A cross-sectional analysis of factors associated with detection of oncogenic human papillomavirus in human immunodeficiency virus-infected and uninfected Kenyan women

Background

Cervical cancer is caused by oncogenic human papillomaviruses (HPV) and is one of the most common malignancies in women living in sub-Saharan Africa. Women infected with the human immunodeficiency virus (HIV) have a higher incidence of cervical cancer, but the full impact on HPV detection is not well understood, and associations of biological and behavioral factors with oncogenic HPV detection have not been fully examined. Therefore, a study was initiated to investigate factors that are associated with oncogenic HPV detection in Kenyan women.

Methods

Women without cervical dysplasia were enrolled in a longitudinal study. Data from enrollment are presented as a cross-sectional analysis. Demographic and behavioral data was collected, and HPV typing was performed on cervical swabs. HIV-uninfected women (n = 105) and HIV-infected women (n = 115) were compared for demographic and behavioral characteristics using t-tests, Chi-square tests, Wilcoxon sum rank tests or Fisher’s exact tests, and for HPV detection using logistic regression or negative binomial models adjusted for demographic and behavioral characteristics using SAS 9.4 software.

Results

Compared to HIV-uninfected women, HIV-infected women were older, had more lifetime sexual partners, were less likely to be married, were more likely to regularly use condoms, and were more likely to have detection of HPV 16, other oncogenic HPV types, and multiple oncogenic types. In addition to HIV, more lifetime sexual partners was associated with a higher number of oncogenic HPV types (aIRR 1.007, 95% CI 1.007–1.012). Greater travel distance to the clinic was associated with increased HPV detection (aOR for detection of ≥ 2 HPV types: 3.212, 95% CI 1.206–8.552). Older age (aOR for HPV 16 detection: 0.871, 95% CI 0.764–0.993) and more lifetime pregnancies (aOR for detection of oncogenic HPV types: 0.706, 95% CI, 0.565–0.883) were associated with reduced detection.

Conclusion

HIV infection, more lifetime sexual partners, and greater distance to health-care were associated with a higher risk of oncogenic HPV detection, in spite of ART use in those who were HIV-infected. Counseling of women about sexual practices, improved access to health-care facilities, and vaccination against HPV are all potentially important in reducing oncogenic HPV infections.

Ultra-deep next-generation sequencing of plasma cell-free DNA in patients with advanced lung cancers: results from the Actionable Genome Consortium

BACKGROUND

Noninvasive genotyping using plasma cell-free DNA (cfDNA) has the potential to obviate the need for some invasive biopsies in cancer patients while also elucidating disease heterogeneity. We sought to develop an ultra-deep plasma next-generation sequencing (NGS) assay for patients with non-small-cell lung cancers (NSCLC) that could detect targetable oncogenic drivers and resistance mutations in patients where tissue biopsy failed to identify an actionable alteration.

PATIENTS AND METHODS

Plasma was prospectively collected from patients with advanced, progressive NSCLC. We carried out ultra-deep NGS using cfDNA extracted from plasma and matched white blood cells using a hybrid capture panel covering 37 lung cancer-related genes sequenced to 50 000× raw target coverage filtering somatic mutations attributable to clonal hematopoiesis. Clinical sensitivity and specificity for plasma detection of known oncogenic drivers were calculated and compared with tissue genotyping results. Orthogonal ddPCR validation was carried out in a subset of cases.

RESULTS

In 127 assessable patients, plasma NGS detected driver mutations with variant allele fractions ranging from 0.14% to 52%. Plasma ddPCR for EGFR or KRAS mutations revealed findings nearly identical to those of plasma NGS in 21 of 22 patients, with high concordance of variant allele fraction (r = 0.98). Blinded to tissue genotype, plasma NGS sensitivity for de novo plasma detection of known oncogenic drivers was 75% (68/91). Specificity of plasma NGS in those who were driver-negative by tissue NGS was 100% (19/19). In 17 patients with tumor tissue deemed insufficient for genotyping, plasma NGS identified four KRAS mutations. In 23 EGFR mutant cases with acquired resistance to targeted therapy, plasma NGS detected potential resistance mechanisms, including EGFR T790M and C797S mutations and ERBB2 amplification.

