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Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment

Werba, Gregor; Weissinger, Daniel; Kawaler, Emily A; Zhao, Ende; Kalfakakou, Despoina; Dhara, Surajit; Wang, Lidong; Lim, Heather B; Oh, Grace; Jing, Xiaohong; Beri, Nina; Khanna, Lauren; Gonda, Tamas; Oberstein, Paul; Hajdu, Cristina; Loomis, Cynthia; Heguy, Adriana; Sherman, Mara H; Lund, Amanda W; Welling, Theodore H; Dolgalev, Igor; Tsirigos, Aristotelis; Simeone, Diane M
The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression; however, in-depth single cell characterization of the PDAC TME and its role in response to therapy is lacking. Here, we perform single-cell RNA sequencing on freshly collected human PDAC samples either before or after chemotherapy. Overall, we find a heterogeneous mixture of basal and classical cancer cell subtypes, along with distinct cancer-associated fibroblast and macrophage subpopulations. Strikingly, classical and basal-like cancer cells exhibit similar transcriptional responses to chemotherapy and do not demonstrate a shift towards a basal-like transcriptional program among treated samples. We observe decreased ligand-receptor interactions in treated samples, particularly between TIGIT on CD8 + T cells and its receptor on cancer cells, and identify TIGIT as the major inhibitory checkpoint molecule of CD8 + T cells. Our results suggest that chemotherapy profoundly impacts the PDAC TME and may promote resistance to immunotherapy.
PMID: 36781852
ISSN: 2041-1723
CID: 5427092

Impact of comprehensive family history and genetic analysis in the multidisciplinary pancreatic tumor clinic setting

Everett, Jessica N; Dettwyler, Shenin A; Jing, Xiaohong; Stender, Cody; Schmitter, Madeleine; Baptiste, Ariele; Chun, Jennifer; Kawaler, Emily A; Khanna, Lauren G; Gross, Seth A; Gonda, Tamas A; Beri, Nina; Oberstein, Paul E; Simeone, Diane M
BACKGROUND:Genetic testing is recommended for all pancreatic ductal adenocarcinoma (PDAC) patients. Prior research demonstrates that multidisciplinary pancreatic cancer clinics (MDPCs) improve treatment- and survival-related outcomes for PDAC patients. However, limited information exists regarding the utility of integrated genetics in the MDPC setting. We hypothesized that incorporating genetics in an MDPC serving both PDAC patients and high-risk individuals (HRI) could: (1) improve compliance with guideline-based genetic testing for PDAC patients, and (2) optimize HRI identification and PDAC surveillance participation to improve early detection and survival. METHODS:Demographics, genetic testing results, and pedigrees were reviewed for PDAC patients and HRI at one institution over 45 months. Genetic testing analyzed 16 PDAC-associated genes at minimum. RESULTS:Overall, 969 MDPC subjects were evaluated during the study period; another 56 PDAC patients were seen outside the MDPC. Among 425 MDPC PDAC patients, 333 (78.4%) completed genetic testing; 29 (8.7%) carried a PDAC-related pathogenic germline variant (PGV). Additionally, 32 (9.6%) met familial pancreatic cancer (FPC) criteria. These PDAC patients had 191 relatives eligible for surveillance or genetic testing. Only 2/56 (3.6%) non-MDPC PDAC patients completed genetic testing (p < 0.01). Among 544 HRI, 253 (46.5%) had a known PGV or a designation of FPC, and were eligible for surveillance at baseline; of the remainder, 15/291 (5.2%) were eligible following genetic testing and PGV identification. CONCLUSION/CONCLUSIONS:Integrating genetics into the multidisciplinary setting significantly improved genetic testing compliance by reducing logistical barriers for PDAC patients, and clarified cancer risks for their relatives while conserving clinical resources. Overall, we identified 206 individuals newly eligible for surveillance or genetic testing (191 relatives of MDPC PDAC patients, and 15 HRI from this cohort), enabling continuity of care for PDAC patients and at-risk relatives in one clinic.
PMID: 35906821
ISSN: 2045-7634
CID: 5277102

Unmet needs in the treatment of intrahepatic cholangiocarcinoma harboring FGFR2 gene rearrangements

