Targeting Progression in Pulmonary Fibrosis: An Overview of Underlying Mechanisms, Molecular Biomarkers, and Therapeutic Intervention

Interstitial lung diseases comprise a heterogenous range of diffuse lung disorders, potentially resulting in pulmonary fibrosis. While idiopathic pulmonary fibrosis has been recognized as the paradigm of a progressive fibrosing interstitial lung disease, other conditions with a progressive fibrosing phenotype characterized by a significant deterioration of the lung function may lead to a burden of significant symptoms, a reduced quality of life, and increased mortality, despite treatment. There is now evidence indicating that some common underlying biological mechanisms can be shared among different chronic fibrosing disorders; therefore, different biomarkers for disease-activity monitoring and prognostic assessment are under evaluation. Thus, understanding the common pathways that induce the progression of pulmonary fibrosis, comprehending the diversity of these diseases, and identifying new molecular markers and potential therapeutic targets remain highly crucial assignments. The purpose of this review is to examine the main pathological mechanisms regulating the progression of fibrosis in interstitial lung diseases and to provide an overview of potential biomarker and therapeutic options for patients with progressive pulmonary fibrosis.

Pulsed electrolysis - explained

Lately, there has been high interest in electrolysis under dynamic conditions, the so-called pulsed electrolysis. Different studies have shown that in pulsed electrolysis, selectivity towards certain products can be improved compared to steady-state operation. Many groups also demonstrated that the selectivity can be tuned by selection of pulsing profile, potential limits, as well as frequency of the change. To explain the origin of this improvement, some modeling studies have been performed. However, it seems that a theoretical framework to study this effect is still missing. In the present contribution, we suggest a theoretical framework of nonlinear frequency response analysis for the evaluation of the process improvement under pulsed electrolysis conditions. Of special interest is the DC component, which determines how much the mean output value under dynamic conditions will be different from the value under steady-state conditions. Therefore, the DC component can be considered as a measure of process improvement under dynamic conditions compared to the steady-state operation. We show that the DC component is directly dependent on nonlinearities of the electrochemical process and demonstrate how this DC component can be calculated theoretically as well as how it can be obtained from measurements.

A fast magnetic vector characterization method for quasi two-dimensional systems and heterostructures

The use of magnetic vector tomography/laminography has opened a 3D experimental window to access the magnetization at the nanoscale. These methods exploit the dependence of the magnetic contrast in transmission to recover its 3D configuration. However, hundreds of different angular projections are required leading to large measurement times. Here we present a fast method to dramatically reduce the experiment time specific for quasi two-dimensional magnetic systems. The algorithm uses the Beer-Lambert equation in the framework of X-ray transmission microscopy to obtain the 3D magnetic configuration of the sample. It has been demonstrated in permalloy microstructures, reconstructing the magnetization vector field with a reduced number of angular projections obtaining quantitative results. The throughput of the methodology is × 10-× 100 times faster than conventional magnetic vector tomography, making this characterization method of general interest for the community.

TSPO acts as an immune resistance gene involved in the T cell mediated immune control of glioblastoma

Glioblastoma (GB) IDH-wildtype is the most malignant primary brain tumor. It is particularly resistant to current immunotherapies. Translocator protein 18 kDa (TSPO) is upregulated in GB and correlates with malignancy and poor prognosis, but also with increased immune infiltration. Here, we studied the role of TSPO in the regulation of immune resistance of human GB cells. The role of TSPO in tumor immune resistance was experimentally determined in primary brain tumor initiating cells (BTICs) and cell lines through genetic manipulation of TSPO expression and subsequent cocultures with antigen specific cytotoxic T cells and autologous tumor-infiltrating T cells. Death inducing intrinsic and extrinsic apoptotic pathways affected by TSPO were investigated. TSPO-regulated genes mediating apoptosis resistance in BTICs were identified through gene expression analysis and subsequent functional analyses. TSPO transcription in primary GB cells correlated with CD8⁺ T cell infiltration, cytotoxic activity of T cell infiltrate, expression of TNFR and IFNGR and with the activity of their downstream signalling pathways, as well as with the expression of TRAIL receptors. Coculture of BTICs with tumor reactive cytotoxic T cells or with T cell-derived factors induced TSPO up-regulation through T cell derived TNFα and IFNγ. Silencing of TSPO sensitized BTICs against T cell-mediated cytotoxicity. TSPO selectively protected BTICs against TRAIL-induced apoptosis by regulating apoptosis pathways. TSPO also regulated the expression of multiple genes associated with resistance against apoptosis. We conclude that TSPO expression in GB is induced through T cell-derived cytokines TNFα and IFNγ and that TSPO expression protects GB cells against cytotoxic T cell attack through TRAIL. Our data thereby provide an indication that therapeutic targeting of TSPO may be a suitable approach to sensitize GB to immune cell-mediated cytotoxicity by circumventing tumor intrinsic TRAIL resistance.

Neoadjuvant plus adjuvant combined or sequenced vemurafenib, cobimetinib and atezolizumab in patients with high-risk, resectable BRAF-mutated and wild-type melanoma: NEO-TIM, a phase II randomized non-comparative study

Background

Following the increased survival of patients with metastatic melanoma thanks to immunotherapy and targeted therapy, neoadjuvant approaches are being investigated to address the unmet needs of unresponsive and intolerant patients. We aim to investigate the efficacy of neoadjuvant plus adjuvant combined or sequenced vemurafenib, cobimetinib and atezolizumab in patients with high-risk, resectable BRAF-mutated and wild-type melanoma.

Methods

The study is a phase II, open-label, randomized non-comparative trial in patients with stage IIIB/C/D surgically resectable, BRAF-mutated and wild-type melanoma, with three possible treatments: (1) vemurafenib 960 mg twice daily from day 1 to 42; (2) vemurafenib 720 mg twice daily from day 1 to 42; (3) cobimetinib 60 mg once daily from day 1 to 21 and from day 29 to 42; and (4) atezolizumab 840 mg for two cycles (day 22 and day 43).Patients will be randomized to three different arms: A) BRAF-mutated patients will receive over 6 weeks (1) + (3); B) BRAF-mutated patients will receive over 6 weeks (2) + (3) + (4); C) BRAF wild-type patients will receive over 6 weeks (3) + (4). All patients will also receive atezolizumab 1200 mg every 3 weeks for 17 cycles after surgery and after a second screening period (up to 6 weeks).

Discussion

Neoadjuvant therapy for regional metastases may improve operability and outcomes and facilitate the identification of biomarkers that can guide further lines of treatment. Patients with clinical stage III melanoma may especially benefit from neoadjuvant treatment, as the outcomes of surgery alone are very poor. It is expected that the combination of neoadjuvant and adjuvant treatment may reduce the incidence of relapse and improve survival.

Clinical trial registration

eudract.ema.europa.eu/protocol.htm, identifier 2018-004841-17.

Glycerol amendment enhances biosulfidogenesis in acid mine drainage-affected areas: An incubation column experiment

Microbial sulfate (SO₄²⁻) reduction in Acid Mine Drainage (AMD) environments can ameliorate the acidity and extreme metal concentrations by consumption of protons via the reduction of SO₄²⁻ to hydrogen sulfide (H₂S) and the concomitant precipitation of metals as metal sulfides. The activity of sulfate-reducing bacteria can be stimulated by the amendment of suitable organic carbon sources in these generally oligotrophic environments. Here, we used incubation columns (IC) as model systems to investigate the effect of glycerol amendment on the microbial community composition and its effect on the geochemistry of sediment and waters in AMD environments. The ICs were built with natural water and sediments from four distinct AMD-affected sites with different nutrient regimes: the oligotrophic Filón Centro and Guadiana acidic pit lakes, the Tintillo river (Huelva, Spain) and the eutrophic Brunita pit lake (Murcia, Spain). Physicochemical parameters were monitored during 18 months, and the microbial community composition was determined at the end of incubation through 16S rRNA gene amplicon sequencing. SEM-EDX analysis of sediments and suspended particulate matter was performed to investigate the microbially-induced mineral (neo)formation. Glycerol amendment strongly triggered biosulfidogenesis in all ICs, with pH increase and metal sulfide formation, but the effect was much more pronounced in the ICs from oligotrophic systems. Analysis of the microbial community composition at the end of the incubations showed that the SRB Desulfosporosinus was among the dominant taxa observed in all sulfidogenic columns, whereas the SRB Desulfurispora, Desulfovibrio and Acididesulfobacillus appeared to be more site-specific. Formation of Fe³⁺ and Al³⁺ (oxy)hydroxysulfates was observed during the initial phase of incubation together with increasing pH while formation of metal sulfides (predominantly, Zn, Fe and Cu sulfides) was observed after 1–5 months of incubation. Chemical analysis of the aqueous phase at the end of incubation showed almost complete removal of dissolved metals (Cu, Zn, Cd) in the amended ICs, while Fe and SO₄²⁻ increased towards the water-sediment interface, likely as a result of the reductive dissolution of Fe(III) minerals enhanced by Fe-reducing bacteria. The combined geochemical and microbiological analyses further establish the link between biosulfidogenesis and natural attenuation through metal sulfide formation and proton consumption.

Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients

Background

Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach to rapidly monitor and tackle emerging variants of concern (VOC) of the COVID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that might escape the immune protection conferred by vaccination strategies or previous virus exposure. It is also becoming clear now that efficient genomic surveillance would require monitoring of the host gene expression to identify prognostic biomarkers of treatment efficacy and disease progression. Here we propose an integrative workflow to both generate thousands of SARS-CoV-2 genome sequences per week and analyze host gene expression upon infection.

Methods

In this study we applied an integrated workflow for RNA extracted from nasal swabs to obtain in parallel the full genome of SARS-CoV-2 and transcriptome of host respiratory epithelium. The RNA extracted from each sample was reverse transcribed and the viral genome was specifically enriched through an amplicon-based approach. The very same RNA was then used for patient transcriptome analysis. Samples were collected in the Campania region, Italy, for viral genome sequencing. Patient transcriptome analysis was performed on about 700 samples divided into two cohorts of patients, depending on the viral variant detected (B.1 or delta).

Results

We sequenced over 20,000 viral genomes since the beginning of the pandemic, producing the highest number of sequences in Italy. We thus reconstructed the pandemic dynamics in the regional territory from March 2020 to December 2021. In addition, we have matured and applied novel proof-of-principle approaches to prioritize possible gain-of-function mutations by leveraging patients’ metadata and isolated patient-specific signatures of SARS-CoV-2 infection. This allowed us to (i) identify three new viral variants that specifically originated in the Campania region, (ii) map SARS-CoV-2 intrahost variability during long-term infections and in one case identify an increase in the number of mutations in the viral genome, and (iii) identify host gene expression signatures correlated with viral load in upper respiratory ways.

