bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of DDPCR blood-based diagnostic tests that simultaneously measure mRNA expression from immune and cancer cells.
Authors: Mellert Hestia S. , Jackson Leisa , Tompkins Chris , Lodge Anne , Pestano Gary Anthony 
Published: November 2019

22 Background: Therapeutic options for patients with non-small cell lung cancer (NSCLC) continue to expand with the advent of immunotherapies. Lack of tissue and drawbacks with available IHC tests have increased the need for blood-based diagnostics. Thus, the detection of circulating nucleic acids has become highly relevant to clinical testing. Methods: We focused on extending the utility of blood-based testing for measurement of intra-cellular transcripts to multiplexed detection of gene expression. Specifically, we addressed maximizing the yield of quality circulating RNA for use in multiplexed droplet digital PCR (ddPCR) assays. Evaluation criteria included droplet counts for biomarkers of cancer and immunotherapy response. The markers evaluated were CD45, CD3, CK8, CK18, CK19, and PD-L1. Specimens included cell lines and prospectively collected samples from normal, healthy donors and donors with NSCLC. Results: Cell lines expressing variable levels of cytokeratins and PD-L1 were used to establish assay sensitivity. In these experiments, the test system could detect these markers in the equivalent of a single cell. We evaluated specificity using RNA from these same cell lines, resting and activated lymphocytes, and monocytes. With the exception of CK8, all assays demonstrated the expected specificities. Given the complexity of assessing PD-L1 in circulation because of its expression on immune cells, a threshold of 30 copies of PD-L1 was established using normal healthy donors (n = 9). Using this cut-off we then measured PD-L1 in circulating RNA from donors with NSCLC (n = 20). By these criteria, PD-L1 expression of sufficient copy number was restricted to a single EGFR wild-type donor (1/10). Previous reports have indicated that for EGFR wild-type patients, PD-L1 over expression may be considered a poor prognostic indicator of OS. Conclusions: We are developing sensitive and specific methods that can be applied to gene expression studies in blood. We have shown feasibility of these methods by evaluating key immune and cancer-specific RNAs. Evaluations are on-going with prospective sample collections to validate thresholds for this assay that may lead to its clinical utility.
Identifying treatment options for triple negative breast cancer patients using RNA-sequencing.
Authors: Pedersen Gitte 
Published: November 2019

31 Background: In the context of diagnostics, RNA is proxy for proteins and proteins are typically targets for drugs; e.g. breast cancer is typically driven by over-expression of various hormone receptors and Her2. In the current standard-of-care setting there is no measurement of mutations. Furthermore, all the markers for response to the new immune therapies are expressed as mRNA. Approximately 15% of the breast cancer patients are triple negative. Due to the poor outcome of chemo, standard-of-care guidelines (NCCN) suggests doctors encourage the patient to enroll in clinical trials. However, with more than 2000 ongoing trials in breast, which trial could potentially benefit the patient? Methods: Using the RNA-seq data from the TCGA study, we analyzed more than 120 triple negative datasets. Results: We found at least one over-expressed checkpoint inhibitor target in almost all the patients, suggesting that if you analyzed for all of the checkpoint targets, it would be possible to find a clinical study for these patients. Furthermore, when we analyzed over-expressed tumor antigens, we realized that it would be possible to design sophisticated combination trials with this information. In addition, we identified patients that were BRCAwt with an impaired DNA repair pathway; e.g. some had BRCA silencing and could potentially benefit from PARP inhibitors. Finally, a small number of patients overexpressed the androgen receptor for which there is a drug approved for prostate cancer. Conclusions: Compared to DNA analysis, tumor RNA profiling has the potential to guide a much broader set of drugs and treatment approaches including immunotherapy and chemotherapy. Messenger RNA (mRNA) analysis can reveal tumor antigens and drug targets expressed by cancer cells, as well as the vital status of the tumor microenvironment including immune response, the integrity of DNA repair mechanisms, and the engagement of angiogenesis and other cancer-related pathways.
Prevalence and clinical implications of T-cell immunoglobulin mucin type-1 (TIM-1) in multiple tumor types.
Authors: Halim Abdel , Bagley Rebecca G. , Turner Christopher D. , Keler Tibor 
Published: November 2019

