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Vivek Naranbhai, Anusha Nathan, Clarety Kaseke, Cristhian Berrios, Ashok Khatri, Shawn Choi, Matthew A Getz, Rhoda Tano-Menka, Onosereme Ofoman, Alton Gayton, Fernando Senjobe, Kerri J St Denis, Evan C Lam, Wilfredo F Garcia-Beltran, Alejandro B Balazs, Bruce D Walker, A John Iafrate, Gaurav D Gaiha
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from infection and vaccine-induced antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recognition is unknown. Here we show that T cell responses in individuals with prior infection, vaccination, both prior infection and vaccination, and boosted vaccination are largely preserved to Omicron spike and non-spike proteins. However, we also identify a subset of individuals (∼21%) with a >50% reduction in T cell reactivity to the Omicron spike...
January 5, 2022: medRxiv
#62
JOURNAL ARTICLE
Wilfredo F Garcia-Beltran, Kerri J St Denis, Angelique Hoelzemer, Evan C Lam, Adam D Nitido, Maegan L Sheehan, Cristhian Berrios, Onosereme Ofoman, Christina C Chang, Blake M Hauser, Jared Feldman, Alex L Roederer, David J Gregory, Mark C Poznansky, Aaron G Schmidt, A John Iafrate, Vivek Naranbhai, Alejandro B Balazs
Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured the neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild-type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that received their primary series recently (<3 months), distantly (6-12 months), or an additional "booster" dose, while accounting for prior SARS-CoV-2 infection...
February 3, 2022: Cell
#63
COMPARATIVE STUDY
Vivek Naranbhai, Kerri J St Denis, Evan C Lam, Onosereme Ofoman, Wilfredo F Garcia-Beltran, Cristhian B Mairena, Atul K Bhan, Justin F Gainor, Alejandro B Balazs, A John Iafrate
Patients with cancer are more likely to have impaired immune responses to SARS-CoV-2 vaccines. We study the breadth of responses against SARS-CoV-2 variants after primary vaccination in 178 patients with a variety of tumor types and after booster doses in a subset. Neutralization of alpha, beta, gamma, and delta SARS-CoV-2 variants is impaired relative to wildtype, regardless of vaccine type. Regardless of viral variant, mRNA1273 is the most immunogenic, followed by BNT162b2, and then Ad26.COV2.S. Neutralization of more variants (breadth) is associated with a greater magnitude of wildtype neutralization, and increases with time since vaccination; advancing age associates with a lower breadth...
January 10, 2022: Cancer Cell
#64
Wilfredo F Garcia-Beltran, Kerri J St Denis, Angelique Hoelzemer, Evan C Lam, Adam D Nitido, Maegan L Sheehan, Cristhian Berrios, Onosereme Ofoman, Christina C Chang, Blake M Hauser, Jared Feldman, David J Gregory, Mark C Poznansky, Aaron G Schmidt, A John Iafrate, Vivek Naranbhai, Alejandro B Balazs
Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of vaccine-induced neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that were vaccinated recently (<3 months), distantly (6-12 months), or recently boosted, and accounted for prior SARS-CoV-2 infection...
December 14, 2021: medRxiv
#65
JOURNAL ARTICLE
Vincenza Granata, Francesca Coppola, Roberta Grassi, Roberta Fusco, Salvatore Tafuto, Francesco Izzo, Alfonso Reginelli, Nicola Maggialetti, Duccio Buccicardi, Barbara Frittoli, Marco Rengo, Chandra Bortolotto, Roberto Prost, Giorgia Viola Lacasella, Marco Montella, Eleonora Ciaghi, Francesco Bellifemine, Federica De Muzio, Ginevra Danti, Giulia Grazzini, Massimo De Filippo, Salvatore Cappabianca, Carmelo Barresi, Franco Iafrate, Luca Pio Stoppino, Andrea Laghi, Roberto Grassi, Luca Brunese, Emanuele Neri, Vittorio Miele, Lorenzo Faggioni
Background: Structured reporting (SR) in radiology is becoming increasingly necessary and has been recognized recently by major scientific societies. This study aims to build structured CT-based reports in Neuroendocrine Neoplasms during the staging phase in order to improve communication between the radiologist and members of multidisciplinary teams. Materials and Methods: A panel of expert radiologists, members of the Italian Society of Medical and Interventional Radiology, was established...