Conclusion

In conclusion, we have successfully generated an optimized and cost-effective strategy to monitor SARS-CoV-2 genetic variability, without the need of automation. Thus, our approach is suitable for any lab with a benchtop sequencer and a limited budget, allowing an integrated genomic surveillance on premises. Finally, we have also identified a gene expression signature defining SARS-CoV-2 infection in real-world patients’ upper respiratory ways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-022-01098-8.

POS0731 ASSOCIATION OF PATIENT-REPORTED OUTCOMES WITH TYPE I INTERFERON GENE SIGNATURE FROM THE INTERNATIONAL SYSTEMIC LUPUS ERYTHEMATOSUS PROSPECTIVE OBSERVATIONAL COHORT STUDY (SPOCS)

Background

The aim of the Systemic Lupus Erythematosus Prospective Observational Cohort Study (SPOCS) is to examine the disease course of patients with systemic lupus erythematosus (SLE) in relation to their type I interferon gene signature (IFNGS) status.1 IFNGS has been associated with SLE disease activity.2

Objectives

To identify associations between IFNGS status and patient-reported outcomes (PROs) among patients receiving clinical care while enrolled in SPOCS.

Methods

This noninterventional, international, prospective, observational cohort study included adult patients (≥18 years) with moderate to severe SLE receiving standard therapy. Short Form 36 Health Survey version 2 (SF-36; 0–100), Lupus Quality of Life (LupusQoL; 0–100) and Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F; 0–52) were assessed at baseline, 6 months, and 12 months. Higher scores indicate better outcomes. Analyses were stratified by high or low IFNGS status (4-gene test) at baseline.

Results

Of 827 patients, mean (standard deviation [SD]) age was 45.1 (14.0) years, 771 (93%) were female, 525 (63%) were IFNGS high, and 219 (26%) were IFNGS low. IFNGS-high patients were younger than IFNGS-low (mean [SD] 43.0 [13.7] vs 50.7 [12.9] years), had fewer comorbidities (83% vs 91%) and similar baseline disease activity (mean [SD]: SLE Disease Activity Index 2000, 9.8 [4.3] vs 9.2 [5.2]; Physician’s Global Assessment, both 1.5 [0.6]). At baseline, there were some differences in PROs between IFNGS-high and -low patients. At Month 12, changes in most domains did not meet the minimal clinically important difference (MCID). Slight improvement was observed only in selected domains in the IFNGS-high group. This group was younger and had fewer comorbidities at baseline. (Table 1, Figure 1).

Table 1.

PRO Scores at Baseline and Month 12 by IFNGS Status

BaselineMonth 12Change From BaselineMCID (≥)PROTotal (n=810)IFNGS HighIFNGS Low (n=219)Total (n=431)IFNGS HighIFNGS Low (n=147)TotalIFNGS HighIFNGS Low(n=525)(n=279)SF-36Physical Component Summary37.4 (10.5)38.3 (10.5)+35.2 (10.6)139.8 (10.8)41.7 (10.4)+35.7 (10.8)2.3 (7.6)3.0 (8.1)*0.6 (6.4)2.5Mental Component Summary43.2 (11.6)43.6 (11.7)42.7 (11.6)44.9 (11.2)45.9 (10.6)43.4 (11.5)0.9 (9.2)1.4 (9.6)-0.3 (8.4)2.5LupusQoLPhysical health56.4 (27.4)58.1 (27.0)+52.1 (27.7)60.5 (26.9)65.0 (25.3)+52.5 (27.7)2.6 (18.1)5.0 (19.2)*-1.4 (16.4)3.4Pain54.3 (30.3)55.7 (29.8)50.2 (30.8)61.4 (28.5)66.0 (26.5)+52.6 (29.1)5.4 (23.8)8.1 (25.2)0.7 (21.3)8.5Planning61.4 (32.2)63.7 (31.8)+57.0 (32.2)66.3 (29.6)70.8 (27.8)+58.5 (30.8)2.9 (24.4)4.2 (24.7)-1.0 (22.9)6.5Intimate relationships58.0 (34.8)61.2 (34.1)+50.9 (34.8)59.8 (33.9)65.6 (32.3)+50.6 (34.7)-0.6 (24.5)-0.7 (25.9)-0.8 (22.3)9.2Burden to others50.7 (32.6)50.7 (32.6)50.4 (33.5)56.4 (30.7)59.7 (29.5)51.8 (31.7)3.1 (25.4)5.6 (26.0)*0.1 (23.9)5.3Emotional health66.3 (25.6)66.1 (26.0)67.8 (24.8)71.1 (24.7)72.9 (23.8)69.2 (24.7)1.8 (19.4)3.1 (20.3)-0.5 (18.1)3.4Body image62.6 (29.4)61.0 (30.1)66.4 (28.3)68.2 (27.6)70.3 (27.4)65.1 (27.0)2.0 (23.9)*4.1 (24.3)*-0.4 (22.1)1.1Fatigue48.6 (27.8)49.9 (27.6)45.5 (28.2)53.7 (26.9)57.4 (26.2)+46.9 (25.7)2.1 (19.3)3.5 (20.0)-0.9 (18.7)3.9FACIT-F25.8 (13.4)26.9 (13.4)+23.4 (12.9)28.7 (13.2)31.1 (12.7)+24.6 (12.9)2.3 (9.6)3.2 (10.2)0.6 (8.5)4.0

Data are mean (SD). Asterisks (*) indicate changes from baseline ≥ MCID. +Comparison between high and low IFNGS status by Mann-Whitney U test (nominal p-value<0.01).

Data for n are patients per subgroup and do not reflect responses per PRO assessment.

Conclusion

In this cohort study, patients with moderate to severe SLE had poor health status, health-related quality of life, and fatigue. A clinically meaningful change was not met in most PROs, suggesting patients continue to have a high need for improved treatment options.

References

[1]Hammond ER. BMJ Open 2020;10:e036563.

[2]Dall’era MC. Ann Rheum Dis 2005;64:1692–7.

Acknowledgements

Writing assistance by Shelley Harris, PhD (Fishawack). This study was sponsored by AstraZeneca.

Disclosure of Interests

Martin Aringer Speakers bureau: AbbVie, AstraZeneca, BMS, Boehringer Ingelheim, Chugai, HEXAL, Lilly, MSD, Mylan, Novartis, Roche, Sanofi, UCB, Consultant of: AbbVie, AstraZeneca, BMS, Boehringer Ingelheim, Galapagos, GSK, Pfizer, Roche, Sanofi, Laurent Arnaud Speakers bureau: AstraZeneca, Consultant of: AstraZeneca, Grant/research support from: AstraZeneca, Christine Peschken Consultant of: AstraZeneca, GSK, Grant/research support from: AstraZeneca, Richard Furie Speakers bureau: AstraZeneca, Genentech, Consultant of: AstraZeneca, Grant/research support from: AstraZeneca, Eric F. Morand Speakers bureau: GSK, Novartis, Paid instructor for: AstraZeneca, Biogen, Eli Lilly, Consultant of: AstraZeneca, Biogen, Bristol Myers Squibb, Eli Lilly, EMD Serono, Genentech, GSK, Janssen, Servier, Grant/research support from: Abbvie, AstraZeneca, Bristol Myers Squibb, GSK, Janssen, Caroline Seo Shareholder of: AstraZeneca, Employee of: AstraZeneca, Eleni Rapsomaniki Employee of: AstraZeneca, Jonatan Hedberg Shareholder of: AstraZeneca, Employee of: AstraZeneca, Jacob Knagenhjelm Shareholder of: AstraZeneca, Employee of: AstraZeneca, Tina Grünfeld Eén Shareholder of: AstraZeneca, Employee of: AstraZeneca, Barnabas Desta Shareholder of: AstraZeneca, Employee of: AstraZeneca, Raj Tummala Shareholder of: AstraZeneca, Employee of: AstraZeneca, Alessandro Sorrentino Shareholder of: Galapagov, Abbott Laboratories, Gilead Sciences, Moderna, Employee of: Janssen, Sanofi, AstraZeneca, Heide Stirnadel-Farrant Shareholder of: AstraZeneca, GSK, Employee of: AstraZeneca

POS0733 DISCORDANCE BETWEEN PATIENT GLOBAL ASSESSMENT AND PHYSICIAN GLOBAL ASSESSMENT OF DISEASE ACTIVITY IN THE MODERATE TO SEVERE SYSTEMIC LUPUS ERYTHEMATOSUS PROSPECTIVE OBSERVATIONAL COHORT STUDY (SPOCS)

Background

Emphasis in clinical research and care has been placed on the need to include evaluations that reflect the perspectives of both patients and physicians.

Objectives

The goal of this study was to analyze patient and physician assessments and to determine characteristics associated with concordance and discordance of these assessments.

Methods

Baseline data of patients with moderate to severe SLE enrolled in the Systemic Lupus Erythematosus Prospective Observational Cohort Study (SPOCS)1 were analyzed. Physician’s Global Assessment (PGA) representing disease activity during the 4-week interval prior to baseline and Patient Global Assessment (PtGA) representing the impact of disease during a 1-month interval prior to baseline were independently scored on visual analogue scales (PGA 0-3; PtGA 0-100). Spearman’s rank (rho) was calculated to assess their correlation. A difference between PGA and PtGA scores ≥25 points defined discordance (after rescaling PGA to 0–100).2 Baseline characteristics associated with concordance and discordance were assessed.

Results

827 patients were included in this analysis. At baseline, the mean PGA score was 1.5 (SD 0.6, n=824), and the mean PtGA score was 51.1 (SD 25.5, n=790). The correlation between PGA and PtGA was low (rho=0.19, P<0.001, n=787) (Figure 1). PGA and PtGA scores were discordant in 301 (38%) of patients. Among those patients exceeding the threshold defining discordance, 152 (19%) had higher PGA scores than PtGA scores, and 149 (19%) had higher PtGA scores than PGA scores. The subgroup of PGA-higher discordant patients had higher mean SLEDAI-2K scores, greater serological activity, and more frequent type 1 interferon gene signature positivity, whereas PtGA-higher discordant patients were more likely to be using analgesics and/or anti-depressants, had higher mean BMI and were less likely to be employed (Table 1).

Table 1.

