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Targeting the Atf7ip-Setdb1 Complex Augments Antitumor Immunity by Boosting Tumor Immunogenicity

Hu, Hai; Khodadadi-Jamayran, Alireza; Dolgalev, Igor; Cho, Hyunwoo; Badri, Sana; Chiriboga, Luis A; Zeck, Briana; Lopez De Rodas Gregorio, Miguel; Dowling, Catríona M; Labbe, Kristen; Deng, Jiehui; Chen, Ting; Zhang, Hua; Zappile, Paul; Chen, Ze; Ueberheide, Beatrix; Karatza, Angeliki; Han, Han; Ranieri, Michela; Tang, Sittinon; Jour, George; Osman, Iman; Sucker, Antje; Schadendorf, Dirk; Tsirigos, Aristotelis; Schalper, Kurt A; Velcheti, Vamsidhar; Huang, Hsin-Yi; Jin, Yujuan; Ji, Hongbin; Poirier, John T; Li, Fei; Wong, Kwok-Kin
Substantial progress has been made in understanding how tumors escape immune surveillance. However, few measures to counteract tumor immune evasion have been developed. Suppression of tumor antigen expression is a common adaptive mechanism that cancers use to evade detection and destruction by the immune system. Epigenetic modifications play a critical role in various aspects of immune invasion, including the regulation of tumor antigen expression. To identify epigenetic regulators of tumor antigen expression, we established a transplantable syngeneic tumor model of immune escape with silenced antigen expression and used this system as a platform for a CRISPR-Cas9 suppressor screen for genes encoding epigenetic modifiers. We found that disruption of the genes encoding either of the chromatin modifiers activating transcription factor 7-interacting protein (Atf7ip) or its interacting partner SET domain bifurcated histone lysine methyltransferase 1 (Setdb1) in tumor cells restored tumor antigen expression. This resulted in augmented tumor immunogenicity concomitant with elevated endogenous retroviral (ERV) antigens and mRNA intron retention. ERV disinhibition was associated with a robust type I interferon response and increased T-cell infiltration, leading to rejection of cells lacking intact Atf7ip or Setdb1. ATF7IP or SETDB1 expression inversely correlated with antigen processing and presentation pathways, interferon signaling, and T-cell infiltration and cytotoxicity in human cancers. Our results provide a rationale for targeting Atf7ip or Setdb1 in cancer immunotherapy.
PMID: 34462284
ISSN: 2326-6074
CID: 5061142

Phase 0 Clinical Trial of Everolimus in Patients with Vestibular Schwannoma or Meningioma

Karajannis, Matthias A; Mauguen, Audrey; Maloku, Ekrem; Xu, Qingwen; Dunbar, Erin M; Plotkin, Scott R; Yaffee, Anna; Wang, Shiyang; Roland, J Thomas; Sen, Chandranath; Placantonakis, Dimitris G; Golfinos, John G; Allen, Jeffrey C; Vitanza, Nicholas A; Chiriboga, Luis A; Schneider, Robert J; Deng, Jingjing; Neubert, Thomas A; Goldberg, Judith D; Zagzag, David; Giancotti, Filippo G; Blakeley, Jaishri O
Inhibition of mTORC1 signaling has been shown to diminish growth of meningiomas and schwannomas in preclinical studies, and clinical data suggest that everolimus, an orally administered mTORC1 inhibitor, may slow tumor progression in a subset of NF2 patients with vestibular schwannoma (VS). To assess the pharmacokinetics, pharmacodynamics and potential mechanisms of treatment resistance, we performed a pre-surgical (phase 0) clinical trial of everolimus in patients undergoing elective surgery for VS or meningiomas. Eligible patients with meningioma or VS requiring tumor resection enrolled on study received everolimus 10 mg daily for 10 days immediately prior to surgery. Everolimus blood levels were determined immediately prior to and after surgery. Tumor samples were collected intraoperatively. Ten patients completed protocol therapy. Median pre- and post-operative blood levels of everolimus were found to be in a high therapeutic range (17.4 ng/ml and 9.4 ng/ml, respectively). Median tumor tissue drug concentration determined by mass spectrometry was 24.3 pg/mg (range 9.2-169.2). We observed only partial inhibition of phospho-S6 in the treated tumors, indicating incomplete target inhibition compared to control tissues from untreated patients (p=0.025). Everolimus led to incomplete inhibition of mTORC1 and downstream signaling. These data may explain the limited anti-tumor effect of everolimus observed in clinical studies for NF2 patients and will inform the design of future pre-clinical and clinical studies targeting mTORC1 in meningiomas and schwannomas.
PMID: 34224367
ISSN: 1538-8514
CID: 4932142