CONCLUSIONS

Ultra-deep plasma NGS with clonal hematopoiesis filtering resulted in de novo detection of targetable oncogenic drivers and resistance mechanisms in patients with NSCLC, including when tissue biopsy was inadequate for genotyping.

Advancing performance evaluation standards for household water treatment technologies

Diarrheal illnesses and fatalities continue to be major issues in many regions throughout the world. Household water treatment (HWT) technologies (including both point-of-use (POU) and point-of-entry (POE) treatment solutions) have been shown as able to deliver safe water in many low-income communities. However, as shown herein, there are important inconsistencies in protocols employed for validating performance of HWTs. The WHO does not stipulate influent concentration as a parameter that could influence removal efficacy, nor does it indicate an influent concentration range that should be used during technology evaluations. A correlation between influent concentration and removal is evidenced herein (R² = 0.88) with higher influent concentrations resulting in higher log-removal values (LRVs). The absence of a recommended standard influent concentration of bacteria (as well as for viruses and protozoa) could have negative consequences in intervention efforts. Recommendations are provided that regulatory bodies should specify an influent concentration range for testing and verification of HWT technologies.

Abstract P3-06-07: Recurrent but not pathognomonic fusion genes in mucinous carcinomas of the breast

Introduction: Mucinous carcinoma of the breast (MCB) is a rare histologic subtype of estrogen receptor (ER)-positive invasive carcinoma, and is characterized by tumor cells floating in pools of mucin. Despite their characteristic histology, MCBs are heterogeneous at the genetic level and no driver genetic alterations have been identified. Notably, MCBs lack the common genetic alterations found in ER-positive invasive ductal carcinomas (i.e. 16q losses, 1q gains and PIK3CA mutations). Fusion genes have been reported in breast cancer, including highly recurrent or pathognomonic fusions genes, such as the ETV6-NTRK3 and MYB/MYBL1 rearrangements in secretory carcinoma and adenoid cystic carcinoma, respectively. In this study we sought to define whether MCBs would be underpinned by a pathognomonic fusion gene.

Materials and methods: Seven pure mucinous A (hypocellular), seven pure mucinous B (hypercellular), and the mucinous component of a mixed MCB were microdissected, and subjected to RNA extraction followed by RNA-sequencing for fusion gene discovery. Read pairs supporting chimeric transcripts were identified using INTEGRATE, FusionCatcher and STARfusion. The Bayesian driver probability of the candidate fusion genes was annotated using OncoFuse. In-frame fusion gene candidates with a high driver probability were validated using orthogonal methods (RT-PCR and Sanger sequencing).

Results: Our analysis identified fusion genes in 47% (7/15) of the MCBs analyzed (29% (2/7) of type A MCBs, 57% (4/7) type B MCBs and in the mucinous component of one mixed MCB). The OAZ1-CSNK1G2 and RFC4-LPP fusion genes were identified in 20% (3/15) and 13% (2/15) of the cases, respectively. The OAZ1-CSNK1G2 chimeric transcript results in the truncation of the kinase domain of CSNK1G2, which represses ER transactivation. The RFC4-LPP chimeric transcript leads to the fusion of exons 1-3 of RFC4 and exons 5-11 of LPP, where the LIM domains of LPP are conserved. LPP is a known partner of fusion genes identified in mesenchymal tumors and reported to mediate TGF-β induced breast oncogenesis via its LIM domain. Additional validated, potentially pathogenic fusion genes identified in MCBs involved kinases, phosphatases or regulators of tyrosine kinase receptor signaling, such as IRAK3-PPM1H (n=1), GIGYF2–GFRA3 (n=1) and PHF20-FAM217B (n=1).

Conclusions: MCBs harbor fusion genes in almost half of the cases with two fusions being recurrent, involving primarily genes encoding kinases, phosphatases or receptor tyrosine kinase signaling regulators. Nevertheless, due to the lack of recurrence of a specific fusion gene, this special histologic type of breast cancer is unlikely to be underpinned by a highly recurrent/ pathognomonic pathogenic fusion gene.

Citation Format: Pareja F, Gularte-Merida R, Da Cruz Paula A, Brown D, Geyer FC, Piscuoglio S, Marchio C, Vincent-Salomon A, Brogi E, Weigelt B, Reis-Filho JS. Recurrent but not pathognomonic fusion genes in mucinous carcinomas of the breast [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 P3-06-07.