Characteristics associated with PGA and PtGA scoresa

Concordant (N=486)PGA higher (N=152)PtGA higher (N=149)P-value-1bP-value-2bAge, years45.5 (13.7)42.7 (14.4)46.4 (14.0)0.0220.043Race, White326 (71%)96 (66%)94 (69%)0.1920.360BMI, kg/m227.6 (7.2)25.6 (5.4)27.2 (6.4)0.0320.011Employed249 (51%)80 (53%)51 (34%)0.0010.001SLEDAI-2K total score10.0 (4.8)10.8 (5.1)8.2 (3.0)<0.001<0.001Positive ANA/anti-dsDNA436 (90%)143 (94%)127 (85%)0.0120.041Low Complement (C3 or C4)132 (46%)58 (60%)41 (43%)0.0140.026High IFNGS313 (71%)101 (78%)89 (64%)0.0140.049≥1 mild flare115 (24%)20 (13%)45 (30%)<0.0010.001≥1 moderate flare88 (18%)37 (24%)23 (16%)0.0570.120≥1 severe flare39 (8%)11 (7%)15 (10%)0.3720.628OCS daily dose0.0520.129No OCS214 (44%)57 (38%)62 (42%)>0–7.5 mg139 (29%)38 (25%)52 (35%)>7.5–15 mg75 (15%)37 (25%)18 (12%)>15 mg57 (12%)19 (13%)17 (11%)Immunosuppressants271 (56%)80 (53%)75 (50%)0.6900.467Biologics106 (22%)25 (16%)19 (13%)0.3640.032Analgesics152 (31%)22 (14%)46 (31%)<0.001<0.001Antidepressants123 (25%)31 (20%)52 (35%)0.0050.013

aMean (SD) for continuous, n (%) for nominal variables. Missing data was <10% of patients for the variables displayed. Denominators exclude missing data. bP-value-1 compares PGA higher vs PtGA higher. P-value-2 compares all 3 groups. Based on the chi-squared test for categorical variables and t-test or ANOVA for continuous variables.

IFNGS, type 1 interferon gene signature; OCS, oral corticosteroid; PGA, physician global assessment; PtGA, patient global assessment

Conclusion

Low correlation between PGA and PtGA suggests both should be used to acquire a broad perspective of the impact of disease on the overall health of patients. Different baseline characteristics were associated with the PGA-higher compared to the PtGA-higher discordant subgroups.

References

[1]Hammond ER, et al. BMJ Open. 2020;10:e036563.

[2]Challa DNV, et al. Rheumatol Ther. 2017;4:201–8.

Acknowledgements

Editing assistance by Rebecca S. Jones, PhD (Fishawack). This study was sponsored by AstraZeneca.

Disclosure of Interests

Laurent Arnaud Speakers bureau: AstraZeneca, Consultant of: AstraZeneca, Grant/research support from: AstraZeneca, Richard Furie Speakers bureau: AstraZeneca, Genentech, Consultant of: AstraZeneca, Grant/research support from: AstraZeneca, Eric F. Morand Speakers bureau: GSK, Novartis, Paid instructor for: AstraZeneca, Biogen, Eli Lilly, Consultant of: AstraZeneca, Biogen, Bristol Myers Squibb, Eli Lilly, EMD Serono, Genentech, GSK, Janssen, Servier, Grant/research support from: Abbvie, AstraZeneca, Bristol Myers Squibb, GSK, Janssen, Christine Peschken Consultant of: AstraZeneca, GSK, Grant/research support from: AstraZeneca, Martin Aringer Speakers bureau: AbbVie, AstraZeneca, BMS, Boehringer Ingelheim, Chugai, HEXAL, Lilly, MSD, Mylan, Novartis, Roche, Sanofi, UCB, Consultant of: AbbVie, AstraZeneca, BMS, Boehringer Ingelheim, Galapagos, GSK, Pfizer, Roche, Sanofi, Eleni Rapsomaniki Employee of: AstraZeneca, Jonatan Hedberg Shareholder of: AstraZeneca, Employee of: AstraZeneca, Jacob Knagenhjelm Shareholder of: AstraZeneca, Employee of: AstraZeneca, Caroline Seo Shareholder of: AstraZeneca, Employee of: AstraZeneca, Tina Grünfeld Eén Shareholder of: AstraZeneca, Employee of: AstraZeneca, Barnabas Desta Shareholder of: AstraZeneca, Employee of: AstraZeneca, Alessandro Sorrentino Shareholder of: Galapagov, Abbott LAboratories, Gilead Sciences, Moderna, Employee of: Janssen, Sanofi, AstraZeneca, Raj Tummala Shareholder of: AstraZeneca, Employee of: AstraZeneca, Heide Stirnadel-Farrant Shareholder of: AstraZeneca, GSK, Employee of: AstraZeneca

Salt-inducible kinase 3 protects tumor cells from cytotoxic T-cell attack by promoting TNF-induced NF-κB activation

BACKGROUND

Cancer immunotherapeutic strategies showed unprecedented results in the clinic. However, many patients do not respond to immuno-oncological treatments due to the occurrence of a plethora of immunological obstacles, including tumor intrinsic mechanisms of resistance to cytotoxic T-cell (TC) attack. Thus, a deeper understanding of these mechanisms is needed to develop successful immunotherapies.

METHODS

To identify novel genes that protect tumor cells from effective TC-mediated cytotoxicity, we performed a genetic screening in pancreatic cancer cells challenged with tumor-infiltrating lymphocytes and antigen-specific TCs.

RESULTS

The screening revealed 108 potential genes that protected tumor cells from TC attack. Among them, salt-inducible kinase 3 (SIK3) was one of the strongest hits identified in the screening. Both genetic and pharmacological inhibitions of SIK3 in tumor cells dramatically increased TC-mediated cytotoxicity in several in vitro coculture models, using different sources of tumor and TCs. Consistently, adoptive TC transfer of TILs led to tumor growth inhibition of SIK3-depleted cancer cells in vivo. Mechanistic analysis revealed that SIK3 rendered tumor cells susceptible to tumor necrosis factor (TNF) secreted by tumor-activated TCs. SIK3 promoted nuclear factor kappa B (NF-κB) nuclear translocation and inhibited caspase-8 and caspase-9 after TNF stimulation. Chromatin accessibility and transcriptome analyses showed that SIK3 knockdown profoundly impaired the expression of prosurvival genes under the TNF-NF-κB axis. TNF stimulation led to SIK3-dependent phosphorylation of the NF-κB upstream regulators inhibitory-κB kinase and NF-kappa-B inhibitor alpha on the one side, and to inhibition of histone deacetylase 4 on the other side, thus sustaining NF-κB activation and nuclear stabilization. A SIK3-dependent gene signature of TNF-mediated NF-κB activation was found in a majority of pancreatic cancers where it correlated with increased cytotoxic TC activity and poor prognosis.

CONCLUSION

Our data reveal an abundant molecular mechanism that protects tumor cells from cytotoxic TC attack and demonstrate that pharmacological inhibition of this pathway is feasible.

Exosomal CD73 from serum of patients with melanoma suppresses lymphocyte functions and is associated with therapy resistance to anti-PD-1 agents

BACKGROUND

CD73 is an ectonucleotidase producing the immunosuppressor mediator adenosine. Elevated levels of circulating CD73 in patients with cancer have been associated with disease progression and poor response to immunotherapy. Immunosuppressive pathways associated with exosomes can affect T-cell function and the therapeutic efficacy of anti-programmed cell-death protein 1 (anti-PD-1) therapy. Here, we conducted a retrospective pilot study to evaluate levels of exosomal CD73 before and early during treatment with anti-PD-1 agents in patients with melanoma and its potential contribution to affect T-cell functions and to influence the clinical outcomes of anti-PD-1 monotherapy.

METHODS

Exosomes were isolated by mini size exclusion chromatography from serum of patients with melanoma (n=41) receiving nivolumab or pembrolizumab monotherapy. Expression of CD73 and programmed death-ligand 1 (PD-L1) were evaluated on exosomes enriched for CD63 by on-bead flow cytometry. The CD73 AMPase activity was evaluated by mass spectrometry, also in the presence of selective inhibitors of CD73. Interferon (IFN)-γ production and granzyme B expression were measured in CD3/28 activated T cells incubated with exosomes in presence of the CD73 substrate AMP. Levels of CD73 and PD-L1 on exosomes were correlated with therapy response. Exosomes isolated from healthy subjects were used as control.

RESULTS

Isolated exosomes carried CD73 on their surface, which is enzymatically active in producing adenosine. Incubation of exosomes with CD3/28 activated T cells in the presence of AMP resulted in a significant reduction of IFN-γ release, which was reversed by the CD73 inhibitor APCP or by the selective A2A adenosine receptor antagonist ZM241385. Expression levels of exosomal CD73 from serum of patients with melanoma were not significantly different from those in healthy subjects. Early on-treatment, expression levels of both CD73 and PD-L1 on exosomes isolated from patients receiving pembrolizumab or nivolumab monotherapy were significantly increased compared with baseline. Early during therapy exosomal PD-L1 increased in responders, while exosomal CD73 resulted significantly increased in non-responders.

CONCLUSIONS

CD73 expressed on exosomes from serum of patients with melanoma produces adenosine and contributes to suppress T-cell functions. Early on-treatment, elevated expression levels of exosomal CD73 might affect the response to anti-PD-1 agents in patients with melanoma who failed to respond to therapy.

T cell-mediated elimination of cancer cells by blocking CEACAM6–CEACAM1 interaction

Carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6), a cell surface receptor, is expressed on normal epithelial tissue and highly expressed in cancers of high unmet medical need, such as non-small cell lung, pancreatic, and colorectal cancer. CEACAM receptors undergo homo- and heterophilic interactions thereby regulating normal tissue homeostasis and angiogenesis, and in cancer, tumor invasion and metastasis. CEACAM6 expression on malignant plasma cells inhibits antitumor activity of T cells, and we hypothesize a similar function on epithelial cancer cells.

The interactions between CEACAM6 and its suggested partner CEACAM1 on T cells were studied. A humanized CEACAM6-blocking antibody, BAY 1834942, was developed and characterized for its immunomodulating effects in co-culture experiments with T cells and solid cancer cells and in comparison to antibodies targeting the immune checkpoints programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), and T cell immunoglobulin mucin-3 (TIM-3).

The immunosuppressive activity of CEACAM6 was mediated by binding to CEACAM1 expressed by activated tumor-specific T cells. BAY 1834942 increased cytokine secretion by T cells and T cell-mediated killing of cancer cells. The in vitro efficacy of BAY 1834942 correlated with the degree of CEACAM6 expression on cancer cells, suggesting potential in guiding patient selection. BAY 1834942 was equally or more efficacious compared to blockade of PD-L1, and at least an additive efficacy was observed in combination with anti-PD-1 or anti-TIM-3 antibodies, suggesting an efficacy independent of the PD-1/PD-L1 axis.

In summary, CEACAM6 blockade by BAY 1834942 reactivates the antitumor response of T cells. This warrants clinical evaluation.

