrolizumab and nivolumab are variable and often <50%, suggesting that additional predictive biomarkers are needed. METHODS Clinicopathologic data were collected from patients with MSI-H mCRC confirmed by hybrid capture-based next-generation sequencing (NGS) treated with PD-1/L1 inhibitors at five institutes. Tumor mutational burden (TMB) was determined on 0.8-1.1 Mb of sequenced DNA and reported as mutations/Mb. Potential biomarkers of response and time to progression were analyzed by univariate and multivariate analyses. Once TMB was confirmed as a predictive biomarker, a larger dataset of 18 140 unique CRC patients was analyzed to define the relevance of the identified TMB cut-point. RESULTS A total of 22 patients were treated with PD-1/L1 inhibitors including 19 with pembrolizumab monotherapy. Among tested variables, TMB showed the strongest association with objective response (OR; P < 0.001) and PFS, by univariate (P < 0.001) and multivariate analysis (P < 0.01). Using log-rank statistics, the optimal predictive cut-point for TMB was estimated between 37 and 41 mutations/Mb. All 13 TMBhigh cases responded, while 6/9 TMBlow cases had progressive disease. The median PFS for TMBhigh has not been reached (median follow-up >18 months) while the median PFS for TMBlow was 2 months. A TMB of 37.4 mutations/Mb in a large MSI-H mCRC population (821/18, 140 cases; 4.5%) evaluated by NGS corresponded to the 35th percentile cut-point. CONCLUSIONS TMB appears to be an important independent biomarker within MSI-H mCRC to stratify patients for likelihood of response to ICPIs. If validated in prospective studies, TMB may play an important role in guiding the sequencing and/or combinations of ICPIs in MSI-H mCRC.
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Khattak SK, Mustafa SH, Zaman H, Rahim A, Ali SM, Zaib Z. Compliance to Antihypertensive Medication: A Tertiary Care Study. Mymensingh Med J 2019; 28:668-672. [PMID: 31391442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hypertension is a global health problem and affects more than one billion people worldwide. Long term hypertension is associated with grave complications and therefore maintaining blood pressure within normal range is essential and ensuring patient's drug compliance is an important sector of patient care. Therefore, the purpose of our study was to find out the causes of poor compliance to antihypertensive medications. This cross sectional study was carried out in Medical Department of Ayub Teaching Hospital Abbottabad, Pakistan from 1st September 2017 to 30th October 2018. One hundred ninety three (193) patients were included through non probability consecutive sampling and were divided into two groups on the basis of compliance. The data was collected with the help of a structured questionnaire and analyzed using SPSS 20. Out of 193 hypertensive patients, 88(45.6%) were male while 105(54.4%) were females, with minimum age of 24 years and maximum age of 95 years and mean age of 61.98±12.81SD. Minimum duration of hypertension was 5 months and maximum was 30 years with mean duration of hypertension and standard deviation (SD) of 6.26±6.51 years. One hundred & Twenty (62.2%) patients were non-compliant, while 73(37.8%) were compliant to medication. Forgetfulness of medicine 85(70.8%) and non-affordability 62(52.5%) were the most common causes of noncompliance. This study documented a significantly higher proportion of medication non-adherence among hypertensive patients, with drug forgetfulness and affordability being found as the most common cause.
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Moku PR, Shepherd LE, Ali SM, Leitzel K, Parulekar WE, Zhu L, Virk S, Nomikos D, Aparicio S, Gelmon KA, Drabick JJ, Cream L, Halstead SE, Umstead T, Mckeone D, Maddukuri A, Polimera HV, Ali A, Poulose J, Pancholy N, Spiegel H, Nagabhairu V, Chen BE, Lipton A. Abstract PD3-10: Higher serum PD-L1 predicts for increased overall survival to lapatinib vs trastuzumab in the phase 3 CCTG MA.31 trial. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-pd3-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: In the CCTG (Canadian Clinical Trials Group) MA.31 randomized phase 3 trial, the trastuzumab-taxane combination led to longer PFS than lapatinib-taxane in HER2-positive metastatic breast cancer (MBC). We previously reported the prognostic utility of pretreatment serum PD-L1 in the trastuzumab arm of MA.31 (ASCO 2018, #1031), and here we evaluate serum PD-L1 in the lapatinib arm, and in the whole trial. Higher serum PD-L1 has been reported to be associated with reduced response to treatment with the immune checkpoint inhibitors in melanoma and lung cancer.