Beri, Nina
Intrahepatic cholangiocarcinoma, a malignancy of the intrahepatic bile ducts, is the second most common primary liver malignancy and has been rising in incidence over the past several decades. Given its poor prognosis and diagnosis at a late stage, novel therapies are urgently needed to improve outcomes. Intrahepatic cholangiocarcinoma harbors a high rate of targetable mutations, spurring an increased interest in drug development in this disease. FGFR2 gene rearrangements occur in approximately 10-16% of these tumors and this underscores the importance of next generation sequencing in this population. There are now several FGFR inhibitors in development, and these agents may help improve outcomes for these patients. However, both primary and secondary resistance remain a challenge.
PMID: 35081733
ISSN: 1744-8301
CID: 5154582

A phase 1b study evaluating IL-1beta and PD-1 targeting with chemotherapy in metastatic pancreatic cancer (PanCAN-SR1) [Meeting Abstract]

Oberstein, P E; Rahma, O E; Beri, N; Stoll-D'Astice, A C; Duliege, A -M; Nazeer, S; Squires, M; Bar-Sagi, D; Wolpin, B M; Dougan, S; Simeone, D M
Background: Pancreatic ductal adenocarcinoma (PDA) is a highly lethal malignancy that is refractory to therapeutic targeting of the immune microenvironment. In preclinical work, IL-1beta was shown to be upregulated in pancreatic cancer tumors, and in mouse models, IL-1beta expression led to activation of pancreatic stellate cells and immunosuppression (Das et al 2020). We hypothesize that blockade of IL-1beta and PD-1 will result in alterations in myeloid, lymphoid, and fibroblast subsets within the pancreatic cancer microenvironment and add therapeutic benefit in combination with chemotherapy in PDA.
Method(s): We are conducting an open-label multicenter Phase Ib study evaluating a 4 drug regimen including gemcitabine and nabpaclitaxel with the addition of canakinumab (ACZ885), a high-affinity human anti-interleukin1beta (IL-1beta) monoclonal antibody (mAb), and spartalizumab (PDR001), a mAb directed against human Programmed Death-1 (PD-1). Eligible subjects have metastatic PDA without prior anticancer therapy for metastatic disease and RECIST measurable disease. The primary objective was to identify a recommended phase II/III dose of combination therapy by evaluating the incidence of dose limiting toxicities in the first 56 days (8 weeks) of dosing in at least 6 evaluable subjects utilizing a Bayesian logistic regression model. All subjects underwent baseline and on-study tissue and blood collection for extensive exploratory correlative studies. Secondary objectives including safety and tolerability of quadruple therapy and preliminary assessment of clinical activity.
Result(s): 10 subjects were enrolled between November 2020 and March 2021, and the first 6 subjects to complete 8 weeks of therapy were included in the dose confirmation analysis. There were no dose limiting toxicities and the recommended Phase II/III dose was established as; gemcitabine (1000 mg/m2 IV) on day 1,8,15; nab-paclitaxel (125 mg/m2 IV) on day 1,8,15, canakinumab (250 mg via subcutaneous injection) on day 1, spartalizumab (400 mg IV) on day 1; of each 28 day cycle. Adverse events were consistent with those seen with chemotherapy and were predominately hematologic. The majority of subjects completed the on-treatment blood and tissue collection for correlative analysis. The study is ongoing with subjects remaining on therapy and all subjects will be evaluated for efficacy.
Conclusion(s): In this Phase Ib study, we demonstrated the feasibility and safety of adding canakinumab and spartalizumab to standard of care chemotherapy in first line metastatic PDA and established the recommended Phase II/III dose. This novel 4 drug combination will be tested in a randomized Phase II/III study through the Precision Promise clinical trial network. Preliminary correlative and efficacy data will be reported
ISSN: 0732-183x
CID: 5164502

A phase II, randomized, controlled trial of nivolumab in combination with BMS-986253 or cabiralizumab in advanced hepatocellular carcinoma (HCC) patients [Meeting Abstract]