308 Transcriptomic analysis of melanoma patients in adjuvant setting treated with anti PD1 therapy: real life study

Background

Adjuvant treatment of melanoma patients with immune-checkpoint inhibition (ICI) significantly improved relapse-free survival (RFS).1 In the phase 3 keynote-054 trial showed that pembrolizumab (anti-PD1) administration in adjuvant setting provided a longer RFS (59,8%) than the placebo group (41,4%) at a 3.5-year median follow-up.2 Moreover, 4 years RFS results from the phase 3 checkmate 238 trial, showed a superior efficacy of nivolumab versus ipilimumab in patients with resected AJCC-7 stage III or IV melanoma. RFS rate was of 58% in the nivolumab arm and 45% in the ipilimumab arm.3 Although treatment with ICIs has improved the RFS of melanoma patients in adjuvant setting, there is still a large proportion of patients who do not respond to the treatment and then relapse. The aim of this study was to investigate the molecular mechanisms underlying resistance to anti-PD1 treatment in the adjuvant setting.

Methods

From December 2018 to July 2020, n. 121 melanoma patients in stage III or IV NED were treated with anti-PD1s as adjuvant (minimum follow up of 12 months, range 12–30 months). These patients received nivolumab (n=95) or pembrolizumab (n=26). Distant and local metastases was observed in 33 (27%) and 7 (6%) patients, respectively (patients baseline characteristics are listed in table1). Gene expression profiles, using NanoString IO 360 panel, were performed from peripheral blood mononuclear cell (PBMCs), collected retrospectively, from n.73 patients (of which n.26 had relapse). All patients have appropriately signed informed consent. Statistical analysis was performed via Bonferroni correction, P< 0.05 was considered statistically significant for median stratification.

Results

At a minimum follow-up of 12 months, the 12-month rate of Relapse-free survival was 72%, confirming the data reported by checkmate 238 trial. In the transcriptomic analysis we observed that in patients with local-regional metastases there was a higher expression of ITGA2 (p<0.05), a gene that promotes malignant tumor aggression by up-regulating PD-L1 expression through STAT3 pathway and the downregulation of DUSP1 (p<0.05) that is linked in promotion of angiogenesis, invasion and metastasis. Moreover, in male group we found a higher expression of HLA-DQB1 and HLA-DQA1 which belonged to HLA class II beta chains.

Abstract 308 Table 1

Conclusions

In this preliminary report we found that RFS 1-yr rate is similar to checkmate 238 study, and that patients with local metastasis have a higher expression of genes related to promote PDL1 levels. Further investigations are needed to get additional information.

Acknowledgements

The study was supported by the Institutional Project ”Ricerca Corrente” of Istituto Nazionale Tumori IRCCS Fondazione ”G. Pascale” of Napoli, Italy.

References

Weber J, Mandala M, Del Vecchio M, et al, CheckMate 238 Collaborators. Adjuvant nivolumab versus ipilimumab in resected stage III or IV melanoma. N Engl J Med 2017 November 9;377(19):1824–1835.

Eggermont AMM, Blank CU, Mandalà M, et al. EORTC melanoma group. Adjuvant pembrolizumab versus placebo in resected stage III melanoma (EORTC 1325-MG/KEYNOTE-054): distant metastasis-free survival results from a double-blind, randomised, controlled, phase 3 trial. Lancet Oncol 2021 May;22(5):643–654.

Ascierto PA, Del Vecchio M, Mandalá M, et al. Adjuvant nivolumab versus ipilimumab in resected stage IIIB-C and stage IV melanoma (CheckMate 238): 4-year results from a multicentre, double-blind, randomised, controlled, phase 3 trial. Lancet Oncol 2020 November;21(11):1465–1477.

Ethics Approval

The study was approved by internal ethics board of the Istituto Nazionale Tumori IRCCS Fondazione ”G. Pascale” of Napoli Italy, approval number of registry 33/17 OSS.

Consent

Written informed consent was obtained from the patient for publication of this abstract and any accompanying images. A copy of the written consent is available for review by the Editor of this journal.

Beta-blocker/ACE inhibitor therapy differentially impacts the steady state signaling landscape of failing and non-failing hearts

Background

The molecular underpinnings of heart failure with reduced ejection fraction (HFrEF) involves a complex remodeling of the contractile, metabolic and electrical functions. Current pharmacotherapy for patients presenting HFrEF includes combination of angiotensin-converting enzyme inhibitors (ACEi) and β-adrenergic receptor blockers (β-AR blockers). Yet, a knowledge gap exists regarding the molecular changes accompanying such treatment.

Purpose

The present study takes an omics approach to study protein and phosphorylation signaling derangement in HFrEF and to define the global changes resulting from treatment with β-AR blocker (metoprolol) and ACE inhibitor (enalapril) in control- and HFrEF hearts.

Methods and results

For induction of HFrEF, a tight and permanent ligature was applied to constrict the transverse aorta in male C57BL6 mice. Eight weeks post-surgery, an osmotic pump was implanted delivering either vehicle or treatment (enalapril, ACE inhibitor, and metoprolol, β-AR blocker) for a two week period. The proteome- and phosphoproteome of left ventricular tissue was resolved using high-resolution liquid chromatography-mass spectrometry. The resulting dataset covered 6,004 proteins and 14,967 phosphorylation events. HFrEF was characterized by profound downregulation of mitochondrial proteins coupled with derangement of β-adrenergic and pyruvate dehydrogenase signaling. Upon treatment, phosphorylation changes consequent to HFrEF were reversed, including a reversal of Pdhk4 activity. In controls, treatment mainly led to downregulation of canonical PKA signaling. Overall, the signaling response elicited by treatment was profoundly different for failing than for control hearts.

Conclusions

We used state-of-the-art proteomics and phosphoproteomics approaches to analyze changes in protein abundance and phosphorylation state of the left ventricle resulting from combination therapy with a β-AR blocker and an ACE inhibitor in failing and non-failing hearts. Our observation of divergent signaling outcomes depending on the disease state of the heart underscores the importance of evaluating drug effects within the context of the specific conditions present in the recipient heart.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): The Danish Council for independent ResearchLundbeck FoundationFondation Leducq Transatlantic Network of Excellence

Novel insights into the disease transcriptome of human diabetic glomeruli and tubulointerstitium

BACKGROUND

Diabetic nephropathy (DN) is the most common cause of end-stage renal disease, affecting ∼30% of the rapidly growing diabetic population, and strongly associated with cardiovascular risk. Despite this, the molecular mechanisms of disease remain unknown.

METHODS

RNA sequencing (RNAseq) was performed on paired, micro-dissected glomerular and tubulointerstitial tissue from patients diagnosed with DN [n = 19, 15 males, median (range) age: 61 (30-85) years, chronic kidney disease stages 1-4] and living kidney donors [n = 20, 12 males, median (range) age: 56 (30-70) years].

RESULTS

Principal component analysis showed a clear separation between glomeruli and tubulointerstitium transcriptomes. Differential expression analysis identified 1550 and 4530 differentially expressed genes, respectively (adjusted P < 0.01). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses highlighted activation of inflammation and extracellular matrix (ECM) organization pathways in glomeruli, and immune and apoptosis pathways in tubulointerstitium of DN patients. Specific gene modules were associated with renal function in weighted gene co-expression network analysis. Increased messengerRNA (mRNA) expression of renal damage markers lipocalin 2 (LCN) and hepatitis A virus cellular receptor1 (HAVCR1) in the tubulointerstitial fraction was observed alongside higher urinary concentrations of the corresponding proteins neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule-1 (KIM-1) in DN patients.

CONCLUSIONS

Here we present the first RNAseq experiment performed on paired glomerular and tubulointerstitial samples from DN patients. We show that prominent disease-specific changes occur in both compartments, including relevant cellular processes such as reorganization of ECM and inflammation (glomeruli) as well as apoptosis (tubulointerstitium). The results emphasize the potential of utilizing high-throughput transcriptomics to decipher disease pathways and treatment targets in this high-risk patient population.

The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles

T lymphocyte activation requires the formation of immune synapses (IS) with antigen-presenting cells. The dynamics of membrane receptors, signaling scaffolds, microfilaments, and microtubules at the IS determine the potency of T cell activation and subsequent immune response. Here, we show that the cytosolic chaperonin CCT (chaperonin-containing TCP1) controls the changes in reciprocal orientation of the centrioles and polarization of the tubulin dynamics induced by T cell receptor in T lymphocytes forming an IS. CCT also controls the mitochondrial ultrastructure and the metabolic status of T cells, regulating the de novo synthesis of tubulin as well as posttranslational modifications (poly-glutamylation, acetylation, Δ1 and Δ2) of αβ-tubulin heterodimers, fine-tuning tubulin dynamics. These changes ultimately determine the function and organization of the centrioles, as shown by three-dimensional reconstruction of resting and stimulated primary T cells using cryo-soft x-ray tomography. Through this mechanism, CCT governs T cell activation and polarity.

Abstract 5529: Proteomic profiling of FFPE tumors samples from melanoma subjects treated with anti-PD-1 immunotherapy identifies proteins associated with response to treatment

Background Immune checkpoint inhibitors (ICI) have greatly improved the treatment options for patients with advanced stage melanoma, with improved clinical responses and overall survival compared to standard systemic therapies. However, a large percentage of melanoma patients do not respond to ICIs, highlighting the need for a greater understanding of the tumor environment and host immune response. Here, we apply unbiased discovery proteomics, based on label-free data independent acquisition (DIA) mass spectrometry, to deeply characterize global tumor proteomes to identify proteins and pathways that are associated with pre-treatment response to anti-PD-1 immunotherapy.

Methods Unbiased, data-independent acquisition (DIA) mass spectrometry was used to analyze formalin fixed paraffin imbedded (FFPE) tumor tissue samples from subjects with Stage III-IV melanoma which were resected prior to initiation of first-line anti-PD-1 ICI therapy. The selected samples represent two distinct clinical subgroups; those who received clinical benefit, with a stable disease or better (SD, PR and CR, n = 13), and those with no clinical benefit (PD, n = 9). Samples were prepared for mass spectrometry using standard procedures. All samples were analyzed using 4-hour gradients on a LC-MS/MS setup operated in DIA mode. Data was extracted using Spectronaut (Biognosys) with a sample specific spectral library which was combined with a large human tissue resource library. Statistical analysis was conducted to identify proteins that are up- or down-regulated with respect to benefit group. Pathway analysis was also conducted to highlight dysregulated biological functions and pathways.

Results In analysis with 2-hour gradients, &gt;7,500 proteins were quantified across all samples. Univariate statistical testing between groups identified 254 proteins are dysregulated (120 up- and 134 down-regulated) in subjects who received clinical benefit, of which a subset of 25 proteins was identified that describe the variance between the two sample groups. When annotated to their sub-cellular location, all up-regulated species are identified as mitochondrial proteins, indicating an enhanced metabolic environment in the responder subgroup. Additionally, GM2A and PLEKHA5 were strong diagnostic predictors of responder status. This updated analysis, conducted with a deeper level of characterization, will focus on additional metabolic pathways as well as known proteins associated with metabolic resistance (e.g. CD39 and CD73) to more fully characterize the tumor metabolic environment.