Abstract P2-01-02: Whole exome sequencing analysis of the progression from ductal carcinoma in situ to invasive ductal carcinoma

Introduction: Ductal carcinoma in situ (DCIS) is a bona fide non-obligate precursor of invasive carcinoma. Single cell sequencing studies have revealed intra-lesion genetic heterogeneity in DCIS and shown that progression to invasive ductal carcinoma (IDC) may occur through different mechanisms, including the selection of a subpopulation of tumor cells, acquisition of new genetic alterations or multi-clonal invasion. Here, we sought to investigate the genetic heterogeneity of DCIS, and to document further the clonal selection process accompanying progression to IDC.

Materials and methods: Synchronous DCIS (n=16) and IDC (n=15) samples from 14 patients were microdissected separately, and DNA samples of tumor and matched normal tissues were subjected to whole-exome sequencing (WES; n=27) or massively parallel targeted sequencing of all coding regions of ≥410 cancer-related genes (n=4). Somatic genetic alterations and mutational signatures were identified using state-of-the-art bioinformatics algorithms. PyClone was employed to define the clonal architecture of each DCIS and IDC and infer the clonal shifts accompanying progression from DCIS to IDC.

Results: DCIS were found to harbor recurrent somatic mutations affecting PIK3CA (50%), GATA3 (44%), TP53 (38%), CBFB (19%), PTEN (13%), and AKT1 (13%), which are genes known to be significantly mutated in invasive breast cancers. Despite the genomic similarities between matched DCIS and IDCs, NOTCH2 and MYC were found to be amplified solely in the IDC component of two cases, and PPM1D amplification was restricted to the DCIS component of another case. The mutational signature ascribed to aging (i.e. signature 1) was the predominant mutational signature in the DCIS and IDCs analyzed. PyClone analysis revealed that all synchronous DCIS and IDC studied here were clonally related and confirmed the previous observation that DCIS displays intra-lesion genetic heterogeneity. Evidence of clonal selection in the progression from DCIS to IDC was observed in three cases, whereby a minor DCIS subclone likely constituted the substrate for the development of IDC. In one of these cases, from a patient with a BRCA1 germline pathogenic mutation, we observed a shift from the mutational signature associated with defective homologous recombination DNA repair (i.e. signature 3) to the APOBEC-related mutational signatures (i.e. signatures 2 and 13) in the progression from DCIS to IDC.

Conclusion: Intra-lesion genetic heterogeneity is a common feature in DCIS synchronously diagnosed with IDC. Our findings corroborate the notion that DCIS is a direct non-obligate precursor of IDC, and that clonal selection in the progression of DCIS to IDC may be present in a subset of cases, but is unlikely to constitute the most frequent mechanism of progression.

Citation Format: Lee JY, Bi R, Pareja F, Geyer FC, Brown D, Wen HY, Norton L, Hicks J, Weigelt B, Reis-Filho JS. Whole exome sequencing analysis of the progression from ductal carcinoma in situ to invasive ductal carcinoma [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 P2-01-02.

Abstract P3-07-02: Metaplastic breast carcinomas and uterine carcinosarcomas are histologically and genetically related

Introduction: Metaplastic breast carcinomas (MBCs) and uterine carcinosarcomas (UCSs) are histologically similar, being often characterized by an admixture of adenocarcinoma areas with areas displaying sarcomatoid differentiation. We sought to investigate whether their histologic similarities would be paralleled by similar patterns of genetic alterations, and to determine whether the different histologic components of MBCs and UCSs would be clonally related.

Methods: Whole exome sequencing (WES) data from 35 MBCs previously analyzed by our group and 57 UCSs from The Cancer Genome Atlas (TCGA) study were reanalyzed. Somatic single nucleotide variants were detected with MuTect and indels with Strelka, Varscan2, Scalpel and Lancet. Copy number alterations were inferred using FACETS and functional annotation of the non-synonymous somatic mutations, amplifications or homozygous deletions was performed. We further microdissected the histologically distinct components of 11 MBCs and six UCSs and subjected each component to WES. Clonal decomposition was performed using PyClone.