Evidence for continuity of interstitial spaces across tissue and organ boundaries in humans

Cenaj, Odise; Allison, Douglas H R; Imam, Rami; Zeck, Briana; Drohan, Lilly M; Chiriboga, Luis; Llewellyn, Jessica; Liu, Cheng Z; Park, Young Nyun; Wells, Rebecca G; Theise, Neil D
Bodies have continuous reticular networks, comprising collagens, elastin, glycosaminoglycans, and other extracellular matrix components, through all tissues and organs. Fibrous coverings of nerves and blood vessels create structural continuity beyond organ boundaries. We recently validated fluid flow through human fibrous tissues, though whether these interstitial spaces are continuous through the body or discontinuous, confined within individual organs, remains unclear. Here we show evidence for continuity of interstitial spaces using two approaches. Non-biological particles (tattoo pigment, colloidal silver) were tracked within colon and skin interstitial spaces and into adjacent fascia. Hyaluronic acid, a macromolecular component of interstitial spaces, was also visualized. Both techniques demonstrate interstitial continuity within and between organs including within perineurium and vascular adventitia traversing organs and the spaces between them. We suggest that there is a body-wide network of fluid-filled interstitial spaces that has significant implications for molecular signaling, cell trafficking, and the spread of malignant and infectious disease.
PMID: 33790388
ISSN: 2399-3642
CID: 4830922

Somatic Focal Copy Number Gains of Noncoding Regions of Receptor Tyrosine Kinase Genes in Treatment-Resistant Epilepsy

Vasudevaraja, Varshini; Rodriguez, Javier Hernaez; Pelorosso, Cristiana; Zhu, Kaicen; Buccoliero, Anna Maria; Onozato, Maristela; Mohamed, Hussein; Serrano, Jonathan; Tredwin, Lily; Garonzi, Marianna; Forcato, Claudio; Zeck, Briana; Ramaswami, Sitharam; Stafford, James; Faustin, Arline; Friedman, Daniel; Hidalgo, Eveline Teresa; Zagzag, David; Skok, Jane; Heguy, Adriana; Chiriboga, Luis; Conti, Valerio; Guerrini, Renzo; Iafrate, A John; Devinsky, Orrin; Tsirigos, Aristotelis; Golfinos, John G; Snuderl, Matija
Epilepsy is a heterogenous group of disorders defined by recurrent seizure activity due to abnormal synchronized activity of neurons. A growing number of epilepsy cases are believed to be caused by genetic factors and copy number variants (CNV) contribute to up to 5% of epilepsy cases. However, CNVs in epilepsy are usually large deletions or duplications involving multiple neurodevelopmental genes. In patients who underwent seizure focus resection for treatment-resistant epilepsy, whole genome DNA methylation profiling identified 3 main clusters of which one showed strong association with receptor tyrosine kinase (RTK) genes. We identified focal copy number gains involving epidermal growth factor receptor (EGFR) and PDGFRA loci. The dysplastic neurons of cases with amplifications showed marked overexpression of EGFR and PDGFRA, while glial and endothelial cells were negative. Targeted sequencing of regulatory regions and DNA methylation analysis revealed that only enhancer regions of EGFR and gene promoter of PDGFRA were amplified, while coding regions did not show copy number abnormalities or somatic mutations. Somatic focal copy number gains of noncoding regulatory represent a previously unrecognized genetic driver in epilepsy and a mechanism of abnormal activation of RTK genes. Upregulated RTKs provide a potential avenue for therapy in seizure disorders.
PMID: 33274363
ISSN: 1554-6578
CID: 4694512

Validation of PD-L1 clone 22C3 immunohistochemical stain on two Ventana DISCOVERY autostainer models: detailed protocols, test performance characteristics, and interobserver reliability analyses