Conclusions Global profiling of the tumor proteome provides a unique characterization of melanoma tumor biology. A pathway level analysis shows increased metabolic processes may underly some of the differences in benefit related to ICI therapy.

Citation Format: Nicholas Dupuis, Jakob Vowinckel, Domenico Mallardo, Mariaelena Capone, Madonna Gabriele, Antonio Sorrentino, Vito Vanella, Daniel Heinzmann, Paolo Ascierto. Proteomic profiling of FFPE tumors samples from melanoma subjects treated with anti-PD-1 immunotherapy identifies proteins associated with response to treatment [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5529.

CAMK1D Triggers Immune Resistance of Human Tumor Cells Refractory to Anti-PD-L1 Treatment

The success of cancer immunotherapy is limited by resistance to immune checkpoint blockade. We therefore conducted a genetic screen to identify genes that mediated resistance against CTLs in anti-PD-L1 treatment-refractory human tumors. Using PD-L1-positive multiple myeloma cells cocultured with tumor-reactive bone marrow-infiltrating CTL as a model, we identified calcium/calmodulin-dependent protein kinase 1D (CAMK1D) as a key modulator of tumor-intrinsic immune resistance. CAMK1D was coexpressed with PD-L1 in anti-PD-L1/PD-1 treatment-refractory cancer types and correlated with poor prognosis in these tumors. CAMK1D was activated by CTL through Fas-receptor stimulation, which led to CAMK1D binding to and phosphorylating caspase-3, -6, and -7, inhibiting their activation and function. Consistently, CAMK1D mediated immune resistance of murine colorectal cancer cells in vivo The pharmacologic inhibition of CAMK1D, on the other hand, restored the sensitivity toward Fas-ligand treatment in multiple myeloma and uveal melanoma cells in vitro Thus, rapid inhibition of the terminal apoptotic cascade by CAMK1D expressed in anti-PD-L1-refractory tumors via T-cell recognition may have contributed to tumor immune resistance.

A Guide to Concentration Alternating Frequency Response Analysis of Fuel Cells

An experimental setup capable of generating a periodic concentration input perturbation of oxygen was used to perform concentration-alternating frequency response analysis (cFRA) on proton-exchange membrane (PEM) fuel cells. During cFRA experiments, the modulated concentration feed was sent to the cathode of the cell at different frequencies. The electric response, which can be cell potential or current depending on the control applied on the cell, was registered in order to formulate a frequency response transfer function. Unlike traditional electrochemical impedance spectroscopy (EIS), the novel cFRA methodology makes it possible to separate the contribution of different mass transport phenomena from the kinetic charge transfer processes in the frequency response spectra of the cell. Moreover, cFRA is able to differentiate between varying humidification states of the cathode. In this protocol, the focus is on the detailed description of the procedure to perform cFRA experiments. The most critical steps of the measurements and future improvements to the technique are discussed.

Increased PD-L1 expression in radioresistant HNSCC cell lines after irradiation affects cell proliferation due to inactivation of GSK-3beta

At present, targeting PD-1/PD-L1 axis for immune checkpoint inhibition has improved treatment of various tumor entities, including head and neck squamous cell carcinoma (HNSCC). However, one part of the patient cohort still shows little improvement or even hyperprogression. We established three radioresistant (RR) and three radiosensitive (RS) HNSCC cell lines. RR cells showed prolonged survival as well as delayed and diminished apoptosis after irradiation with vimentin expression but no E-cadherin expression, whereas RS cell lines died early and exhibited early apoptosis after irradiation and high vimentin expression. Here, we present results demonstrating differential basal PD-L1 gene and protein expression in RR and RS HNSCC cell lines. Moreover, we observed a radiation dose dependent increase of total PD-L1 protein expression in RR cell lines up to 96h after irradiation compared to non-irradiated (non-IRR) cells. We found a significant GSK-3beta phosphorylation, resulting in an inactivation, after irradiation of RR cell lines. Co-immunoprecipitation experiments revealed decreased interaction of GSK-3beta with PD-L1 in non-IRR compared to irradiated (IRR) RR cells leading to PD-L1 stabilization in RR cells. PD-L1 knockdown in RR cells showed a strong decrease in cell survival. In summary, our results suggest an irradiation dependent increase in basal PD-L1 expression in RR HNSCC cell lines via GSK-3beta inactivation.

Characterization of sustainable polyhydroxyls, produced from bio-based feedstock, and polyurethane and copolymer urethane-amide foams

This manuscript presents data related to the research article entitled "Synthesis and characterization of sustainable polyurethane foams based on polyhydroxyls with different terminal groups" (DOI: 10.1016/j.polymer.2018.06.077) [1]. We provide Supplementary data on the chemical properties, in terms of FTIR characterization, of polyhydroxyls produced starting from bio-based feedstock (biosuccinic acid and 1,4 butandiol) and thermal properties (glass transition temperature-Tg and thermal degradation behavior) of polyurethane and copolymer urethane-amide foams manufactured from the aforementioned polyhydroxyls. The FTIR characterization elucidates the chemical structure of polyhydroxyls and allows to make some hypothesis on their reaction routes with the isocyanate molecules. The thermal characterization revealed that the addition of bio-based polyhydroxyls to the sample formulations improves both the glass transition and degradation temperature of the foams. These foamed products exhibit potential performances to be applied as a substitute for conventional polyurethane foams.

Human PRDM2: Structure, function and pathophysiology

PRDM2/RIZ is a member of a superfamily of histone/protein methyltransferases (PRDMs), which are characterized by the conserved N-terminal PR domain, with methyltransferase activity and zinc finger arrays at the C-terminus. Similar to other family members, two main protein types, known as RIZ1 and RIZ2, are produced from the PRDM2 locus differing by the presence or absence of the PR domain. The imbalance in their respective amounts may be an important cause of malignancy, with the PR-positive isoform commonly lost or downregulated and the PR-negative isoform always being present at higher levels in cancer cells. Interestingly, the RIZ1 isoform also represents an important target of estradiol action downstream of the interaction with hormone receptor. Furthermore, the imbalance between the two products could also be a molecular basis for other human diseases. Thus, understanding the molecular mechanisms underlying PRDM2 function could be useful in the pathophysiological context, with a potential to exploit this information in clinical practice.

Effect of miR-204&211 and RUNX2 control on the fate of human mesenchymal stromal cells

MiR-204 and 211 enforced expression in murine mesenchymal stromal cells (MSCs) has been shown to induce adipogenesis and impair osteogenesis, through RUNX2 down-modulation. This mechanism has been suggested to play a role in osteoporosis associated with obesity. However, two further fundamental MSC functions, chondrogenesis and hematopoietic supporting activity, have not yet been explored. To this end, we transduced, by a lenti-viral vector, miR-204 and 211 in a model primary human MSC line, opportunely chosen among our MSC collection for displaying all properties of canonical bone marrow MSCs, except adipogenesis. Enforced expression of miR-204&211 in these cells, rescued adipogenesis, and inhibited osteogenesis, as previously reported in murine MSCs, but, surprisingly, also damaged cartilage formation and hematopoietic supporting activity, which were never explored before. RUNX2 has been previously indicated as the target of miR-204&211, whose down modulation is responsible for the switch from osteogenesis to adipogenesis. However, the additional disruption of chondrogenesis and hematopoietic supporting activity, which we report here, might depend on diverse miR-204&211 targets. To investigate this hypothesis, permanent RUNX2 knock-down was performed. Sh-RUNX2 fully reproduced the phenotypes induced by miR-204&211, confirming that RUNX2 down modulation is the major event leading to the reported functional modification on our MSCs. It seems thus apparent that RUNX2, a recognized master gene for osteogenesis, might rule all four MSC commitment and differentiation processes. Hence, the formerly reported role of miR204&211 and RUNX2 in osteoporosis and obesity, coupled with our novel observation showing inhibition of cartilage differentiation and hematopoietic support, strikingly resemble the clinical traits of metabolic syndrome, where osteoarthritis, osteoporosis, anaemia and obesity occur together. Our observations, corroborating and extending previous observations, suggest that miR-204&211-RUNX2 axis in human MSCs is possibly involved in the pathogenesis of this rapidly growing disease in industrialized countries, for possible therapeutic intervention to regenerate former homeostasis.

Differences between graphene and graphene oxide in gelatin based systems for transient biodegradable energy storage applications

A comparison between graphene flakes and graphene oxide as filler in gelatin based systems for low-cost transient biodegradable energy storage applications has been carried out. The two bio-composites have been prepared and characterized by rheological measurements, cyclic voltammetry measurements, chronopotentiometry measurements and impedance spectroscopy. Differences in dielectric and mechanical properties have been correlated to the different structural organizations determinate by the hydrophobic/hydrophilic character of the used filler. In particular, the addition of the graphene oxide to the gelatin causes an increase in the elastic modulus with a parallel increase in the mechanical stability with time as compared to the composites obtained by adding graphene. Conversely, the surface capacitance is slightly increased by the graphene oxide addition compared to the pure gelatin sample. On the other hand, the introduction of the graphene flakes into the gelatin leads to a marked increase of the dielectric properties of the resulting bio-composite.

Light irradiation tuning of surface wettability, optical, and electric properties of graphene oxide thin films

In this work the preparation of flexible polymeric films with controlled electrical conductivity, light transmission and surface wettability is reported. A drop casted graphene oxide thin film is photo-reduced at different levels by UV light or laser irradiation. Optical microscopy, IR spectroscopy, electrical characterization, Raman spectroscopy and static water contact angle measurements are used in order to characterize the effects of the various reduction methods. Correlations between the optical, electrical and structural properties are reported and compared to previous literature results. These correlations provide a useful tool for independently tuning the properties of these films for specific applications.

Abstract 2339: RNAi discovery platform to identify novel genes that prevent immune surveillance in pancreatic ductal adenocarcinoma (PDAC)

BACKGROUND: Being one of the most treatment-resistant cancer types, pancreatic ductal adenocarcinoma (PDAC) is characterized by its ability to escape immune surveillance by developing many immunological obstacles. These include a plethora of mechanisms that either dampen immune cell functionality, or foster tumor cell resistance towards immune attack. Immunotherapeutic strategies, such as immune checkpoint blockade, have proven clinical success in many cancer entities, but showed little clinical benefit in PDAC patients, emphasizing the need to identify more key players that could radically improve immunotherapy.

AIM: We aim to systematically identify the whole arsenal of tumor-associated immune modulators by performing a high-throughput RNAi screen and subsequently validate novel therapeutic targets, whose blockade could potentially enhance anti-tumor immune response in PDAC patients.