Results: The most frequent somatic mutations identified in MBCs were TP53 (69%), PIK3CA (29%), FAT3 (26%) and PTEN (14%), whereas the most frequently mutated genes in UCSs were TP53 (84%), FBXW7 (35%), PIK3CA (29%), PTEN (15%) and PPP2R1A (15%). MBCs displayed a significantly higher frequency of mutations targeting FAT3 (26% vs 4%, P<0.01), FAT1 (11% vs 0%, P<0.05) and CHERP (11% vs 0%, P<0.05) than UCSs. UCSs more frequently harbored mutations affecting FBXW7 (35% vs 0%; P<0.01) and PPP2R1A (15% vs 0%, P<0.05) than MBCs. MBCs and UCSs displayed similar copy number alteration profiles, with frequent gains/ amplification of 8q, 3q and 1q, and losses of 8p. Pathway analysis based on the genes targeted by somatic genetic alterations revealed that both MBCs and UCSs were underpinned by genetic alterations resulting in activation of similar pathways, including PI3K, p53, Wnt and Notch signaling. Analysis of the separate components of MBCs and UCSs revealed that the histologically distinct components of MBCs and UCSs are clonally-related, with a median of 71% (range 26%-93%) and 78% (range 30%-93%) of somatic mutations being shared by the distinct components in MBCs and UCSs, respectively. In MBCs, clonal TP53, NOTCH3, KMT2D, FAT4 and PIK3CA mutations and several copy number alterations were shared by the histologically distinct components. Mutations private to each of the histologically distinct components included PIK3R1, CHERP and MAPK14 mutations. The carcinomatous and sarcomatous components of UCSs shared clonal TP53, PIK3CA, CDKN2A, ITGB7 and FGFR2 mutations. Private KMT2B mutations were identified in the UCS carcinomatous components. PyClone analysis revealed that the clonally-related histologically distinct components of each case harbored intra-component genetic heterogeneity coupled with parallel evolution.

Conclusions: Our findings support the contention that UCSs constitute the uterine counterpart of MBCs due to their similar histology and patterns of genetic alterations affecting the same signaling pathways (i.e. TP53, PI3K, Wnt and Notch). In each MBC and UCS analyzed here, the histologically distinct components were found to be clonally related.

Citation Format: Da Cruz Paula A, Brown D, Geyer FC, Smith E, Pareja F, Papanastasiou AD, Fusco N, Marchio C, Brogi E, Wen HY, Vincent-Salomon A, Norton L, Weigelt B, Reis-Filho JS. Metaplastic breast carcinomas and uterine carcinosarcomas are histologically and genetically related [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 P3-07-02.