34 Background: TIM-1 (KIM-1, HAVcr-1) is a type 1 transmembrane glycoprotein. Expression is limited in healthy tissues but upregulated after kidney injury, in ovarian cancer and renal cell carcinoma (RCC). TIM-1 is associated with a more malignant RCC phenotype and immune response regulation. CDX-014, an antibody drug conjugate, contains a fully human IgG1 monoclonal antibody (mAb) conjugated to the potent cytotoxin MMAE. CDX-014 is in a Ph 1/2 trial for RCC (NCT02837991). The prevalence of TIM-1 in other cancers was investigated to explore the broader potential for CDX-014. Methods: Tumors and normal adjacent tissues (NAT) were provided (Mosaic Labs) via IRB-reviewed protocol MOS001 for in vitro analysis of remnant, anonymized human samples. The study included 188 tumors: 30 renal, 45 ovarian, 34 endometrial, 2 cervical, 2 vaginal, 15 bile duct, 15 CRC, 30 NSCLC and 15 thymoma plus 75 NAT. Mosaic performed a validated immunohistochemistry assay on FFPE tissues. A FITC-conjugated, anti-TIM-1 mAb was applied after slide deparaffinization and antigen retrieval. Anti-FITC (Novus Bio), Envision+ HRP and DAB (Dako) were used for visualization. A pathologist scored hematoxylin-counterstained slides for % positive cells and staining intensity. A cut-off of > 2% of cells staining at any intensity was deemed positive. Results: TIM-1 was universally prevalent in renal papillary (14/14) and clear cell carcinoma (CCC [13/13]) plus vaginal CCC (2/2). TIM-1 was also seen in ovarian CCC (12/15; 80%), endometrial CCC (9/21; 43%), adeno NSCLC (2/15; 13%), serous ovarian (1/10; 10%), adeno endometrial (1/13; 8%) and CRC (1/15; 7%). There was no staining in chromophobe RCC (3/3), cervical CCC, endometrioid or mucinous ovarian (10 each), bile duct carcinoma, squamous NSCLC or thymoma. There was minimal to no TIM-1 in NAT except for 7/10 kidney samples (possibly from unappreciated kidney injury). Conclusions: The data suggest that in addition to renal and ovarian cancer, TIM-1 targeted therapy such as CDX-014 warrants exploration in patients with endometrial CCC, vaginal CCC and adeno NCSLC. These results support the ongoing first in human Ph 1/2 study in RCC and potential broader clinical development of CDX-014 in other indications.
Mutation burden as a biomarker of response to immune checkpoint therapy in nine solid cancers.
Authors: Ganesan Shridar , Bhanot Gyan , Mehnert Janice M. , Silk Ann W. , Ross Jeffrey S. , Pavlick Dean , Ali Siraj Mahamed , Markowski Paul , Kaufman Howard L. , Sullivan Ryan J. , Lovly Christine Marie , Sosman Jeffrey Alan , Johnson Douglas Buckner , Betigeri Anil , Subramanian Kalyanasundaram , Panda Anshuman 
Published: November 2019