2021: Frontiers in Endocrinology
#66
JOURNAL ARTICLE
Elena Canzi, Francesca V Danioni, Miriam Parise, Giulia Lopez, Laura Ferrari, Sonia Ranieri, Raffaella Iafrate, Margherita Lanz, Camillo Regalia, Rosa Rosnati
Objective: The current study was aimed at exploring Italian parents' perceived negative and positive changes in family life during the COVID-19 pandemic, taking into account the role of the stage of the family life and family size. Background: During the emergency of the COVID-19 pandemic, millions of families drastically changed their daily life and routines. Little evidence exists on how family characteristics, such as family size or presence of children, are related to families' experience of family change...
December 2021: Family Relations
#67
JOURNAL ARTICLE
Vivek Naranbhai, Wilfredo F Garcia-Beltran, Christina C Chang, Cristhian Berrios Mairena, Julia C Thierauf, Grace Kirkpatrick, Maristela L Onozato, Ju Cheng, Kerri J St Denis, Evan C Lam, Clarety Kaseke, Rhoda Tano-Menka, Diane Yang, Maia Pavlovic, Wendy Yang, Alexander Kui, Tyler E Miller, Michael G Astudillo, Jennifer E Cahill, Anand S Dighe, David J Gregory, Mark C Poznansky, Gaurav D Gaiha, Alejandro B Balazs, A John Iafrate
BACKGROUND: Understanding immunogenicity and effectiveness of SARS-CoV-2 vaccines is critical to guide rational use. METHODS: We compared the immunogenicity of mRNA-1273, BNT-162b2 or Ad26.COV2.S in healthy ambulatory adults in Massachusetts, USA. To correlate immunogenicity with effectiveness of the three vaccines, we performed an inverse-variance meta-analysis of population level effectiveness from public health reports in >40 million individuals. RESULTS: A single dose of either mRNA vaccine yielded comparable antibody and neutralization titers to convalescent individuals...
December 9, 2021: Journal of Infectious Diseases
#68
JOURNAL ARTICLE
Giulia Siravegna, Connor J O'Boyle, Shohreh Varmeh, Natalia Queenan, Alexa Michel, Jarrod Stein, Julia Thierauf, Peter M Sadow, William C Faquin, Simon K Perry, Adam Z Bard, Wei Wang, Daniel G Deschler, Kevin S Emerick, Mark A Varvares, Jong C Park, John R Clark, Annie W Chan, Vanessa Carlota Andreu Arasa, Osamu Sakai, Jochen Lennerz, Ryan B Corcoran, Lori J Wirth, Derrick T Lin, A John Iafrate, Jeremy D Richmon, Daniel L Faden
PURPOSE: HPV-associated Head and Neck Squamous Cell Carcinoma(HPV+HNSCC) is the most common HPV-associated malignancy in the United States and continues to increase in incidence. Current diagnostic approaches for HPV+HNSCC rely on tissue biopsy followed by histomorphologic assessment and detection of HPV indirectly by p16 immunohistochemistry. Such approaches are invasive and have variable sensitivity. EXPERIMENTAL DESIGN: We conducted a prospective observational study in 140 subjects (70 cases and 70 controls) to test the hypothesis that a non-invasive diagnostic approach for HPV+HNSCC would have improved diagnostic accuracy, lower cost, and shorter Diagnostic Interval compared to standard approaches...