Methods: MA.31 accrued 652 centrally and/or locally-identified HER2-positivepatients; 186 in the trastuzumab arm, and 202 in the lapatinib armhad pretreatment serum available. TheELLA immunoassay platform (ProteinSimple, San Jose, CA) was used to quantitate serum PD-L1. Step-wise forward Cox multivariate analysis was used for PFS and OS, and testing for treatment-biomarker interaction was based on the local partial-likelihood method (Liu Y, Jiang W, and Chen BE, Statistics in Medicine 34, 3516-3530, 2015).
Results: In the total study population, pretreatment serum PD-L1 concentration had a median of 86.2 pg/ml, and 25% and 75% interquartiles of 64.1 and 134.3 pg/ml, respectively. In univariate analysis in the whole trial, and within both treatment arms, serum PD-L1 was not a significant biomarker for PFS. For OS, higher serum PD-L1 (as a continuous variable) was significant for shorter OS within the trastuzumab arm (HR=3.84, p=0.04), but was not associated with OS in the lapatinib arm (p=0.37). In the whole trial, in multivariate analysis for OS [15 covariates included: age, race, ECOG status, anthracyclines, other chemo, endocrine, radio, other prior adjuvant therapy, disease status, ER status, PR status, Ki67 (log transformed), CK5, EGFR, treatment arm, and serum PD-L1 (with median cut point)], serum PD-L1 remained a significant independent covariate (HR= 2.27, p= 0.001 (Table).There was significant interaction between treatment arm and continuous serum PD-L1 (Bootstrap method, p=0.0025); above 214.2 pg/ml serum PD-L1 (89% percentile), higher pretreatment serum PD-L1 was associated with a shorter OS to trastuzumab treatment, but longer OS to lapatinib treatment.
Conclusions: In the CCTG MA.31 trial, serum PD-L1 was a significant predictive factor: higher pretreatment serum PD-L1 was associated with a shorter OS to trastuzumab treatment, but longer OS to lapatinib treatment. Immune evasion may decrease the effectiveness of trastuzumab therapy. Further evaluation of elevated serum PD-L1 in the advanced breast cancer setting is warranted to identify HER2-positive MBC patients who may benefit from novel immune-targeted therapies in addition to trastuzumab.
Multivariate Analysis (whole trial): Significant Independent CovariatesCovariateP-ValueHRLower 95% CIHigher 95% CISerum PD-L1 (pretreatment) (>median vs <median)0.0012.271.403.68EGFR Status (continuous IHC score)0.0031.0121.0041.019Other Chemotherapy (yes vs no)0.0081.911.193.07Treatment Arm (trastuzumab vs. lapatinib)0.0100.530.330.86ECOG Performance Status (0 vs 1 or 2)0.0250.590.370.94Ki67 (log)0.0461.451.0062.081
Citation Format: Moku PR, Shepherd LE, Ali SM, Leitzel K, Parulekar WE, Zhu L, Virk S, Nomikos D, Aparicio S, Gelmon KA, Drabick JJ, Cream L, Halstead SE, Umstead T, Mckeone D, Maddukuri A, Polimera HV, Ali A, Poulose J, Pancholy N, Spiegel H, Nagabhairu V, Chen BE, Lipton A. Higher serum PD-L1 predicts for increased overall survival to lapatinib vs trastuzumab in the phase 3 CCTG MA.31 trial [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD3-10.