Marie M, Stickney K, VanBuecken D, Vellek B, Webber C, Allen L, Bollyk J, Hilderman N, Ismail H, Lamola S, Sanda S, Vendettuoli H, Tridgell D, Monzavi R, Bock M, Fisher L, Halvorson M, Jeandron D, Kim M, Wood J, Geffner M, Kaufman F, Parkman R, Salazar C, Goland R, Clynes R, Cook S, Freeby M, Pat Gallagher M, Gandica R, Greenberg E, Kurland A, Pollak S, Wolk A, Chan M, Koplimae L, Levine E, Smith K, Trast J, DiMeglio L, Blum J, Evans-Molina C, Hufferd R, Jagielo B, Kruse C, Patrick V, Rigby M, Spall M, Swinney K, Terrell J, Christner L, Ford L, Lynch S, Menendez M, Merrill P, Pescovitz M, Rodriguez H, Alleyn C, Baidal D, Fay S, Gaglia J, Resnick B, Szubowicz S, Weir G, Benjamin R, Conboy D, deManbey A, Jackson R, Jalahej H, Orban T, Ricker A, Wolfsdorf J, Zhang HH, Wilson D, Aye T, Baker B, Barahona K, Buckingham B, Esrey K, Esrey T, Fathman G, Snyder R, Aneja B, Chatav M, Espinoza O, Frank E, Liu J, Perry J, Pyle R, Rigby A, Riley K, Soto A, Gitelman S, Adi S, Anderson M, Berhel A, Breen K, Fraser K, Gerard-Gonzalez A, Jossan P, Lustig R, Moassesfar S, Mugg A, Ng D, Prahalod P, Rangel-Lugo M, Sanda S, Tarkoff J, Torok C, Wesch R, Aslan I, Buchanan J, Cordier J, Hamilton C, Hawkins L, Ho T, Jain A, Ko K, Lee T, Phelps S, Rosenthal S, Sahakitrungruang T, Stehl L, Taylor L, Wertz M, Wong J, Philipson L, Briars R, Devine N, Littlejohn E, Grant T, Gottlieb P, Klingensmith G, Steck A, Alkanani A, Bautista K, Bedoy R, Blau A, Burke B, Cory L, Dang M, Fitzgerald-Miller L, Fouts A, Gage V, Garg S, Gesauldo P, Gutin R, Hayes C, Hoffman M, Ketchum K, Logsden-Sackett N, Maahs D, Messer L, Meyers L, Michels A, Peacock S, Rewers M, Rodriguez P, Sepulbeda F, Sippl R, Steck A, Taki I, Tran BK, Tran T, Wadwa RP, Zeitler P, Barker J, Barry S, Birks L, Bomsburger L, Bookert T, Briggs L, Burdick P, Cabrera R, Chase P, Cobry E, Conley A, Cook G, Daniels J, DiDomenico D, Eckert J, Ehler A, Eisenbarth G, Fain P, Fiallo-Scharer R, Frank N, Goettle H, Haarhues M, Harris S, Horton L, Hutton J, Jeffrrey J, Jenison R, Jones K, Kastelic W, King MA, Lehr D, Lungaro J, Mason K, Maurer H, Nguyen L, Proto A, Realsen J, Schmitt K, Schwartz M, Skovgaard S, Smith J, Vanderwel B, Voelmle M, Wagner R, Wallace A, Walravens P, Weiner L, Westerhoff B, Westfall E, Widmer K, Wright H, Schatz D, Abraham A, Atkinson M, Cintron M, Clare-Salzler M, Ferguson J, Haller M, Hosford J, Mancini D, Rohrs H, Silverstein J, Thomas J, Winter W, Cole G, Cook R, Coy R, Hicks E, Lewis N, Marks J, Pugliese A, Blaschke C, Matheson D, Pugliese A, Sanders-Branca N, Ray Arce LA, Cisneros M, Sabbag S, Moran A, Gibson C, Fife B, Hering B, Kwong C, Leschyshyn J, Nathan B, Pappenfus B, Street A, Boes MA, Peterson Eck S, Finney L, Albright Fischer T, Martin A, Jacqueline Muzamhindo C, Rhodes M, Smith J, Wagner J, Wood B, Becker D, Delallo K, Diaz A, Elnyczky B, Libman I, Pasek B, Riley K, Trucco M, Copemen B, Gwynn D, Toledo F, Rodriguez H, Bollepalli S, Diamond F, Eyth E, Henson D, Lenz A, Shulman D, Raskin P, Adhikari S, Dickson B, Dunnigan E, Lingvay I, Pruneda L, Ramos-Roman M, Raskin P, Rhee C, Richard J, Siegelman M, Sturges D, Sumpter K, White P, Alford M, Arthur J, Aviles-Santa ML, Cordova E, Davis R, Fernandez S, Fordan S, Hardin T, Jacobs A, Kaloyanova P, Lukacova-Zib I, Mirfakhraee S, Mohan A, Noto H, Smith O, Torres N, Wherrett D, Balmer D, Eisel L, Kovalakovska R, Mehan M, Sultan F, Ahenkorah B, Cevallos J, Razack N, Jo Ricci M, Rhode A, Srikandarajah M, Steger R, Russell WE, Black M, Brendle F, Brown A, Moore D, Pittel E, Robertson A, Shannon A, Thomas JW, Herold K, Feldman L, Sherwin R, Tamborlane W, Weinzimer S, Toppari J, Kallio T, Kärkkäinen M, Mäntymäki E, Niininen T, Nurmi B, Rajala P, Romo M, Suomenrinne S, Näntö-Salonen K, Simell O, Simell T, Bosi E, Battaglia M, Bianconi E, Bonfanti R, Grogan P, Laurenzi A, Martinenghi S, Meschi F, Pastore M, Falqui L, Teresa Muscato M, Viscardi M, Bingley P, Castleden H, Farthing N, Loud S, Matthews C, McGhee J, Morgan A, Pollitt J, Elliot-Jones R, Wheaton C, Knip M, Siljander H, Suomalainen H, Colman