December 2, 2021: Clinical Cancer Research
#69
JOURNAL ARTICLE
Cynthia L Bowes, Vivek Naranbhai, Kerri J St Denis, Evan C Lam, Brittany Bertaux, Florence K Keane, Melin J Khandekar, Alejandro B Balazs, John A Iafrate, Justin F Gainor, Henning Willers
The immunogenicity of SARS-CoV-2 vaccines in cancer patients receiving radiotherapy is unknown. This prospective cohort study demonstrates that anti-SARS-CoV-2 spike antibody and neutralization titers are reduced in a subset of thoracic radiotherapy patients, possibly due to immunosuppressive conditions. Antibody testing may be useful to identify candidates for additional vaccine doses.
November 25, 2021: Radiotherapy and Oncology
#70
REVIEW
Nikolay L Malinin, GaHyun Lee, Cicera R Lazzarotto, Yichao Li, Zongli Zheng, Nhu T Nguyen, Matthew Liebers, Ved V Topkar, A John Iafrate, Long P Le, Martin J Aryee, J Keith Joung, Shengdar Q Tsai
Genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) is a sensitive, unbiased, genome-wide method for defining the activity of genome-editing nucleases in living cells. GUIDE-seq is based on the principle of efficient integration of an end-protected double-stranded oligodeoxynucleotide tag into sites of nuclease-induced DNA double-stranded breaks, followed by amplification of tag-containing genomic DNA molecules and high-throughput sequencing. Here we describe a detailed GUIDE-seq protocol including cell transfection, library preparation, sequencing and bioinformatic analysis...
December 2021: Nature Protocols
#71
JOURNAL ARTICLE
Vivek Naranbhai, Claire A Pernat, Alexander Gavralidis, Kerri J St Denis, Evan C Lam, Laura M Spring, Steven J Isakoff, Jocelyn R Farmer, Leyre Zubiri, Gabriela S Hobbs, Joan How, Andrew M Brunner, Amir T Fathi, Jennifer L Peterson, Mustafa Sakhi, Grace Hambelton, Elyssa N Denault, Lindsey J Mortensen, Lailoo A Perriello, Marissa N Bruno, Brittany Y Bertaux, Aleigha R Lawless, Monica A Jackson, Elizabeth Niehoff, Caroline Barabell, Christian N Nambu, Erika Nakajima, Trenton Reinicke, Cynthia Bowes, Cristhian J Berrios-Mairena, Onosereme Ofoman, Grace E Kirkpatrick, Julia C Thierauf, Kerry Reynolds, Henning Willers, Wilfredo-Garcia Beltran, Anand S Dighe, Rebecca Saff, Kimberly Blumenthal, Ryan J Sullivan, Yi-Bin Chen, Arthur Kim, Aditya Bardia, Alejandro B Balazs, A John Iafrate, Justin F Gainor
PURPOSE: The immunogenicity and reactogenicity of SARS-CoV-2 vaccines in patients with cancer are poorly understood. METHODS: We performed a prospective cohort study of adults with solid-organ or hematologic cancers to evaluate anti-SARS-CoV-2 immunoglobulin A/M/G spike antibodies, neutralization, and reactogenicity ≥ 7 days following two doses of mRNA-1273, BNT162b2, or one dose of Ad26.COV2.S. We analyzed responses by multivariate regression and included data from 1,638 healthy controls, previously reported, for comparison...
January 1, 2022: Journal of Clinical Oncology
#72
JOURNAL ARTICLE
Johannes F Scheid, Matthew W Rosenbaum, Eric M Przybyszewski, Kumar Krishnan, David G Forcione, Anthony J Iafrate, Kyle D Staller, Joseph Misdraji, Jochen K Lennerz, Martha Bishop Pitman, Daniel S Pratt
BACKGROUND: Primary sclerosing cholangitis (PSC) is a well-described risk factor for the development of cholangiocarcinoma (CCA). Early detection of CCA in these patients is of great importance because it expands options for therapeutic interventions, including liver transplantation. Current diagnostic tests for the evaluation of biliary strictures are limited to biliary brushing (BB) cytology and fluorescence in situ hybridization (FISH). Next-generation sequencing (NGS) has become an important diagnostic tool in oncology and may be a useful tool for diagnosing CCA on BBs...