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Pope RM, Ali SM, Muir CD, Schulte AA. Communicating, consulting, and caring differently. BMJ 2018; 362:k3103. [PMID: 30006477 DOI: 10.1136/bmj.k3103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ali SM, Chen D, Ali A, Krecko L, Leitzel K, Vasekar M, Nagabhairu V, Marks E, Polimera H, Richardson A, May M, He W, Patel P, Lavin M, Hofsess S, Sweetman R, Hortobagyi G, Baselga J, Lipton A. Abstract P1-07-09: Serum activin A and outcomes in HR+ /HER2- metastatic breast cancer patients treated with everolimus: Results from BOLERO-2. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p1-07-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Everolimus (EVE) plus exemestane (EXE) doubled progression-free survival (PFS) while maintaining quality of life versus EXE alone in postmenopausal women with hormone receptor positive (HR+), HER2-negative metastatic breast cancer (mBC) (BOLERO-2 phase 3; NCT00863655). Pretreatment serum activin A was previously reported as a prognostic factor in first-line hormone therapy (letrozole vs tamoxifen) (Novartis P025) and anti-HER2 mBC (lapatinib vs trastzmab) (CCTG MA.31) trials. Here we investigate the prognostic and predictive ability of activin A in BOLERO-2.
Methods: Activin A levels were determined on pretreatment serum samples using ELISA. Cox-proportional hazards model was used to assess the efficacy of EVE in the activin A low and high subgroups (median cut-point), and the prognostic effect of activin A on PFS and overall survival (OS).
Results: Baseline activin A levels were determined in 513 patients (71% of 725 BOLERO-2 patients randomized 2:1 to EVE+EXE or EXE). Predictive and prognostic signals are shown in the table below
Predictive and prognostic signalsPredictive/PrognosticEnd-pointAct-ivin ATreatmentNEventsMedian PFSHR (95% CI); p valuepredictivePFSHEXE93832.5 (1.5-2.8)-predictivePFSHEVE+EXE1631325.4 (4.1-6.8)0.46 (0.34 - 0.60); <0.0001predictivePFSLEXE89774.2 (2.0 -5.4)-predictivePFSLEVE+EXE1681059.9 (8.1-12.5)0.38 (0.28 - 0.51); <0.0001predictiveOSHEXE936820.1 (13.8-22.6)-predictiveOSHEVE+EXE16312917.7 (15.7-22.3)1.04 (0.78 - 1.40); 0.78predictiveOSLEXE8939NA (34.7-NA)-predictiveOSLEVE+EXE1687241.4 (36.4-NA)1.02 (0.69 - 1.50); 0.93prognosticPFSH 2562154.1 (2.9-4.2)-prognosticPFSL 2571826.9 (6.7-8.5)0.54 (0.45 - 0.66); <0.0001prognosticOSH 25619718.0 (16.5-21.1)-prognosticOSL 25711142.3 (38.5-NA)0.34 (0.27 - 0.42); <0.0001
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In multivariate analysis (including sensitivity to prior hormone therapy and visceral disease), activin A remained a significant independent prognostic factor for PFS and OS [HR 0.57 (0.46-0.69) and 0.34 (0.27-0.43), respectively].
Conclusions: Higher serum activin A was strongly associated with shorter PFS and OS in HR+/HER2- mBC patients. Everolimus was efficacious regardless of serum activin A level. These results are similar to our previous studies in phase 3 trials of letrozole-tamoxifen (Novartis P025), and HER2-targeted therapy, lapatinib vs trastuzmab (CCTG MA.31): pretreatment serum activin A was prognostic for outcome, but was not a predictive factor for treatment arm selection.
Citation Format: Ali SM, Chen D, Ali A, Krecko L, Leitzel K, Vasekar M, Nagabhairu V, Marks E, Polimera H, Richardson A, May M, He W, Patel P, Lavin M, Hofsess S, Sweetman R, Hortobagyi G, Baselga J, Lipton A. Serum activin A and outcomes in HR+ /HER2- metastatic breast cancer patients treated with everolimus: Results from BOLERO-2 [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-07-09.