Welling, T; Beri, N; Siolas, D; Cohen, D J; Becker, D J; Zhong, H; Wu, J J; Oberstein, P E; Karasic, T B
Background: Tyrosine kinase inhibitors can prolong survival in advanced HCC patients, but response rates have been minimal. Recently, immune checkpoint inhibition with nivolumab (nivo) demonstrated objective response rates (ORR) of 15% (escalation phase) and 20% (expansion phase) in the Checkmate 040 study. Pre-clinical and translational studies have demonstrated that IL-8 and tumor associated macrophages (TAMs) contribute to HCC progression and recurrence following treatment. Therefore, rationale exists to evaluate combinatorial approaches to target TAM function combined with checkpoint inhibitory therapy. This phase II, randomized study will evaluate the safety and efficacy of combined anti-CSF1R (Cabiralizumab) or anti-IL-8 (BMS-986253) in combination with Nivo in advanced HCC. Method(s): Advanced HCC patients without prior systemic treatment and disease measurable by RECISTv1.1 with Childs A liver function are eligible. Patients will be enrolled (n=25 per arm) to Nivo 240 mg IV Q2 weeks monotherapy, Nivo 240 mg IV + BMS-986253 1200 mg IV Q2 weeks, or Nivo 240 mg IV + Cabiralizumab 4 mg/kg IV Q2 weeks. Primary endpoints include safety and ORR determined by RECISTv1.1. Secondary endpoints include time to response, duration of response, progression free survival, and overall survival. Exploratory endpoints include analysis of tumor microenvironment immune and tumor cell profiling of pre- and on-treatment tumor tissue
ISSN: 1527-7755
CID: 4326202

A phase I/II multisite study of nivolumab and carboplatin/paclitaxel with radiation therapy (RT) in patients with locally advanced esophageal squamous cell carcinoma (ESCC) [Meeting Abstract]

Wu, J J; Atkinson, E C; Leichman, L P; Patel, H; Iqbal, S; Lee, Du K; Bizekis, C; Goldberg, J D; Thomas, C R; Cohen, D J; Becker, D J; Siolas, D; Beri, N; Oberstein, P E; Ku, G Y
Background: Preoperative chemoRT is a standardof- care as shown in the CROSS trial (N Engl J Med 2012;366:2074-2084), Surgery is sometimes deferred in pts with clinical CR (cCR) based on lack of overall survival benefit (J Clin Oncol 2005;23:2310-2317, J Clin Oncol2007;25:1160-1168). Nivolumab has activity in advanced ESCC (Lancet Oncol 2017;18:631-639), and adding it to chemoRT may improve outcomes.
Method(s): This phase I/II study was designed to assess the safety and tolerability and efficacy of nivolumab added to chemoRT (6 weekly carboplatin AUC 2, paclitaxel 50mg/m2, RT 50.4 Gy in 1.8 Gy fractions 5/7 days) for pts with TanyN1-3 or T3-4N0M0 ESCC. The phase I primary endpoint is 'unacceptable toxicity' at 28 days after the last dose of chemotherapy. The phase II primary endpoints are cCR (endoscopy + PET/CT) and pCR rates for pts undergoing surgery. Nivolumab is given q2W x2, then concurrent chemoRT with nivolumab q2W x3. If no cCR, pt proceeds to esophagectomy, then adjuvant nivolumab q2W x3; if cCR, pt has an option of no surgery but receives nivolumab q2W x3.
Result(s):From 7/20/17 to 12/27/18, 6 pts were enrolled. No unacceptable or grade 5 toxicities were observed. The most common grade 1/2 AEs in >1 pt were anorexia, myelosuppression, elevated AST and nausea. Grade 3/4 AEs in >1 pt were lymphopenia and leukocytopenia. 2 pts required hospitalizations (dyspnea 1, colitis 1). All pts completed therapy; 1 pt had dose delay due to grade 2 esophagitis; 2 pts progressed, 4 achieved cCR. Of 4 pts with cCR, 2 pts chose surgery and both achieved pCR. None of the 4 pts recurred.
Conclusion(s): ChemoRT with nivolumab is tolerable with manageable toxicities in locally advanced ESCC. Enrollment to the phase II portion ended because of slow accrual. Adverse Events. Grade 1 &2 in > 1 pt: 4/6: Anorexia & Anemia 3/6: Leukocytopenia Neutropenia Thrombocytopenia Nausea & Elevated AST 2/6: Hypomagnesemia Hypokalemia Grade 3 & 4 in > 1 pt: 5/6: Lymphopenia, 2/6: Leukocytopenia
ISSN: 1527-7755
CID: 4326192

Breast cancer screening utilization and understanding of current guidelines among rural U.S. women with private insurance