March 2022: Cancer Cytopathology
#73
REVIEW
A Desai, C M Rivera, W C Faquin, A J Iafrate, M N Rivera, A Jaquinet, M J Troulis
This comprehensive literature review represents a summary of all cases of clear cell carcinoma (CCC) of the salivary glands that are documented in the literature. PubMed was used to collect available reports of CCC; 97 reports detailing 254 cases, published between 1983 and 2020, were retrieved. Clinically the tumor manifests most commonly as a painless mass or swelling on the palate, and the duration of symptoms prior to seeking care ranges from 1 week to 6 years. Local tumor recurrence was present in 18.8% of the cases...
October 19, 2021: International Journal of Oral and Maxillofacial Surgery
#74
Vivek Naranbhai, Wilfredo F Garcia-Beltran, Christina C Chang, Cristhian Berrios Mairena, Julia C Thierauf, Grace Kirkpatrick, Maristela L Onozato, Ju Cheng, Kerri J St Denis, Evan C Lam, Clarety Kaseke, Rhoda Tano-Menka, Diane Yang, Maia Pavlovic, Wendy Yang, Alexander Kui, Tyler E Miller, Michael G Astudillo, Jennifer E Cahill, Anand S Dighe, David J Gregory, Mark C Poznansky, Gaurav D Gaiha, Alejandro B Balazs, A John Iafrate
Background: Understanding immunogenicity and effectiveness of SARS-CoV-2 vaccines is critical to guide rational use. Methods: We compared the immunogenicity of mRNA-1273, BNT-162b2 or Ad26.COV2.S in ambulatory adults in Massachusetts, USA. To correlate immunogenicity with effectiveness of the three vaccines, we performed an inverse-variance meta-analysis of population level effectiveness from public health reports in >40 million individuals. Results: A single dose of either mRNA vaccine yielded comparable antibody and neutralization titers to convalescent individuals...
October 13, 2021: medRxiv
#75
JOURNAL ARTICLE
Sarah B Mueller, Paola Dal Cin, Long P Le, Dora Dias-Santagata, Jochen K Lennerz, A John Iafrate, Hetal Desai Marble, Andrew M Brunner, Matthew J Weinstock, Marlise R Luskin, Daniel J De Angelo, Richard M Stone, Valentina Nardi
Acute myeloid leukemia (AML) with t(4;12)(q12;p13) translocation is rare and often associated with an aggressive clinical course and poor prognosis. Previous reports based on fluorescence in situ hybridization (FISH) analysis have suggested that ETV6::PDGFRA fusions are present in these patients, despite the absence of eosinophilia, which is typically found in other hematopoietic malignancies with PDGFRA-containing fusions. We first detected an ETV6-SCFD2 fusion by targeted RNA sequencing in a patient with t(4;12)(q12;p13) who had been diagnosed with an ETV6-PDGFRA fusion by FISH analysis but failed to respond to imatinib...
January 8, 2022: Blood Advances
#76
REVIEW
Alessandro Morlacco, Fabio Zattoni, Matteo Soligo, Valeria Lami, Massimo Iafrate, Nicola Zanovello, Fabrizio Dal Moro
Metabolic syndrome (MetS) has been linked with several human cancers. Prostate cancer is the most common neoplasm in male adults and is often treated with radical prostatectomy (RP). Given the complex hormonal and metabolic alteration present in MetS, a possible role in the development and progression of prostate cancer (PCa) has been hypothesized. Several studies have investigated the connections between MetS and the risk of developing prostate cancer, as well as the oncological outcomes of patients who already suffer from PCa and receive a radical treatment...