METHODS: We generated a luciferase-expressing PANC-1 cell line and knocked down 2514 genes using a siRNA library. Our library includes G-protein coupled receptors, protein kinases and 1117 surface proteins. We co-cultured HLA-A201+ matched tumor infiltrating lymphocytes (TILs) derived from a PDAC patient with the transfected tumor cells. We then measured the remaining luciferase intensity of the tumor cells as an estimation of TIL-mediated cytotoxicity. In order to exclude genes whose knock-down affected cell viability per se, we cultivated tumor cells with the siRNA library in the absence of TILs.

RESULTS: We identified 155 candidate genes whose knock-down enhances TIL-mediated killing more efficiently than PD-L1 down-regulation. 35% of these genes are surface molecules and are most likely to directly mediate tumor immune evasion. Beside novel undescribed genes, our list contains well characterized immune modulators, supporting the reliability of our approach. Of note 13 of our hits were also found in a related melanoma screen and might play a role in the regulation of immune surveillance of different tumor entities. Among our candidates, 4 hits were chosen for further validation. We confirmed the expression of our selected candidates in several tumor cell lines and assessed the siRNA on-target effect using several non-overlapping siRNA sequences targeting the same hit. Transfection of PANC-1 with different siRNA sequences showed knock-down of the target gene as assessed via qPCR. Additionally we observed increased T-cell mediated killing as measured via luciferase-based killing assay and Chromium release assay.

CONCLUSION: We set up a robust and systematic method to unravel novel key players of pancreatic cancer immune surveillance. Further functional validation of our candidate genes will prove their potential to be used as relevant therapeutic targets in the clinic.

Citation Format: Antonio Sorrentino, Ayse Nur Menevse, Tillmann Michels, Nisit Khandelwal, Marco Breinig, Isabel Poschke, Valentina Volpin, Sabrina Wagner, Rienk Offringa, Michael Boutros, Philipp Beckhove. RNAi discovery platform to identify novel genes that prevent immune surveillance in pancreatic ductal adenocarcinoma (PDAC). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2339.

Optical pseudomotors for soft x-ray beamlines

Optical elements of soft x-ray beamlines usually have motorized translations and rotations that allow for the fine alignment of the beamline. This is to steer the photon beam at some positions and to correct the focus on slits or on sample. Generally, each degree of freedom of a mirror induces a change of several parameters of the beam. Inversely, several motions are required to actuate on a single optical parameter, keeping the others unchanged. We define optical pseudomotors as combinations of physical motions of the optical elements of a beamline, which allow modifying one optical parameter without affecting the others. We describe a method to obtain analytic relationships between physical motions of mirrors and the corresponding variations of the beam parameters. This method has been implemented and tested at two beamlines at ALBA, where it is used to control the focus of the photon beam and its position independently.

Abstract C88: Genomics, advocacy, and emerging therapeutics to address triple-negative breast cancer (TNBC) outcome disparities

Background: Collaborative team science provides a starting point for comprehensive change, and advocates have a unique and important role developing and engaging in transdisciplinary collaboratives that focus on new questions and new possibilities to advance the science of ethnic and medically underserved health care disparities.

Participating in four areas : 1) research and programmatic support, 2) education and outreach, 3) policy and strategy, and 4) representation and advisory, the UCSF Breast Science Advocacy Core (BSAC) Program, a volunteer affiliate of the Breast Oncology Program (BOP), one of ten multidisciplinary research programs under the umbrella of the UCSF Helen Diller Comprehensive Cancer Center promotes a transformative, transdisciplinary, integrated environment to study the biological basis of the diseases that comprise breast cancer; to define the risk of developing or progressing with specific types of breast cancer; to develop novel interventions that work locally and globally to reduce morbidity and mortality from breast cancer and its treatment; and to leverage new collaborative research, education, and mentoring/training opportunities that address cancer outcome disparities.

Advocates involved in KOMEN, DOD, PCORI, AND CBCRP funded research and training grants apply four core principles that forge synergy with NCI Advocacy Research Working Group Recommendations: 1)strategic innovation, 2)collaborative execution, 3)evidence based decision-making, and 4) ethical codes of conduct.

Embracing transdisciplinary professionalism, researchers and advocates build on their track record as shared value partners committed to furthering the collective impact of science advocacy exchange (SAE).

Study Objectives: Genomic analyses of patient tumors have unearthed an overwhelming number of recurrent somatic alterations in genes that have dramatic effects on tumor biology, patient drug responses, and clinical outcomes. In one study, high grade triple negative breast cancer (TNBC) accounts for 34% of breast cancers in African American women versus 21% in white women. A growing body of evidence has shown that African American women have biologically more aggressive disease, independent of social determinants, and suffer the highest mortality rates. While biological breakthroughs of the last decade have greatly advanced our understanding of cancer, in advanced TNBC, a poor prognosis subtype, there is an urgent need to translate this evolving patient genomic data into new therapeutic paradigms.

Our study focuses on the intersection of synthetic lethal approaches, MYC driven human cancers, and immunotherapy as an “innovation agenda”. A distinct MYC vision highlights how overexpression is associated with aggressive outcomes and poor patient outcomes, and synthetic lethal strategies to target MYC (CDK inhibitors, PIM2, as well as the PDI immune pathways) have potential for addressing outcome disparities In African American Women with Triple Negative Breast Cancer (TNBC).

Key Findings: We have developed a screening technique that can be used to rapidly and accurately identify potential synthetic lethal interactions in TNBC. This platform utilizes an isogenic cell line system that we have developed to model oncogene activation in TNBC. A growing body of evidence has shown that:

1) Quantitative approach maps genotype-specific drug responses in isogenic cells

2) Systematic discovery of biomarkers for cancer drugs under clinical investigation

3) Clinically actionable synthetic lethal interaction between MYC and dasatinib is discovered

4) Mechanism of dasatinib action through inhibition of LYN kinase is described

Key Take-Away Message: The inclusion of advocates in convergent science settings remind academic stakeholders that research is there to benefit the patient as they attempt to spark innovation, democratize science, and support smarter interventions that expedite the incredible potential of future investments in bioscience within disparities arenas.

Citation Format: Susan Samson, Alicia Y. Zhou, Maria Martins, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John Gordan, Rebecca Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul Clemens, Alykhan Shamji, Stuart Schreiber, Nevan Krogan, Kevan Shokat, Frank McCormick, Sourav Bandyopadhyay, Andrei Goga. Genomics, advocacy, and emerging therapeutics to address triple-negative breast cancer (TNBC) outcome disparities. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr C88.

Abstract A070: Genetic knockdown screens across tumor types unravel a diverse tumor “immune-modulatome” landscape

Clinical trials with immune-checkpoint blockade antibodies have bolstered the importance of immune therapy as the standard of care for cancer patients, but it has also simultaneously highlighted the heterogeneity in patient responses to such treatment. These heterogeneities can be explained to a certain extent by the lack of tumor-specific expression of the targeted immune checkpoint molecules. But in many cases it can also be conceived that tumors either develop resistance to a targeted immune-checkpoint node by circumventing it or more than one player is involved in a concerted action to subvert the T cell response. In either scenario, we lack a holistic understanding of the putative genes in the tumor genome that could functionally suppress the immune response. To bridge this gap, we employed a high-throughput RNAi-mediated knockdown of upto 2800 genes (~50% associated with surface molecules) in MCF7 (breast), M579-A2 (melanoma) and PANC-1 (pancreatic) tumor cell lines and co-cultured them with either antigen-specific T cell clones or respective patient-derived and tumor-specific infiltrating lymphocytes (TILs) to assess the impact on anti-tumor immunity using a luciferase-based readout. Primary hit-list was further subjected to a secondary screen based on multi-cytokine profiling of the T cells. Our investigation revealed a few salient caveats of tumor-mediated immune suppression. Firstly, we discovered a family of orphan receptors, which were never attributed to the immune system before, to actively suppress the T cells in a manner comparable to the currently defined immune-checkpoint molecules, such as PD-L1. Secondly, the trans-versatility of these novel molecules across the tumor types was highly limited, with only 3-14 common molecules being involved in two or more tumor types. This leads us to our third observation that there exists a complex organ-specific orchestration of peripheral immune tolerance, which needs to be taken into account when devising immune-checkpoint blockade therapies. Amongst the key immunosuppressive candidate genes, CCR9 was validated to directly subvert T cell responses in melanoma, breast and pancreatic cancer in the in vitro and in vivo tumor models. Additionally we have verified TiMi1, an orphan G-protein coupled receptor, to mediate strong immunosuppression in melanoma and pancreatic cancer against the respective TILs. Knockdown of both CCR9 and TiMi1, either via siRNAs or shRNAs, in tumor cells significantly increased Th1 cytokine secretion by TILs along with elevated tumor lysis in vitro and in vivo xenotransplanted mouse models. Moreover, they both induce a highly immunosuppressive genetic signature in the encountering TILs. While TiMi1 appeared to modulate calcium-dependent signaling, CCR9 regulated STAT signaling in T cells leading to an immunosuppressed phenotype. Overall, these candidates represent attractive targets for cancer immunotherapy either through function blocking antibodies or small molecules.

In conclusion, we here report an effective genetic screen strategy in multiple tumor types that has the potential to uncover novel modifiers of anti-tumor immunity. Extensively validated candidates from these screens are attractive targets for cancer immunotherapy that will allow us to further expand our limited arsenal of immune-checkpoint inhibitors, with the overall goal of increasing patient responses to such treatments.

Citation Format: Nisit Khandelwal, Tillmann Michels, Marco Breinig, Antonio Sorrentino, Isabel Poschke, Rienk Offringa, Michal Lotem, Michael Boutros, Philipp Beckhove. Genetic knockdown screens across tumor types unravel a diverse tumor “immune-modulatome” landscape. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A070.

A high-throughput RNAi screen for detection of immune-checkpoint molecules that mediate tumor resistance to cytotoxic T lymphocytes

The success of T cell-based cancer immunotherapy is limited by tumor's resistance against killing by cytotoxic T lymphocytes (CTLs). Tumor-immune resistance is mediated by cell surface ligands that engage immune-inhibitory receptors on T cells. These ligands represent potent targets for therapeutic inhibition. So far, only few immune-suppressive ligands have been identified. We here describe a rapid high-throughput siRNA-based screening approach that allows a comprehensive identification of ligands on human cancer cells that inhibit CTL-mediated tumor cell killing. We exemplarily demonstrate that CCR9, which is expressed in many cancers, exerts strong immune-regulatory effects on T cell responses in multiple tumors. Unlike PDL1, which inhibits TCR signaling, CCR9 regulates STAT signaling in T cells, resulting in reduced T-helper-1 cytokine secretion and reduced cytotoxic capacity. Moreover, inhibition of CCR9 expression on tumor cells facilitated immunotherapy of human tumors by tumor-specific T cells in vivo. Taken together, this method allows a rapid and comprehensive determination of immune-modulatory genes in human tumors which, as an entity, represent the ‘immune modulatome’ of cancer.