P, Healy F, Mesfin S, Redl L, Wentworth J, Willis J, Farley M, Harrison L, Perry C, Williams F, Mayo A, Paxton J, Thompson V, Volin L, Fenton C, Carr L, Lemon E, Swank M, Luidens M, Salgam M, Sharma V, Schade D, King C, Carano R, Heiden J, Means N, Holman L, Thomas I, Madrigal D, Muth T, Martin C, Plunkett C, Ramm C, Auchus R, Lane W, Avots E, Buford M, Hale C, Hoyle J, Lane B, Muir A, Shuler S, Raviele N, Ivie E, Jenkins M, Lindsley K, Hansen I, Fadoju D, Felner E, Bode B, Hosey R, Sax J, Jefferies C, Mannering S, Prentis R, She J, Stachura M, Hopkins D, Williams J, Steed L, Asatapova E, Nunez S, Knight S, Dixon P, Ching J, Donner T, Longnecker S, Abel K, Arcara K, Blackman S, Clark L, Cooke D, Plotnick L, Levin P, Bromberger L, Klein K, Sadurska K, Allen C, Michaud D, Snodgrass H, Burghen G, Chatha S, Clark C, Silverberg J, Wittmer C, Gardner J, LeBoeuf C, Bell P, McGlore O, Tennet H, Alba N, Carroll M, Baert L, Beaton H, Cordell E, Haynes A, Reed C, Lichter K, McCarthy P, McCarthy S, Monchamp T, Roach J, Manies S, Gunville F, Marosok L, Nelson T, Ackerman K, Rudolph J, Stewart M, McCormick K, May S, Falls T, Barrett T, Dale K, Makusha L, McTernana C, Penny-Thomas K, Sullivan K, Narendran P, Robbie J, Smith D, Christensen R, Koehler B, Royal C, Arthur T, Houser H, Renaldi J, Watsen S, Wu P, Lyons L, House B, Yu J, Holt H, Nation M, Vickers C, Watling R, Heptulla R, Trast J, Agarwal C, Newell D, Katikaneni R, Gardner C, Del A, Rio A, Logan H, Collier C, Rishton G, Whalley A, Ali S, Ramtoola T, Quattrin L, Mastrandea A, House M, Ecker C, Huang C, Gougeon J, Ho D, Pacuad D, Dunger J, May C, O’Brien C, Acerini B, Salgin A, Thankamony R, Williams J, Buse G, Fuller M, Duclos J, Tricome H, Brown D, Pittard D, Bowlby A, Blue T, Headley S, Bendre K, Lewis K, Sutphin C, Soloranzo J, Puskaric H, Madison M, Rincon M, Carlucci R, Shridharani B, Rusk E, Tessman D, Huffman H, Abrams B, Biederman M, Jones V, Leathers W, Brickman P, Petrie D, Zimmerman J, Howard L, Miller R, Alemzadeh D, Mihailescu R, Melgozza-Walker N, Abdulla C, Boucher-Berry D, Ize-Ludlow R, Levy C, Swenson, Brousell N, Crimmins D, Edler T, Weis C, Schultz D, Rogers D, Latham C, Mawhorter C, Switzer W, Spencer P, Konstantnopoulus S, Broder J, Klein L, Knight L, Szadek G, Welnick B, Thompson R, Hoffman A, Revell J, Cherko K, Carter E, Gilson J, Haines G, Arthur B, Bowen W, Zipf P, Graves R, Lozano D, Seiple K, Spicer A, Chang J, Fregosi J, Harbinson C, Paulson S, Stalters P, Wright D, Zlock A, Freeth J, Victory H, Maheshwari A, Maheshwari T, Holmstrom J, Bueno R, Arguello J, Ahern L, Noreika V, Watson S, Hourse P, Breyer C, Kissel Y, Nicholson M, Pfeifer S, Almazan J, Bajaj M, Quinn K, Funk J, McCance E, Moreno R, Veintimilla A, Wells J, Cook S, Trunnel J, Henske S, Desai K, Frizelis F, Khan R, Sjoberg K, Allen P, Manning G, Hendry B, Taylor S, Jones W, Strader M, Bencomo T, Bailey L, Bedolla C, Roldan C, Moudiotis B, Vaidya C, Anning S, Bunce S, Estcourt E, Folland E, Gordon C, Harrill J, Ireland J, Piper L, Scaife K, Sutton S, Wilkins M, Costelloe J, Palmer L, Casas C, Miller M, Burgard C, Erickson J, Hallanger-Johnson P, Clark W, Taylor A, Lafferty S, Gillett C, Nolan M, Pathak L, Sondrol T, Hjelle S, Hafner J, Kotrba R, Hendrickson A, Cemeroglu T, Symington M, Daniel Y, Appiagyei-Dankah D, Postellon M, Racine L, Kleis K, Barnes S, Godwin H, McCullough K, Shaheen G, Buck L, Noel M, Warren S, Weber S, Parker I, Gillespie B, Nelson C, Frost J, Amrhein E, Moreland A, Hayes J, Peggram J, Aisenberg M, Riordan J, Zasa E, Cummings K, Scott T, Pinto A, Mokashi K, McAssey E, Helden P, Hammond L, Dinning S, Rahman S, Ray C, Dimicri S, Guppy H, Nielsen C, Vogel C, Ariza L, Morales Y, Chang R, Gabbay L, Ambrocio L, Manley R, Nemery W, Charlton P, Smith L, Kerr B, Steindel-Kopp M, Alamaguer D, Liljenquist G, Browning T, Coughenour M, Sulk E, Tsalikan M, Tansey J, Cabbage N. Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Critical care usage after major gastrointestinal and liver surgery: a prospective, multicentre observational study