Basu, Atreyee; Chiriboga, Luis; Narula, Navneet; Zhou, Fang; Moreira, Andre L
Immunohistochemical (IHC) stain for PD-L1 as a biomarker for immunotherapy is recommended in non-small cell lung cancer (NSCLC). Under the FDA, the selection of patients for pembrolizumab requires companion diagnostic testing using the Dako Agilent PD-L1 IHC 22C3 pharmDx kit performed on the Dako Autostainer Link 48 platform. However, because it is not widely available, there is need for cross-platform validation. Existing studies provide incomplete protocol detail. In our study, 73 lung tumors were stained using the FDA-approved test ('gold standard'). The same blocks were stained using two different models of the Ventana DISCOVERY platform (ULTRA, n = 73 and XT, n = 70) using different parameters, and interpreted by three pathologists. The ULTRA group met College of American Pathologists (CAP) validation criteria (concordance 91.8%) while the XT group did not (concordance 67.1%). Using tumor proportion score (TPS) ≥1% and TPS ≥50% as cut-offs, the ULTRA protocol had higher sensitivity (97.8% and 91.7%) than XT (73.3% and 60.9%) and similar specificity (ULTRA 88.9% and 100%, XT 88% and 100%). Discordance between ULTRA and XT was 27%, and in all these cases ULTRA was concordant with gold standard. Interobserver reliability was substantial for ULTRA and almost perfect for XT, providing evidence that staining rather than observer variability accounts for XT's inferior performance. Cross-validation of the clinically used 22C3 anti PD-L1 antibody test with substantial interobserver agreement is possible on the commonly used the Ventana DISCOVERY ULTRA automated instrument, while the validation failed on the XT. Cautious attention to detail must be paid when choosing cross-validation parameters.
PMID: 33245263
ISSN: 2046-0236
CID: 4681492

Keratin 19 and mesenchymal markers for evaluation of epithelial-mesenchymal transition and stem cell niche components in primary biliary cholangitis by sequential elution-stripping multiplex immunohistochemistry

Paulsen, John David; Zeck, Briana; Sun, Katherine; Simoes, Camila; Theise, Neil D; Chiriboga, Luis
Multiplexed immunohistochemical techniques give insight into contextual cellular relationships by offering the ability to collect cell-specific data with spatial information from formalin-fixed, paraffin-embedded tissue sections. We established an automated sequential elution-stripping multiplex immunohistochemical assay to address two controversial scientific questions in the field of hepatopathology: 1) whether epithelial-to-mesenchymal transition or mesenchymal-to-epithelial transition occurs during liver injury and repair of a chronic liver disease and 2) if there is a stromal:epithelial relationship along the canals of Hering that would support the concept of this biliary structure being a stem/progenitor cell niche. Our 4-plex assay includes both epithelial and mesenchymal clinical immunohistochemical markers and was performed on clinical human liver specimens in patients with primary biliary cholangitis. The assay demonstrated that in each specimen, co-expression of epithelial and mesenchymal markers was observed in extraportal cholangiocytes. In regard to possible mesenchymal components in a stem cell niche, 82.3% ± 5.5% of extraportal cholangiocytes were intimately associated with a vimentin-positive cell. Co-expression of epithelial and mesenchymal markers by extraportal cholangiocytes is evidence for epithelial to mesenchymal transition in primary biliary cholangitis. Vimentin-positive stromal cells are frequently juxtaposed to extraportal cholangiocytes, supporting an epithelial:mesenchymal relationship within the hepatobiliary stem cell niche. Our automated sequential elution-stripping multiplex immunohistochemical assay is a cost-effective multiplexing technique that can be readily applied to a small series of clinical pathology samples in order to answer scientific questions involving cell:cell relationships and cellular antibody expression.
PMID: 32998669
ISSN: 2046-0236
CID: 4617662

Renal Tubular Complement C9 Deposition Is Associated with Renal Tubular Damage and Fibrosis in Lupus Nephritis [Meeting Abstract]