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Ross JS, Chung J, Elvin JE, Vergilio JA, Ramkissoon S, Suh J, Severson E, Daniel S, Frampton GM, Fabrizio D, Hartmaier RJ, Albacker LA, Ali SM, Schrock AB, Miller VA, Stephens PJ, Gay LM. Abstract PD8-01: CDH1 mutated classic and pleomorphic invasive lobular breast carcinomas differ in genomic signatures and opportunities for targeted and immunotherapies. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-pd8-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Typically defined by negative IHC staining for E-cadherin, classic (CILC) and pleomorphic (PILC) are often combined as a single breast cancer subtype. We queried whether patients with relapsed metastatic disease, mCILC and mPILC, would harbor contrasting genomic alterations (GA)and that molecular information could further differentiate the 2 tumor types and thereby influence therapy selection.
Methods: DNA was extracted from 40 µm of FFPE sections of 10,784 invasive breast carcinomas. 454 (4%) CDH1 mutated mILC were selected including 428 classic mCILC (94%) and 26 mPLIC (6%) subtypes. Comprehensive genomic profiling (CGP) was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth >600X for up to 315 cancer-related genes. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA.
Results: mCILC and mPILC patients featured a median age of 63 years (Table). Slide based ER+ status and HER2+ status was significantly different in both groups (P<0.0001). The frequency of base substitutions in ESR1 was significantly higher in mCILC, and this difference was also significantly higher in mCILC metastasis biopsies exposed to hormonal therapy than in pre-treatment primary tumors (P<0.0001). ERBB2 (HER2) GA (amp + non-amp) detected by CGP were higher in mPILC than mCILC in both pre-and post-treatment samples (P<0.0001 for both). The ERBB2 GA frequency was nearly twice as high after hormonal therapy in both mCILC and mPILC. ESR1 and ERBB2 GA were mutually exclusive overall and especially in the mCILC group. PIK3CA GA were the most frequent GA in both mCILC and mPILC. TP53 GA were significantly more frequent in mPILC than mCILC. At 19%, the frequency of TMB > 15 mutations/MB in mPILC was more than twice as frequent than in mCILC (P=0.046). All (100%) of both the CILC and PILC groups were negative for mis-match repair deficiency or MSI high status. mCILC and mPILC patients with post primary therapy associated ESR1 and ERBB2 GA responding to targeted and immunotherapies will be presented.
Contrasting Clinical and Genomic Features of CILC and PILC Classic CILC (428 cases)Pleomorphic PILC (26 cases)Median Age6363*ER+98%74%*HER2 IHC/FISH+12 (3%)6 (22%)ESR1 GA Primary Pre-Rx6%0%ESR1 GA Metastatic Post-Rx17%0%ERBB2 GA Primary Pre-Rx7%18%ERBB2 GA Metastatic Post-Rx12%34%Other Significant GAPIK3CA (55%), CCND1 (21%), TP53 (17%), ARID1A, AKT3, MDM4, PTEN (all 11%)PIK3CA (58%), TP53 (30%), AKT1 22%), FGFR4, CCND1, PTEN (all 17%)TMB median (mut/Mb)2.73.6TMB > 15%8%19%*when clinical status available
Conclusions: CGP of mCILC and mPILC reveals significant differences in the panorama of GA both in pre-treatment primary and metastatic disease lesions especially in therapy-impacting GA in ESR1 and ERBB2. mCILC is more often driven by ESR1 GA and mPILC by ERBB2 GA. Although both mCILC and mPILC feature subsets of tumors with high TMB, this is more frequent for mPILC likely indicating different potentials for immunotherapies to benefit these patients.
Citation Format: Ross JS, Chung J, Elvin JE, Vergilio J-A, Ramkissoon S, Suh J, Severson E, Daniel S, Frampton GM, Fabrizio D, Hartmaier RJ, Albacker LA, Ali SM, Schrock AB, Miller VA, Stephens PJ, Gay LM. CDH1 mutated classic and pleomorphic invasive lobular breast carcinomas differ in genomic signatures and opportunities for targeted and immunotherapies [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-01.