BACKGROUND

Patient selection for critical care admission must balance patient safety with optimal resource allocation. This study aimed to determine the relationship between critical care admission, and postoperative mortality after abdominal surgery.

METHODS

This prespecified secondary analysis of a multicentre, prospective, observational study included consecutive patients enrolled in the DISCOVER study from UK and Republic of Ireland undergoing major gastrointestinal and liver surgery between October and December 2014. The primary outcome was 30-day mortality. Multivariate logistic regression was used to explore associations between critical care admission (planned and unplanned) and mortality, and inter-centre variation in critical care admission after emergency laparotomy.

RESULTS

Of 4529 patients included, 37.8% (n=1713) underwent planned critical care admissions from theatre. Some 3.1% (n=86/2816) admitted to ward-level care subsequently underwent unplanned critical care admission. Overall 30-day mortality was 2.9% (n=133/4519), and the risk-adjusted association between 30-day mortality and critical care admission was higher in unplanned [odds ratio (OR): 8.65, 95% confidence interval (CI): 3.51-19.97) than planned admissions (OR: 2.32, 95% CI: 1.43-3.85). Some 26.7% of patients (n=1210/4529) underwent emergency laparotomies. After adjustment, 49.3% (95% CI: 46.8-51.9%, P<0.001) were predicted to have planned critical care admissions, with 7% (n=10/145) of centres outside the 95% CI.

CONCLUSIONS

After risk adjustment, no 30-day survival benefit was identified for either planned or unplanned postoperative admissions to critical care within this cohort. This likely represents appropriate admission of the highest-risk patients. Planned admissions in selected, intermediate-risk patients may present a strategy to mitigate the risk of unplanned admission. Substantial inter-centre variation exists in planned critical care admissions after emergency laparotomies.

Implementation of evidence-based practice for benign paroxysmal positional vertigo: DIZZTINCT- A study protocol for an exploratory stepped-wedge randomized trial

Background

Benign paroxysmal positional vertigo (BPPV) is the most common peripheral vestibular disorder, and accounts for 8% of individuals with moderate or severe dizziness. BPPV patients experience substantial inconveniences and disabilities during symptomatic periods. BPPV therapeutic processes – the Dix-Hallpike Test (DHT) and the Canalith Repositioning Maneuver (CRM) – have an evidence base that is at the clinical practice guideline level. The most commonly used CRM is the modified Epley maneuver. The DHT is the gold standard test for BPPV and the CRM is supported by numerous randomized controlled trials and systematic reviews. Despite this, BPPV care processes are underutilized.