Wu, M; Chiriboga, L; Goilav, B; Wang, S; Putterman, C; Schwartz, D; Pullman, J; Broder, A; Belmont, H M
Background/Purpose: Tubulointerstitial damage in lupus nephritis (LN) is a strong predictor of progression to chronic kidney disease (CKD) and end stage renal disease (ESRD). While prior studies showed complement activation mediates glomerular injury, the role of complement in renal tubular damage has not been evaluated. The objective of this study is to investigate the association between complement activation as measured by tubular complement 9 (C9) deposition with interstitial fibrosis and tubular atrophy (IFTA) in LN.
Method(s): LN biopsies from July 2014 to July 2016 were evaluated. Chromogenic immunohistochemistry was performed on formalin-fixed, paraffin-embedded, 4-mum human renal biopsy sections using unconjugated, murine anti-human Complement C9 (Hycult Biotech, clone X197) as a marker of the membrane attack complex (MAC) activation. C3 glomerulopathy was used as a positive control and normal kidney served as a negative control. Tubular basement membrane C9 staining intensity was analyzed as absent (0) versus present (1 to 3) scored on a semi-quantitative scale by a renal pathologist. IFTA was categorized as 0-10%, 11-20%, and >20%. Clinical parameters were assessed at the time of biopsy and 6 months post biopsy.
Result(s): Renal biopsies from 30 LN patients were studied, of which 23 (77%) were proliferative LN. There were 24 (80%) women, mean age 33 (standard deviation) (12) years. Positive tubular C9 staining (C9+) was observed in 7 (23%) biopsies. At the time of renal biopsy, C9+ patients had significantly higher proteinuria, compared to C9- patients: median (interquartile range) 6.2g (3.3-13.1) vs. 2.4g (1.3-4.6), p< 0.01. The differences persisted at 6 months after induction therapy: 1.08g (1.0-8.3) in C9+ vs. 0.68g (0.2-2.1) in C9- patients, p=0.06. Tubular C9 deposition was associated with the finding of interstitial fibrosis on biopsy: 3 out of 7 (42.9%) had >20% interstitial fibrosis as compared to none in the C9- group, p=< 0.01. Higher proportion of C9+ patients had moderate NIH Chronicity index: 3 out of 7 (42.9%) vs 2 out of 23 (8.7%) in the C9- group, p=0.07. There was no significant difference in eGFR at renal biopsy between the two groups.
Conclusion(s): Tubular C9 deposition is associated with proteinuria, interstitial fibrosis and increased chronicity which are predictors of progression to ESRD. Complement activation may play an important role in tubulointerstitial damage in LN
EMBASE:634233054
ISSN: 2326-5205
CID: 4811982

Experimental Variables that Affect Human Hepatocyte AAV Transduction in Liver Chimeric Mice

Zou, Chenhui; Vercauteren, Koen O A; Michailidis, Eleftherios; Kabbani, Mohammad; Zoluthkin, Irene; Quirk, Corrine; Chiriboga, Luis; Yazicioglu, Mustafa; Anguela, Xavier M; Meuleman, Philip; High, Katherine A; Herzog, Roland W; de Jong, Ype P
Adeno-associated virus (AAV) vector serotypes vary in their ability to transduce hepatocytes from different species. Chimeric mouse models harboring human hepatocytes have shown translational promise for liver-directed gene therapies. However, many variables that influence human hepatocyte transduction and transgene expression in such models remain poorly defined. Here, we aimed to test whether three experimental conditions influence AAV transgene expression in immunodeficient, fumaryl-acetoactetate-hydrolase-deficient (Fah-/-) chimeric mice repopulated with primary human hepatocytes. We examined the effects of the murine liver injury cycle, human donor variability, and vector doses on hepatocyte transduction with various AAV serotypes expressing a green fluorescent protein (GFP). We determined that the timing of AAV vector challenge in the liver injury cycle resulted in up to 7-fold differences in the percentage of GFP expressing human hepatocytes. The GFP+ hepatocyte frequency varied 7-fold between human donors without, however, changing the relative transduction efficiency between serotypes for an individual donor. There was also a clear relationship between AAV vector doses and human hepatocyte transduction and transgene expression. We conclude that several experimental variables substantially affect human hepatocyte transduction in the Fah-/- chimera model, attention to which may improve reproducibility between findings from different laboratories.
PMCID:7326722
PMID: 32637450
ISSN: 2329-0501
CID: 4514632

The diagnostic utility of EZH2 H-score and Ki-67 index in non-invasive breast apocrine lesions