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Chung JH, Pavlick D, Hartmaier R, Schrock AB, Young L, Forcier B, Ye P, Levin MK, Goldberg M, Burris H, Gay LM, Hoffman AD, Stephens PJ, Frampton GM, Lipson DM, Nguyen DM, Ganesan S, Park BH, Vahdat LT, Leyland-Jones B, Mughal TI, Pusztai L, O'Shaughnessy J, Miller VA, Ross JS, Ali SM. Hybrid capture-based genomic profiling of circulating tumor DNA from patients with estrogen receptor-positive metastatic breast cancer. Ann Oncol 2017; 28:2866-2873. [PMID: 28945887 PMCID: PMC5834148 DOI: 10.1093/annonc/mdx490] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genomic changes that occur in breast cancer during the course of disease have been informed by sequencing of primary and metastatic tumor tissue. For patients with relapsed and metastatic disease, evolution of the breast cancer genome highlights the importance of using a recent sample for genomic profiling to guide clinical decision-making. Obtaining a metastatic tissue biopsy can be challenging, and analysis of circulating tumor DNA (ctDNA) from blood may provide a minimally invasive alternative. PATIENTS AND METHODS Hybrid capture-based genomic profiling was carried out on ctDNA from 254 female patients with estrogen receptor-positive breast cancer. Peripheral blood samples were submitted by clinicians in the course of routine clinical care between May 2016 and March 2017. Sequencing of 62 genes was carried out to a median unique coverage depth of 7503×. Genomic alterations (GAs) in ctDNA were evaluated and compared with matched tissue samples and genomic datasets of tissue from breast cancer. RESULTS At least 1 GA was reported in 78% of samples. Frequently altered genes were TP53 (38%), ESR1 (31%) and PIK3CA (31%). Temporally matched ctDNA and tissue samples were available for 14 patients; 89% of mutations detected in tissue were also detected in ctDNA. Diverse ESR1 GAs including mutation, rearrangement and amplification, were observed. Multiple concurrent ESR1 GAs were observed in 40% of ESR1-altered cases, suggesting polyclonal origin; ESR1 compound mutations were also observed in two cases. ESR1-altered cases harbored co-occurring GAs in PIK3CA (35%), FGFR1 (16%), ERBB2 (8%), BRCA1/2 (5%), and AKT1 (4%). CONCLUSIONS GAs relevant to relapsed/metastatic breast cancer management were identified, including diverse ESR1 GAs. Genomic profiling of ctDNA demonstrated sensitive detection of mutations found in tissue. Detection of amplifications was associated with ctDNA fraction. Genomic profiling of ctDNA may provide a complementary and possibly alternative approach to tissue-based genomic testing for patients with estrogen receptor-positive metastatic breast cancer.
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Oztan A, Fischer S, Schrock AB, Erlich RL, Lovly CM, Stephens PJ, Ross JS, Miller V, Ali SM, Ou SHI, Raez LE. Emergence of EGFR G724S mutation in EGFR-mutant lung adenocarcinoma post progression on osimertinib. Lung Cancer 2017; 111:84-87. [PMID: 28838405 DOI: 10.1016/j.lungcan.2017.07.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 11/26/2022]
Abstract
Mutations in the epidermal growth factor receptor (EGFR) are drivers for a subset of lung cancers. Osimertinib is a third-generation tyrosine kinase inhibitor (TKI) recently approved for the treatment of T790M-positive non-small cell lung cancer (NSCLC); however, acquired resistance to osimertinib is evident and resistance mechanisms remain incompletely defined. The EGFR G724S mutation was detected using hybrid-capture based comprehensive genomic profiling (CGP) and a hybrid-capture based circulating tumor DNA (ctDNA) assays in two cases of EGFR-driven lung adenocarcinoma in patients who had progressed on osimertinib treatment. This study demonstrates the importance of both tissue and blood based hybrid-capture based genomic profiling at disease progression to identifying novel resistance mechanisms in the clinic.