Abstract PR15: Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism

There is an urgent need in oncology to link molecular aberrations in tumors with altered cellular behaviors, such as metabolic derangements, and to identify novel therapeutics for cancer treatment. We have sought to identify synthetic-lethal genetic interactions that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to PI3K/AKT pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner. These studies provide new drug and biomarker pairs for clinical investigation. We have also performed global metabolomics analysis in a subset of the isogenic cell lines demonstrating alterations in metabolic pathways that are shared across multiple oncogenes, as well as those that are distinct to specific oncogenic drivers. This scalable approach enables the prediction of drug responses from patient data and can be used to accelerate the development of new genotype-directed therapies.

Citation Format: Maria M. Martins, Alicia Y. Zhou, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart Schreiber, Stuart Schreiber, Nevan J. Krogan, Kevan M. Shokat, Kevan M. Shokat, Frank McCormick, Daniel Nomura, Sourav Bandyopadhyay, Andrei Goga. Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr PR15.

Abstract PR07: Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism

There is an urgent need in oncology to link molecular aberrations in tumors with altered cellular behaviors, such as metabolic derangements, and to identify novel therapeutics for cancer treatment. We have sought to identify synthetic-lethal genetic interactions that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to PI3K/AKT pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner. These studies provide new drug and biomarker pairs for clinical investigation. We have also performed global metabolomics analysis in a subset of the isogenic cell lines demonstrating alterations in metabolic pathways that are shared across multiple oncogenes, as well as those that are distinct to specific oncogenic drivers. This scalable approach enables the prediction of drug responses from patient data and can be used to accelerate the development of new genotype-directed therapies.

This abstract is also presented as a poster at the Translation of the Cancer Genome conference.

Citation Format: Maria M. Martins, Alicia Y. Zhou, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart Schreiber, Stuart Schreiber, Nevan J. Krogan, Kevan M. Shokat, Kevan M. Shokat, Frank McCormick, Daniel Nomura, Sourav Bandyopadhyay, Andrei Goga. Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR07.

Abstract B48: Identification of novel drug interactions with MYC via a quantitative chemical-genetic interaction map

There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or emergent dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to AKT/PI3K pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner, providing new drug and biomarker pairs for clinical investigation. This scalable approach enables the prediction of drug responses from patient data and can be used to accelerate the development of new genotype-directed therapies.

Citation Format: Alicia Y. Zhou, Maria M. Martins, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart L. Schreiber, Nevan J. Krogan, Kevan M. Shokat, Frank McCormick, Andrei Goga, Sourav Bandyopadhyay. Identification of novel drug interactions with MYC via a quantitative chemical-genetic interaction map. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr B48.

Abstract B44: A systems approach combining genomics, advocacy, and emerging novel therapeutics to address triple-negative breast cancer (TNBC) outcomes disparities

Background: Genomic analyses of patient tumors have unearthed an overwhelming number of recurrent somatic alterations in genes that have dramatic effects on tumor biology, patient drug responses, and clinical outcomes. In one study, high-grade triple negative breast cancer (TNBC) accounts for 34% of breast cancers in African American women versus 21% in white women. African American women have biologically more aggressive disease, independent of social determinants, and suffer the highest mortality rates. In advanced TNBC, a poor prognosis subtype, there is an urgent need to translate this emerging patient genomic data into new therapeutic paradigms.

Objectives: Our study focuses on emerging compounds that are already approved (i.e., Dasatinib) or in testing for human use and we expect that this work will serve as a prelude to one or more clinical trials in TNBC. We seek to determine if the treatment of metastatic TNBC recurrence with more targeted genotype-specific agents could improve the outcomes/survival of all women in this particularly aggressive poor prognosis subset, including African American women.

Methods: To guide the development of genotype-specific therapies in TNBC, we have established an isogenic cell-line drug screen that measures the impact of gene activation on a panel of emerging, clinically relevant compounds targeting a variety of cancer pathways. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. We believe that this approach can identify core synthetic lethal interactions, which underlie drug sensitivity and can be used as a foundation to identify patient populations that will selectively respond to drug treatments.

Results: Using our systems approach, our interaction map highlights both known and novel connections between oncogene activation and drug responses and provides a modular roadmap for the exploration of synthetic lethal relationships. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to AKT/PI3K pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner. Ensuring that the voice of the patient is represented in our scientific inquiry, advocacy has played a significant role in the development and realization of this project. Aligning experiential and professionalized expertise, trained advocates explore relentless challenges and opportunities for moving the science forward.

Conclusion: A novel systems biology approach that uses module maps of oncogenes and emerging therapeutics can define synthetic-lethal interactions and actionable therapeutics to help decrease TNBC outcomes/survival disparities in African American women.

Citation Format: Alicia Y. Zhou, Maria M. Martins, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart Schreiber, Nevan J. Krogan, Kevan M. Shokat, Frank McCormick, Susan Samson, Andrei Goga, Sourav Bandyopadhyay. A systems approach combining genomics, advocacy, and emerging novel therapeutics to address triple-negative breast cancer (TNBC) outcomes disparities. [abstract]. In: Proceedings of the Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 9-12, 2014; San Antonio, TX. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2015;24(10 Suppl):Abstract nr B44.

Nanoscale imaging of buried topological defects with quantitative X-ray magnetic microscopy

Advances in nanoscale magnetism increasingly require characterization tools providing detailed descriptions of magnetic configurations. Magnetic transmission X-ray microscopy produces element specific magnetic domain images with nanometric lateral resolution in films up to ∼100 nm thick. Here we present an imaging method using the angular dependence of magnetic contrast in a series of high resolution transmission X-ray microscopy images to obtain quantitative descriptions of the magnetization (canting angles relative to surface normal and sense). This method is applied to 55–120 nm thick ferromagnetic NdCo₅ layers (canting angles between 65° and 22°), and to a NdCo₅ film covered with permalloy. Interestingly, permalloy induces a 43° rotation of Co magnetization towards surface normal. Our method allows identifying complex topological defects (merons or ½ skyrmions) in a NdCo₅ film that are only partially replicated by the permalloy overlayer. These results open possibilities for the characterization of deeply buried magnetic topological defects, nanostructures and devices.

Transmission X-ray microscopy allows for the imaging of magnetic domains in thin film materials. Here, the authors exploit the angular dependence of the magnetic contrast to extract out-of-plane canting angles of stripe domains and topological defects in NdCo₅ films buried under a NiFe layer.

Abstract 970: Broad therapy resistance is induced by suppression of apoptotic priming by lineage programs and oncogenic activation

Understanding the mechanisms of resistance to anticancer therapies may improve personalized treatment regimens and responses to therapy. The mitochondrial apoptosis pathway is activated by most targeted and cytotoxic therapies and represents a node that may be modulated for broad therapy resistance. It has been shown that some cancers, especially those of hematopoietic origin, are primed for apoptosis (as measured by BH3 Profiling) and consequently undergo apoptosis readily in response to therapies while others are unprimed and resistant. However, despite the importance of apoptotic priming in governing response to anticancer therapies, the upstream molecular determinants of apoptotic priming are unknown. Prior work has shown that oncogenes, including c-Myc, can sensitize some cells to apoptosis. We therefore hypothesized that lineage programming and activation of oncogenes may modulate apoptotic priming in normal cells undergoing neoplastic transformation.

Using numerous in vitro and in vivo ovarian, breast, kidney and liver tumorigenesis models we discovered that the strongest determinant of apoptotic priming and chemosensitivity in a cancer cell is the level of priming measured in the cell of origin. To illustrate, ovarian adenocarcinomas, which originate from primed ovarian or fallopian tube epithelia, are considerably more primed than hepatocellular carcinomas originating from unprimed precursors. Notably, we also found that activation of certain oncogenes can meaningfully increase apoptotic priming and chemosensitivity while others decrease it. For example, transformation of normal epithelial cells via forced expression of the c-Myc oncogene increased priming and chemosensitivity. In contrast, activation of Ras in isogenic cells dramatically decreased both priming and chemosensitivity. We have systematically characterized the effects of 27 oncogenes on apoptotic priming and chemosensitivity including PI3K, Notch, Src, BRAF, β-catenin, Akt, and Aurora B kinase. Certain subsets of oncogenes consistently reduced apoptotic priming in cells undergoing transformation and, in combination with cell lineage programs, established broad resistance to targeted and cytotoxic therapies. Importantly, our experimental findings are complemented by clinical correlates. Overall, this work may aid efforts to deploy personalized and efficacious cancer treatments and enhance our knowledge of how cancers evade cell death, which is a hallmark of cancer.

Citation Format: Kristopher A. Sarosiek, Alison Karst, Peter Winter, Antonio Sorrentino, Sourav Bandyopadhyay, Andrei Goga, Kris C. Wood, Ronny Drapkin, Anthony Letai. Broad therapy resistance is induced by suppression of apoptotic priming by lineage programs and oncogenic activation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 970. doi:10.1158/1538-7445.AM2015-970

Abstract 2569: Synergistic antitumor interaction between valproic acid, capecitabine and radiotherapy in colorectal cancer as a rationale for the innovative V-shoRT-R3 trial in locally advanced rectal cancer patients

We have recently demonstrated that the histone deacetylase-inhibitor (HDACi) vorinostat induces synergistic antitumour effects in combination with capecitabine by up-regulating, in vitro and in vivo, in colorectal cancer cells but not in ex vivo treated peripheral blood lymphocytes, the mRNA and protein expression of thymidine phosphorylase (TP), the key enzyme converting capecitabine to 5-FU (Di Gennaro, Brit J Cancer 2010). We confirmed a time and dose-dependent induction of TP mRNA and protein expression by several other HDACi, including valproic acid (VPA). We investigated potential antitumor interaction between capecitabine metabolite 5′-deoxy-5-fluorouridine (5′-DFUR) and several HDACi showing synergistic/additive antiproliferative and pro-apoptotic effects in all cancer cells tested, with good results with VPA. Interestingly, TP protein induction is achieved also at low doses of VPA (0.5-1 mM), corresponding to a plasma level between 50 and 100 μg/ml, easily reached in patients with normal anticonvulsant doses. Although at these doses VPA did not induce growth inhibition as single agents, a significant synergistic antitumor effect was still demonstrated in combination with 5′-DFUR, suggesting a specific mechanism of interaction. TP knockdown experiments confirmed a crucial role of TP protein modulation in the observed synergism. Radiotherapy further potentiated in colorectal cancer cells the antiproliferative, pro-apoptotic and DNA damage effects induced by 5′-DFUR/VPA combination, as demonstrated by clonogenic assay, Caspase-3 cleavage and γH2AX foci formation, respectively. On these bases we launched a phase I/II clinical study (V-ShoRT-R3 trial) to explore whether the addition of both VPA and capecitabine to short-course radiotherapy (SCRT) before optimal radical surgery, might increase the pathologic complete tumor regression rate in low-moderate risk rectal cancer patients (ClinicalTrials.gov number NCT01898104). Several biomarkers will be evaluated comparing normal mucosa with tumor and on blood samples. Tumor metabolism will be measured by 18FDG-PET at baseline and 11 days after the beginning of SCRT. Currently phase I clinical study is ongoing. We have also optimized a protocol to evaluate histones and proteins acetylation in peripheral blood mononuclear cells of recruited patients by flow cytometry, as pharmacodynamic/predictive specific marker of VPA HDACi activity and preliminary results will be presented.