Vougiouklakis, Theodore; Belovarac, Brendan J; Lytle, Andrew; Chiriboga, Luis; Ozerdem, Ugur
In diagnostic breast pathology, there is no reliable applicable immunostain to help discern atypical and in situ apocrine lesions from benign apocrine tissue. At present, the diagnosis of non-invasive apocrine lesions remains challenging with current diagnoses rendered based on discrete morphologic characteristics on conventional hematoxylin and eosin staining. Interobserver variability is significant even among subspecialists partly due to lack of adjuvant diagnostic immunohistochemical stains. Herein, we set to elucidate the potential utility of EZH2 and Ki-67 immunostains as tangible tools in non-invasive apocrine proliferations. A cohort of apocrine breast lesions [Benign apocrine hyperplasia (BAH), n = 10; Atypical apocrine hyperplasia (AAH), n = 16; Apocrine ductal carcinoma in situ (ADCIS), n = 12] were subjected to EZH2 immunostaining and analyzed via H-scoring of nuclear expression. Mean H-scores for EZH2 progressively increased from BAH (23.5), to AAH (47.4) and ADCIS (196.4), and showed a significant difference utilizing the Kruskal-Wallis test (p < 0.0001). Further interrogation of Ki-67 demonstrated incremental expression from BAH to AAH and ADCIS at 1.6 %, 4.7 % and 24.7 %, respectively (p < 0.0001, Kruskal-Wallis test), suggesting an association with increased proliferation. Our results demonstrate that a combination of EZH2 and Ki-67 immunostaining may be employed in differentiating among challenging apocrine breast lesions and suggest a putative diagnostic utility for EZH2 and Ki-67 in non-invasive apocrine breast lesions.
PMID: 32825929
ISSN: 1618-0631
CID: 4574932

Continuity of interstitial spaces within skin and colon and with their underlying fascia: Pathways for spread of malignancy and infection [Meeting Abstract]

Cenaj, O; Allison, D; Zeck, B; Drohan, L; Chiriboga, L; Park, Y N; Theise, N
Background: Fibroconnective tissues of the body are traditionally conceived as layers of densely compacted collagen. Recent in vivo microscopy, however, demonstrates that at least some, including visceral submucosae, dermis, fascia, adventitia and perineurium, are actually a reticular network of fluid-filled sinuses supported by a complex scaffold of thick collagen bundles (Benias et al Sci Rep 2018: 8). The interstitial fluid is rich in hyaluronic acid (HA). Whether these large scale interstitial spaces are continuous between tissues/organs or separate is unclear. Continuity was investigated by two methods: 1. movement of non-biological pigment (tattoo pigment, colloidal silver) in colon and skin specimens; 2. localization of HA by IHC.
Design(s): H&E-stained sections of FFPE tissues from resected colons following endoscopic submucosal tattoo for malignant polyps (n=5) and from skin biopsies with either cosmetic tattoos (n=3) or colloidal silver (n=2) were examined. Location of particles was assessed. The slides were then scanned, decolorized, and stained by multiplex chromogenic IHC assay (Discovery Ultra, Ventana) for HA-binding protein (brown), vimentin (magenta) and CD34 (teal) to label interstitial lining cells.
Result(s): Tattoo pigment and colloidal silver within the interstitial spaces was identified in the dermis (Fig. 1) and colonic submucosa and in the dependent mesenteric and subcutaneous fascias. In all colon specimens HA IHC highlighted the spatial continuity of all layers of the colon from lamina propria through muscularis mucosae to submucosa (Fig. 2A), then through the muscularis propria into mesenteric fascia (Fig. 2B, C). Continuity between these spaces and perivascular stroma/adventitia and perineurium in the bowel wall was also evident. Continuity of HA-filled spaces is also demonstrated from papillary to reticular dermis and then to subcutaneous fascia interface. (Figure presented)
Conclusion(s): Interstitial spaces are neither virtual nor a result of processing artifact, but are filled with physiologically relevant fluid rich in HA. Their continuity across tissue compartments is demonstrated by movement of non-biological pigments and by spatial continuity of HA. The implications of such multisystem continuity are protean, but may particularly explain commonly observed modes of discontinuous cancer spread through tissue planes, such as mesenteric tumor deposits in colon cancer and subcutaneous in-transit melanoma metastasis, and spread of infection (e.g. necrotizing fasciitis)
EMBASE:631877765
ISSN: 1530-0285
CID: 4472612