Methods/design

This is a stepped-wedge, randomized clinical trial of a multi-faceted educational and care-process-based intervention designed to improve the guideline-concordant care of patients with BPPV presenting to the emergency department (ED) with dizziness. The unit of randomization and target of intervention is the hospital. After an initial observation period, the six hospitals will undergo the intervention in five waves (two closely integrated hospitals will be paired). The order will be randomized. The primary endpoint is measured at the individual patient level, and is the presence of documentation of either the Dix-Hallpike Test or CRM. The secondary endpoints are referral to a health care provider qualified to treat dizziness for CRM and 90-day stroke rates following an ED dizziness visit. Formative evaluations are also performed to monitor and identify potential and actual influences on the progress and effectiveness of the implementation efforts.

Discussion

If this study safely increases documentation of the DHT/CRM, this will be an important step in implementing the use of these evidenced-based processes of care. Positive results will support conducting larger-scale follow-up studies that assess patient outcomes. The data collection also enables evaluation of potential and actual influences on the progress and effectiveness of the implementation efforts.

Trial registration

ClinicalTrials.gov, ID: NCT02809599. The record was first available to the public on 22 June 2016 prior to the enrollment of the first patients in October 2016.

Electronic supplementary material

The online version of this article (10.1186/s13063-018-3099-0) contains supplementary material, which is available to authorized users.

Percutaneous sentinel node removal using a vacuum-assisted needle biopsy in women with breast cancer: a feasibility and acceptability study

AIMS

To assess the feasibility and acceptability of large-gauge percutaneous removal of the axillary sentinel lymph node (SLN) using dual gamma probe and ultrasound guidance.

MATERIALS AND METHODS

Technetium nanocolloid was administered the day before surgery. On the day of surgery, potential SLNs were identified with gamma probe and ultrasound scanning. A 7 G vacuum-assisted biopsy (VAB) device was inserted percutaneously deep to the target node and the node(s) removed. The gamma probe was used to confirm removal of radiolabelled tissue. At surgery, any residual radiolabelled or blue nodes were removed. Morbidity was assessed via (1) a pain questionnaire immediately after the percutaneous procedure, (2) relevant items from the FACT B+4 questionnaire 7-10 days after surgery, and (3) case note review 1 month after surgery.

RESULTS

Twenty-two patients consented and 20 patients underwent the procedure. Radiolabelled nodal tissue was obtained in 18/20 (90%). The mean procedure time was 11 minutes. Four of 18 patients had metastatic disease identified in the VAB excision tissue with 100% sensitivity for axillary metastasis. At axillary surgery, additional intact SLN or fragments were found in 14 patients. No additional metastatic disease was found at surgery. One patient suffered a pneumothorax during instillation of local anaesthetic. The median pain score was 10/100 by visual analogue scale. Immediate post-procedure haematoma was common (14 of 20) and prolonged manual compression frequent.

CONCLUSION

VAB removal of sentinel nodes using dual scanning is feasible. Although preliminary sensitivity and specificity levels are encouraging, complications may discourage widespread implementation.

Improving Gene Editing Outcomes in Human Hematopoietic Stem and Progenitor Cells by Temporal Control of DNA Repair

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated system (Cas9)-mediated gene editing of human hematopoietic stem cells (hHSCs) is a promising strategy for the treatment of genetic blood diseases through site-specific correction of identified causal mutations. However, clinical translation is hindered by low ratio of precise gene modification using the corrective donor template (homology-directed repair, HDR) to gene disruption (nonhomologous end joining, NHEJ) in hHSCs. By using a modified version of Cas9 with reduced nuclease activity in G1 phase of cell cycle when HDR cannot occur, and transiently increasing the proportion of cells in HDR-preferred phases (S/G2), we achieved a four-fold improvement in HDR/NHEJ ratio over the control condition in vitro, and a significant improvement after xenotransplantation of edited hHSCs into immunodeficient mice. This strategy for improving gene editing outcomes in hHSCs has important implications for the field of gene therapy, and can be applied to diseases where increased HDR/NHEJ ratio is critical for therapeutic success. Stem Cells 2019;37:284-294.