Peppercorn, Jeffrey; Houck, Kevin; Beri, Nina; Villagra, Victor; Wogu, Adane F; Lyman, Gary H; Wheeler, Stephanie B
Women living in rural areas of the U.S. face disparities in screening mammography and breast cancer outcomes. We sought to evaluate utilization of mammography, awareness of screening guidelines, and attitudes towards screening among rural insured U.S. women. We conducted a cross-sectional self-administered anonymous survey among 2000 women aged 40-64 insured by the National Rural Electric Cooperative Association, a non-profit insurer for electrical utility workers in predominantly rural areas across the U.S. Outcomes included mammographic screening in the past year, screening interval, awareness of guidelines, and perceived barriers to screening. 1588 women responded to the survey (response rate 79.4 %). 74 % of respondents lived in a rural area. Among women aged 40-49, 66.5 % reported mammographic screening in the past year. 46 % received annual screening, 32 % biennial screening, and 22 % rare/no screening. Among women aged 50-64, 77.1 % reported screening in the past year. 63 % received annual screening, 25 % biennial screening, and 12 % rare/no screening. The majority of women (98 %) believed that the mammography can find breast cancer early and save lives. Less than 1 % of younger women, and only 14 % of women over age 50 identified the recommendations of the U.S. Preventative Services Screening Task Force as the current expert recommendations for screening. Screening practices tended to follow perceived guideline recommendations. When rural U.S. women over age 40 have insurance, most receive breast cancer screening. The screening guidelines of cancer advocacy groups and specialty societies appear more influential and widely recognized than those of the U.S. preventative services taskforce.
PMID: 26386956
ISSN: 1573-7217
CID: 3177962

Metabolite signatures of exercise training in human skeletal muscle relate to mitochondrial remodelling and cardiometabolic fitness

Huffman, Kim M; Koves, Timothy R; Hubal, Monica J; Abouassi, Hiba; Beri, Nina; Bateman, Lori A; Stevens, Robert D; Ilkayeva, Olga R; Hoffman, Eric P; Muoio, Deborah M; Kraus, William E
AIMS/HYPOTHESIS/OBJECTIVE:Targeted metabolomic and transcriptomic approaches were used to evaluate the relationship between skeletal muscle metabolite signatures, gene expression profiles and clinical outcomes in response to various exercise training interventions. We hypothesised that changes in mitochondrial metabolic intermediates would predict improvements in clinical risk factors, thereby offering novel insights into potential mechanisms. METHODS:Subjects at risk of metabolic disease were randomised to 6 months of inactivity or one of five aerobic and/or resistance training programmes (n = 112). Pre/post-intervention assessments included cardiorespiratory fitness ([Formula: see text]), serum triacylglycerols (TGs) and insulin sensitivity (SI). In this secondary analysis, muscle biopsy specimens were used for targeted mass spectrometry-based analysis of metabolic intermediates and measurement of mRNA expression of genes involved in metabolism. RESULTS:Exercise regimens with the largest energy expenditure produced robust increases in muscle concentrations of even-chain acylcarnitines (median 37-488%), which correlated positively with increased expression of genes involved in muscle uptake and oxidation of fatty acids. Along with free carnitine, the aforementioned acylcarnitine metabolites were related to improvements in [Formula: see text], TGs and SI (R = 0.20-0.31, p < 0.05). Muscle concentrations of the tricarboxylic acid cycle intermediates succinate and succinylcarnitine (R = 0.39 and 0.24, p < 0.05) emerged as the strongest correlates of SI. CONCLUSIONS/INTERPRETATION/CONCLUSIONS:The metabolic signatures of exercise-trained skeletal muscle reflected reprogramming of mitochondrial function and intermediary metabolism and correlated with changes in cardiometabolic fitness. Succinate metabolism and the succinate dehydrogenase complex emerged as a potential regulatory node that intersects with whole-body insulin sensitivity. This study identifies new avenues for mechanistic research aimed at understanding the health benefits of physical activity. Trial registration NCT00200993 and NCT00275145 Funding This work was supported by the National Heart, Lung, and Blood Institute (National Institutes of Health), National Institute on Aging (National Institutes of Health) and National Institute of Arthritis and Musculoskeletal and Skin Diseases (National Institutes of Health).
PMID: 25091629
ISSN: 1432-0428
CID: 3177952

Molecular and Clinical Associations Between Vitamin D and Chronic Lymphocytic Leukemia [Meeting Abstract]

Beri, Nina; Friedman, Daphne R.; Simms, Tiffany M.; Kuchibhatla, Maragatha; Weinberg, J. Brice; Lanasa, Mark C.
ISSN: 0006-4971
CID: 3177992