September 2022: Panminerva Medica
#77
JOURNAL ARTICLE
Alexander M Strait, Julia A Bridge, Anthony J Iafrate, Marilyn M Li, Feng Xu, Gregory J Tsongalis, Konstantinos Linos
Myofibroblastoma is a rare, benign stromal tumor with a diverse morphologic spectrum. Mammary-type myofibroblastoma (MTMF) is the extra-mammary counterpart of this neoplasm and its occurrence throughout the body has become increasingly recognized. Similar morphologic variations of MTMF have now been described which mirror those seen in the breast. We describe a case of intra-abdominal MTMF composed of short fascicles of eosinophilic spindle cells admixed with mature adipose tissue. The spindle cells stained diffusely positive for CD34, desmin, smooth muscle actin, and h-caldesmon by immunohistochemistry...
August 2, 2021: International Journal of Surgical Pathology
#78
JOURNAL ARTICLE
Francesca Danioni, Angela Sorgente, Daniela Barni, Elena Canzi, Laura Ferrari, Sonia Ranieri, Raffaella Iafrate, Camillo Regalia, Rosa Rosnati, Margherita Lanz
The strong restrictive measures adopted in 2020 against the spread of the COVID-19 pandemic in Italy have deeply affected the general population's mental health. In the current longitudinal study, we specifically focus on sense of coherence (SOC), both in terms of comprehensibility/manageability and meaningfulness, among a large sample of Italian adults; SOC is a potential resource likely to foster the ability to cope with stressors. A total of 2,191 Italian participants (65.8% female) aged 18-82 completed an anonymous online self-report questionnaire at Time 1 (during the lockdown, March 2020) and at Time 2 (at the resumption of most activities, July 2020)...
2021: Journal of Psychology
#79
JOURNAL ARTICLE
Anusha Nathan, Elizabeth J Rossin, Clarety Kaseke, Ryan J Park, Ashok Khatri, Dylan Koundakjian, Jonathan M Urbach, Nishant K Singh, Arman Bashirova, Rhoda Tano-Menka, Fernando Senjobe, Michael T Waring, Alicja Piechocka-Trocha, Wilfredo F Garcia-Beltran, A John Iafrate, Vivek Naranbhai, Mary Carrington, Bruce D Walker, Gaurav D Gaiha
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that escape convalescent and vaccine-induced antibody responses has renewed focus on the development of broadly protective T-cell-based vaccines. Here, we apply structure-based network analysis and assessments of HLA class I peptide stability to define mutationally constrained CD8+ T cell epitopes across the SARS-CoV-2 proteome. Highly networked residues are conserved temporally among circulating variants and sarbecoviruses and disproportionately impair spike pseudotyped lentivirus infectivity when mutated...
August 19, 2021: Cell
#80
JOURNAL ARTICLE
F De Felice, G D'Ambrosio, F Iafrate, A Gelibter, F M Magliocca, D Musio, S Caponetto, G Casella, I Clementi, A Picchetto, G Sirgiovani, M Parisi, C Orciuoli, G Torrese, G De Toma, V Tombolini, E Cortesi
AIMS: We assessed the efficacy and safety of total neoadjuvant therapy, including targeted agent plus FOLFOXIRI (5-fluorouracil, leucovorin, oxaliplatin and irinotecan) induction chemotherapy followed by intensified chemoradiotherapy (CRT) and surgical resection, in patients with locally advanced rectal cancer. MATERIALS AND METHODS: This was a single-arm, single-centre phase II trial. Eligible patients had non-metastatic locally advanced rectal adenocarcinoma. Based on Ras-BRAF status, patients were treated with bevacizumab (mutated Ras-BRAF) or panitumumab/cetuximab (wild-type Ras-BRAF) plus FOLFOXIRI regimen followed by oxaliplatin-5-fluorouracil-based CRT and surgery...
June 24, 2021: Clinical Oncology: a Journal of the Royal College of Radiologists
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