Citation Format: Manuela Terranova Barberio, Biagio Pecori, Serena Imbimbo, Alessandra Leone, Francesca Bruzzese, Maria Carmela Piccirillo, Paolo Delrio, Franco Bianco, Luigi Aloj, Antonio Sorrentino, Fabiana Tatangelo, Antonella Petrillo, Secondo Lastoria, Paolo Muto, Francesco Perrone, Antonio Avallone, Alfredo Budillon, Elena Di Gennaro. Synergistic antitumor interaction between valproic acid, capecitabine and radiotherapy in colorectal cancer as a rationale for the innovative V-shoRT-R3 trial in locally advanced rectal cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2569. doi:10.1158/1538-7445.AM2015-2569

Abstract 254: TiMi1 is a novel immune-checkpoint in solid tumors identified via a tumor-infiltrating lymphocyte (TIL)-based RNAi screening

Immunotherapeutic treatment of melanoma achieved major progress in recent years leading for the first time to improved survival. However, since melanoma cells employ various suppressive mechanisms in order to evade recognition and destruction by immune effector cells many patients still do not benefit from immunotherapy. These mechanisms are far more diverse than reflected by currently used immune modulatory drugs. In this study, we established and utilized a novel high throughput RNAi screening to identify new immune checkpoint molecules in melanoma using antigen-specific patient-derived tumor infiltrating lymphocytes (TILs) in conjunction with primary HLA-matched melanoma cells. Using this approach, we screened a siRNA library targeting more than 1200 surface receptors and kinases to explore novel targets for immunotherapy.

Briefly, HLA-A2 and luciferase positive M579-A2-luc melanoma cells were reversely transfected with the siRNA library and then co-cultured with MART1- and gp100-specific TILs to validate the TIL-mediated tumor lysis. Local regression models (LOESS) were applied to generate a hit list of 48 candidates that negatively regulated CTL cytotoxicity. Interestingly, four candidates of a related breast cancer screen were among the top hits. To streamline the discovery process for large scale molecule libraries, we established a secondary screen assaying multiple T cell activation markers, including effector cytokines.

One of the strongest candidates from our primary and secondary screening is TiMi1 (name altered), a cell surface receptor belonging to the class of GPCRs. We found that knock-down of TiMi1 increased TIL-mediated killing of M579-A2-luc without affecting their viability. TiMi1 knock-down increased TIL activity measured by production of type 1-associated cytokines (e.g. IFN γ and TNF-α), reduced TC apoptosis and increased markers associated with raised activity and cytotoxicity (4-1BB and CD107a). We were able to verify the immune checkpoint function of TiMi1 in melanoma patients using an autologous set of melanoma cells and TILs. Phosphoplex analysis in T cells revealed an involvement of the transcription factor CREB in the mode of action of TiMi1. Preliminary experiments suggest that TiMi1 inhibits anti-tumor immune responses in pancreatic (PDAC) and colorectal (CRC) cancers as well.

In summary, we established a novel antigen-specific screening approach for immune checkpoints expressed in melanoma and were able to identify TiMi1 as a promising candidate. Moreover, TiMi1 inhibits T cell responses in melanoma, PDAC and CRC and might be an interesting target for immunotherapy. Our novel high-throughput screening offers a systematic platform to uncover the “immune-modulatome” of cancer and subsequently discover novel targets for immunotherapy. Since the presented work is considered for patent protection, some gene targets are masked in the presented study.

Citation Format: Tillmann Michels, Christina A. Hartl, Nisit Khandelwal, Marco Breinig, Antonio Sorrentino, Christina Mäder, Ludmila Umansky, Isabel Poschke, Rienk Offringa, Michael Boutros, Galit Eisenberg, Michal Lotem, Philipp Beckhove. TiMi1 is a novel immune-checkpoint in solid tumors identified via a tumor-infiltrating lymphocyte (TIL)-based RNAi screening. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 254. doi:10.1158/1538-7445.AM2015-254

Abstract 245: Identification of novel immune checkpoints as potential therapeutic targets in pancreatic ductal adenocarcinoma (PDAC) using RNAi screening

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of pancreatic cancers and constitutes the fourth leading cause of cancer related death worldwide. In contrast to other malignancies, PDAC is highly resistant to chemotherapy and radiotherapy. Additionally, few immunotherapies are currently available because this malignancy was thought to be poorly immunogenic. Recent studies have shown that infiltration of immune cells in biopsies of PDAC patients correlates with improved clinical outcome. Nevertheless, tumor cells can elude the immune system through several inhibitory mechanisms including the expression of immune checkpoints. These are a plethora of molecules that can either boost or dampen the T-cell receptor (TCR) signaling. Some of these molecules, such as PD-L1, have been successfully used as therapeutic targets of novel anticancer drugs.

AIM: We hypothesize that many immune checkpoint molecules on tumor cells remain undiscovered and we performed a high-throughput RNAi screen to unravel the whole arsenal of immune modulators.

METHODS: We generated a luciferase-expressing PANC-1 cell line and knocked down 2514 genes using a siRNA library. Our library included G-protein coupled receptors, protein kinases and 1117 surface proteins. We co-cultured HLA-A201+ matched tumor infiltrating lymphocytes (TILs) derived from a PDAC patient with the transfected tumor cells. We then measured the remaining luciferase intensity of the tumor cells as an estimation of TIL-mediated cytotoxicity. In order to exclude genes whose knock-down affected cell viability per se, we cultivated tumor cells with the siRNA library in the absence of TILs. Data were analyzed with the cellHTS2 R package.

RESULTS: Our screen revealed 155 candidate genes whose knock-down enhances TIL-mediated killing more efficiently than PD-L1 down-regulation. 35% of these genes are surface molecules and are most likely to directly mediate tumor immune evasion. Beside novel undescribed immune checkpoints, our list contains well characterized immune modulators, supporting the reliability of our approach. Of note 13 of our hits were also found in a related melanoma screen and might play a role in the regulation of immune surveillance of many solid tumors. Among our candidates, TONI1 was one of the most prominent hits. So far, we confirmed the role of TONI1 in inhibiting TIL-mediated killing both in chromium release and luciferase based kill assays. Additionally we detected increased T-cell activity upon TONI1 down-regulation, as measured with interferon-γ ELISPOT and TNF-α ELISA. Since the presented work is considered for patent protection, some gene targets are masked.

CONCLUSION: We set up a robust and systematic method to identify novel immune checkpoints for pancreatic cancer. Further functional validation of our candidate genes will prove their use as therapeutic targets.

Citation Format: Antonio Sorrentino, Tillmann Michels, Ayse Nur Menevse, Nisit Khandelwal, Marco Breinig, Isabel Poschke, Rienk Offringa, Michael Boutros, Philipp Beckhove. Identification of novel immune checkpoints as potential therapeutic targets in pancreatic ductal adenocarcinoma (PDAC) using RNAi screening. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 245. doi:10.1158/1538-7445.AM2015-245

Activity-Based Protein Profiling of Oncogene-Driven Changes in Metabolism Reveals Broad Dysregulation of PAFAH1B2 and 1B3 in Cancer

Targeting dysregulated metabolic pathways is a promising therapeutic strategy for eradicating cancer. Understanding how frequently altered oncogenes regulate metabolic enzyme targets would be useful in identifying both broad-spectrum and targeted metabolic therapies for cancer. Here, we used activity-based protein profiling to identify serine hydrolase activities that were consistently upregulated by various human oncogenes. Through this profiling effort, we found oncogenic regulatory mechanisms for several cancer-relevant serine hydrolases and discovered that platelet activating factor acetylhydrolase 1B2 and 1B3 (PAFAH1B2 and PAFAH1B3) activities were consistently upregulated by several oncogenes, alongside previously discovered cancer-relevant hydrolases fatty acid synthase and monoacylglycerol lipase. While we previously showed that PAFAH1B2 and 1B3 were important in breast cancer, our most recent profiling studies have revealed that these enzymes may be dysregulated broadly across many types of cancers. Here, we find that pharmacological blockade of both enzymes impairs cancer pathogenicity across multiple different types of cancer cells, including breast, ovarian, melanoma, and prostate cancer. We also show that pharmacological blockade of PAFAH1B2 and 1B3 causes unique changes in lipid metabolism, including heightened levels of tumor-suppressing lipids. Our results reveal oncogenic regulatory mechanisms of several cancer-relevant serine hydrolases using activity-based protein profiling, and we show that PAFAH1B2 and 1B3 are important in maintaining cancer pathogenicity across a wide spectrum of cancer types.

Differential expression of plasma miRNAs in patients with unprovoked venous thromboembolism and healthy control individuals

BACKGROUND

Venous thromboembolism (VTE) remains the third most common cardiovascular disease with a vague pathogenesis. Circulating miRNAs are small regulatory RNAs found in plasma, serum and other body fluids in an apparently stable form. Although circulating miRNAs, a novel family of regulatory molecules, emerge as a promising class of biomarkers in many cardiovascular diseases and malignancies, knowledge on plasma miRNA levels in VTE remains sparse.

AIMS

The present work was conducted as a pilot study in order to estimate the plasma levels of miRNAs in patients with unprovoked VTE and to assess miRNAs as potential novel biomarkers of VTE.

METHODS

Twenty patients with a history of unprovoked VTE 1-5 years prior to inclusion in the study and twenty age- and sex-matched healthy control participants were enrolled in a case-control study (Tromsø IV). Plasma levels of 742 miRNAs were assessed after RNA extraction and reverse transcription. Profiling of miRNA was conducted on the Universal RT microRNA PCR Human panels I and II (Exiqon, Denmark). For normalization of the data, the average of the assays detected in all samples (n=40 samples) was applied.

RESULTS

Ninety-seven miRNAs were detected throughout all samples. Of these, miR-10b-5p, -320a, -320b, -424-5p, and -423-5p were upregulated, whereas miR-103a-3p, -191-5p, -301a-3p, and 199b-3p were downregulated in plasmas of VTE patients versus controls (P≤0.05). These miRNAs were confined to the extracellular vesicles-depleted plasma fraction, and yielded clear clustering distinguishing samples from the VTE and control groups.

CONCLUSIONS

The results of this pilot study indicate that plasma miRNAs profiling can provide novel biomarkers of unprovoked VTE.