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Heilmann AM, Schrock AB, He J, Nahas M, Curran K, Shukla N, Cramer S, Draper L, Verma A, Erlich R, Ross J, Stephens P, Miller VA, Ali SM, Verglio JA, Tallman MS, Mughal TI. Novel PDGFRB fusions in childhood B- and T-acute lymphoblastic leukemia. Leukemia 2017; 31:1989-1992. [PMID: 28552906 DOI: 10.1038/leu.2017.161] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wang K, McDermott JD, Schrock AB, Elvin JA, Gay L, Karam SD, Raben D, Somerset H, Ali SM, Ross JS, Bowles DW. Comprehensive genomic profiling of salivary mucoepidermoid carcinomas reveals frequent BAP1, PIK3CA, and other actionable genomic alterations. Ann Oncol 2017; 28:748-753. [PMID: 28327999 DOI: 10.1093/annonc/mdw689] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Indexed: 12/15/2022] Open
Abstract
Background We sought to identify genomic alterations (GAs) in salivary mucoepidermoid carcinomas. Patients and methods DNA was extracted from 48 mucoepidermoid carcinomas. Comprehensive genomic profiling (CGP) including the calculation to tumor mutational burden (TMB) was performed on hybridization-captured adaptor ligation-based libraries of 315 cancer-related genes plus introns from 28 genes frequently rearranged for cancer and evaluated for all classes of GAs. Results A total of 183 GAs were found in 80 unique genes. High-grade tumors had more GAs (mean 5 ± 3.8) compared with low (2.3 ± 1.4) or intermediate (2.6 ± 1.5) (P = 0.019). TP53 GAs were seen in all tumor grades (41.7%) but were most common in high-grade malignancies (56%) (P = 0.047). CDKN2A GAs were seen in 41.6% of tumors. PI3K/mTOR pathway activation, including PI3KCA mutations, were more common in high grade (52%) than in low- and intermediate-grade tumors (4.3%) (P = 0.007). BAP1 GAs were observed in 20.8% of tumors and BRCA1/2 GAs present in 10.5% of specimens. ERBB2 amplifications were seen in only 8.3% of tumors. The TMB for this patient group was relatively low with only 5 (10%) of cases having greater than 10 mutations/megabase of sequenced DNA. Conclusion CGP of salivary mucoepidermoid carcinomas revealed diverse GAs that may lead to customized treatment options for patients with these rare tumors.
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Hirshfield KM, Paratala BS, Hindoyan A, Dolfi SC, Yilmazel B, Schrock A, Gay L, Ali SM, Ross JS, Williams CB, Nair P, Ganesan S, Leyland-Jones B. Abstract P3-07-02: Are we missing actionable targets in breast cancer? Novel insights into recurrent Ret alterations. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p3-07-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Recurrent gene fusions in breast cancer have been rarely reported suggesting that they either are not present or are not easily detected by standard sequencing methods. Comprehensive genomic profiling (CGP) by hybrid capture-based, high depth next-generation sequencing approaches, can be used to detect recurrent rearrangements and other genomic alterations involving target genes. We found that CGP can identify recurrent alterations involving RET, a known oncogenic tyrosine receptor kinase, in a subset of breast cancer.
Methods: CGP using FoundationOne platform was performed interrogating the entire coding region for up to 315 cancer-related genes and introns of up to 28 genes involved in rearrangements at a depth of 500-1000X in formalin-fixed, paraffin embedded tumor tissue (Foundation Medicine, MA). Engineered representative RET fusion vectors were synthesized and expressed in non-tumorigenic cell lines (breast MCF10A and mouse 3T3 fibroblasts), and cells were evaluated for RET kinase signaling, drug response, and tumorigenicity. Patient-derived xenografts (PDX) generated from two triple negative breast cancers (TNBCs) were used in an ex vivo assay (Response3DXTM, Molecular Response LLC, San Diego, CA).
Results: Twenty-two RET rearrangements were identified in 8119 (0.27%) breast cancer cases. Of these, 5 rearrangements were activating RET fusions including CCDC6-RET (n=4) and NCOA4-RET (n=1), that have been described in other cancer types. Five other cases had clear evidence of genomic rearrangement involving RET, but the 5' partners could not be definitively identified. The remaining twelve cases had complex rearrangements of RET including internal duplications. RET amplification was also observed, both in TNBC and in a HER2+ breast cancer at onset of resistance to HER2-targeted therapy.
Both NCOA4-RET and a novel RASGEF1A-RET fusion were characterized in vitro. Non-tumorigenic cells engineered to stably overexpress either RET fusions demonstrated transformed phenotypes. The fusions were constitutively active, as shown by endogenous phosphorylation of the kinase domain, and drove activation of downstream signaling as shown by increased phosphorylation of ERK and AKT. Cells transformed by RET-fusions were exquisitely sensitive to treatment with RET inhibitors. Interestingly, a PDX model of RET-amplified TNBC was sensitive to treatment with a PIK3CA inhibitor. An index case of ER+/PR-/HER2+, metastatic breast cancer that had radiographic evidence of disease progression while on trastuzumab, pertuzumab, and anastrazole was found to have a NCOA4-RET fusion by CGP. Subsequent treatment with with cabozantinib plus anastrazole led a rapid clinical and radiographic response.
Conclusions: CGP can identify recurrent RET rearrangements in breast cancer that act as primary oncogenic drivers and can be therapeutically targeted. RET alterations may also play a role in acquired resistance to HER2-targeted therapies, suggesting a role for combined RET and HER2-targeted therapy in this setting. Our data demonstrate that RET alterations can be identified by clinical-grade CGP and are promising candidates as therapeutic targets in selected breast cancer patients.
Citation Format: Hirshfield KM, Paratala BS, Hindoyan A, Dolfi SC, Yilmazel B, Schrock A, Gay L, Ali SM, Ross JS, Williams CB, Nair P, Ganesan S, Leyland-Jones B. Are we missing actionable targets in breast cancer? Novel insights into recurrent Ret alterations [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-07-02.
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Ali SM, Leitzel K, Li M, Udd K, Wang J, Sanchez E, Chen H, Berenson J, Lipton A. Abstract P1-02-10: Reduced serum B-cell maturation antigen levels predict poor outcome in metastatic breast cancer patients in a phase 3 randomized 2nd-line hormone therapy trial. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-02-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: B-cell maturation antigen (BCMA) is a member of the tumor necrosis factor receptor family and has two ligands, B-cell activating factor (BAFF) and a proliferation inducing ligand (APRIL). These ligands activate cell proliferation and inhibit apoptosis of normal and malignant B-cells including in multiple myeloma (MM) cell lines. Berenson et al have recently reported that circulating BCMA levels are elevated in B-cell malignancies and can be used to monitor disease and predict PFS and OS for patients with MM, Waldenstroms's macroglobulinemia and chronic lymphocytic leukemia (CLL). On the other hand, recent studies have shown that serum BCMA levels are very low among patients with MM in complete remission with low antibody levels and those with primary immune deficiencies specifically those with combined variable immune deficiency and X-linked agammaglobulinemia. Studies of the potential role of serum BCMA for patients with solid tumors has not been evaluated to date.
Methods: The pretreatment serum from 139 patients with hormone receptor-positive metastatic breast cancer who were enrolled in a phase 3 randomized clinical trial of second-line hormone therapy was evaluated using an ELISA for BCMA. The BCMA ELISA was from R&D Systems (Minneapolis, MN). Serum BCMA was correlated with TTP using categorical serum BCMA cutpoints.
Results: Pretreatment serum BCMA levels had a median of 55.61 ng/ml, an interquartile range of 34.20 and 78.79 ng/ml, and full range from 3.99 to 1193.26 ng/ml. In univariate analysis for TTP, reduced serum BCMA correlated with shorter TTP at the following dichotomous cutpoints: 15 ng/ml [HR=2.60, p=0.064, n=6 (4.3%) of patients below cutpoint]; 20 ng/ml [HR=2.88, p=0.005, n=10 (7.2%) of patients below cutpoint]; 25 ng/ml [HR=2.16, p=0.023, n=13 (9.4%) of patients below cutpoint]; and 30 ng/ml [HR=1.77, p=0.016, n=27 (19.4%) of patients below the cutpoint].
Conclusions: In a phase 3 randomized clinical trial of second-line hormone therapy among patients with hormone receptor-positive metastatic breast cancer, reduced pretreatment serum BCMA was associated with shorter TTP. This may be due to the association of reduced serum BCMA with immune deficiency; and, thus, lead to shorter TTP among patients with metastatic breast cancer. Evaluation of serum BCMA as a new biomarker to predict outcomes for breast cancer and other solid tumor patients deserves further study.
Citation Format: Ali SM, Leitzel K, Li M, Udd K, Wang J, Sanchez E, Chen H, Berenson J, Lipton A. Reduced serum B-cell maturation antigen levels predict poor outcome in metastatic breast cancer patients in a phase 3 randomized 2nd-line hormone therapy trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-02-10.
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Ravi V, Madison R, Schrock AB, Cote G, Millis S, Alvarez R, Choy E, Katz D, Chung J, Gay L, Miller VA, Ross JS, Ali SM, Schnitt S. Abstract P2-12-01: Comprehensive genomic profiling of 34 cases of breast angiosarcoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p2-12-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Angiosarcoma of the breast (BAS) is a rare but lethal neoplasia, either arising de novo or secondary to radiation therapy, with incidence of the latter disease increasing. We queried a database of more than 70,000 advanced cancer patients assayed with comprehensive genomic profiling (CGP) in the course of clinical care to uncover the frequency, type and associated genomic alterations (GA) in BAS and to highlight possible routes to benefit from targeted therapy.
Methods: CGP was performed for 34 BAS cases using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 315 genes to a mean coverage depth of >500X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes. RNA sequencing for 265 genes was also performed for 24 cases. Limited clinical histories from submitted pathology reports were reviewed under IRB permission.
Results: Clinical specimens from 34 BAS patients, all females, were assayed. The cases harbored 87 total GA for a mean of 2.59 per case, 25% of which were copy number amplifications. The most commonly altered genes were MYC (41%, 14/34), PIK3CA (26%, 9/34), and KDR (26%, 9/34). All MYC alterations were amplifications with a mean copy number of 39, and alterations in other MYC family members (MYCN and MYCL1) were not observed. KDR was recurrently altered as T771R (7/9) and T771K (1/9) and amplified in one case (1/9).
MYC and KDR alterations were mutually exclusive (p<0.0001). 6/14 MYC amplified cases had prior histories of breast carcinoma, with 3/6 noted as being treated with radiation therapy. For the remainder of MYC amplified cases (8/14), no relevant clinical history was available.
Two cases harboring gene fusions were identified including CIC-MEGF8 and NTRK1-PEAR1. Two rearrangements of potential functional significance including CIC-DEDD2 and HT-ALK (exon1 HT - exon5-29 ALK including kinase domain) were also observed. The case harboring HT-ALK also had MYC amplification and known prior radiation therapy. Two other MYC amplified cases also harbored targetable kinase alterations, including FLT4 amplification (described as targetable in Ravi et al JNCCN 2016) and FGFR3 S249C, a known activating mutation.
Conclusions: MYC amplification defines over 40% (14/34) of advanced BAS cases. Of MYC amplified cases, 28% (4/14) harbored targetable alterations of tyrosine kinases including a potential novel ALK fusion. FLT4 amplification only co-occurred with MYC amplification, but this result was not statistically significant in this small series. KDR and MYC alteration were mutually exclusive, and 45% of non-MYC altered cases (9/20) harbored KDR alterations, which were predominantly mutations of T771. Further clinico-pathologic correlation, particularly history of radiation therapy, will be explored in this series, as well defining BAS that harbor neither MYC nor KDR alterations.
Citation Format: Ravi V, Madison R, Schrock AB, Cote G, Millis S, Alvarez R, Choy E, Katz D, Chung J, Gay L, Miller VA, Ross JS, Ali SM, Schnitt S. Comprehensive genomic profiling of 34 cases of breast angiosarcoma [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-12-01.
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