35 Background: A high mutation burden a biomarker of response to immune checkpoint therapy in melanoma, non-small cell lung cancer, and colorectal cancer. It is unknown whether mutation burden is predictive of response in other cancer types, and whether it is identifiable using available clinical assays. Methods: Using data for 10,745 tumors from 33 solid cancer types in TCGA, we looked for a mutation burden threshold (iCAM) in each cancer type associated with gene expression signatures of a blocked immune response of robust CD8+T cell response and up-regulation of immune checkpoint genes. Results: A unique iCAM threshold was identified in nine cancers: melanoma and lung, colon, endometrial, and gastric adenocarcinoma; serous ovarian, bladder urothelial, cervical, and ER+ HER2− breast cancer. iCAM thresholds applied to published clinical data for patients treated with immune checkpoint therapy showed that iCAM+ patients had significantly better response. iCAM+ tumors can be identified from clinical-grade NGS assays with high accuracy . In a prospective melanoma cohort of patients treated with anti- PD-1 patients with iCAM+ tumors had significantly better objective response rates, progression free survival, and overall survival compared patients to iCAM− tumors. Pattern of somatic mutations were different in iCAM+ and iCAM− tumors, suggesting different mechanism of carcinogenesis in iCAM+ versus iCAM− tumors. Higher fractions of leukocytes were NK (Natural Killer) cells and macrophages were M1 polarized, and a lower fraction of T cells were regulatory T cells in iCAM+ tumors compared to iCAM− tumors. Over 75% of the genes significantly up-regulated in iCAM+ tumors in every cancer types were in the immune response pathway, confirming immune response to be the main differentiator in iCAM+ veruss iCAM− tumors. Conclusions: In nine cancer types, a clinically useful mutation burden threshold (iCAM) associated with gene expression signatures of blocked immune response can identify likely responders to immune checkpoint therapy, and iCAM status is identifiable using currently available clinical NGS assays.
Blood-based predictive biomarkers for overall survival (OS) in patients (pts) receiving the immunotherapy sipuleucel-T (sip-T).
Authors: Oh William K. , Kandadi Harini , Sheikh Nadeem Anwar , Galsky Matt D. 
Published: November 2019

36 Background: Sip-T is an FDA-approved immunotherapy for the treatment of asymptomatic or minimally symptomatic metastatic castration-resistant prostate cancer (mCRPC). While baseline prostate-specific antigen level correlates with prolonged OS in pts treated with sip-T, biomarkers predictive of OS remain elusive. Gene expression signatures in peripheral blood (PB) correlate with prognosis in mCRPC (Ross et al, Lancet Oncol. 2012). This study sought to identify a candidate PB gene signature predictive of OS benefit with sip-T. Methods: PB mononuclear cells from sip-T or control (CN) mCRPC pts in the IMPACT trial (NCT00065442) were collected prior to leukapheresis. Affymetrix gene chip (HGU133P2) screening evaluated gene expression; association of gene expression with OS was performed using a multivariate Cox proportional hazards regression model, where OS was fit to gene expression and the 2003 baseline Halabi prognostic variables. The top 50 gene candidates were selected for qPCR confirmation. Results: Out of the 50 gene candidates selected for qPCR confirmation, 5 genes were associated with OS. High expression of SNTB1 and CHI3L2 and low expression of SYNGR3, AURKC, and ZNF268 were associated with improved OS in sip-T–treated pts but not in CN arm pts. A composite gene score (CGS) was calculated incorporating expression of these genes. In a CGS tertile analysis, OS in the top and middle sip-T tertiles was significantly better compared with the corresponding CN groups (Table). The lowest sip-T tertile had a median OS similar to that of the CN arm. Conclusions: CGS based on baseline gene expression may predict OS outcomes for mCRPC pts receiving sip-T. Compared with the CN arm, OS was significantly improved in the top two tertiles of sip-T–treated pts; OS in the bottom tertile was similar to the CN arm. Clinical trial information: NCT00065442. [Table: see text]
Tumor mutational load in gynecological and breast cancer.
Authors: Lynce Filipa , Xiu Joanne , Obeid Elias , Tan Antoinette R. , Gatalica Zoran , Isaacs Claudine , Pohlmann Paula Raffin 
Published: November 2019

44 Background: Lack of test standardization and conflicting results on PD1 and PD-L1 immunohistochemistry (IHC) assays challenge their use as predictive biomarkers for checkpoint inhibitors. High tumor mutational load (TML) has been linked to therapeutic response with immune checkpoint inhibition in melanoma, lung and colorectal cancer. Herein, we explore association of TML and PD1/PD-L1 expression in gynecological (GC) and breast cancer (BC). As secondary aim we explore the association of TML with BRCA1/2 mutations. Methods: De-identified data from molecular profiling on GC and BC tumors from the CARIS Life Sciences database was analyzed after obtaining IRB approval. TML was defined as the total number of nonsynonymous, somatic mutations per Mb sequenced with a 592-gene panel. PD-1 IHC was tested on Tumor Infiltrating Lymphocytes (TIL) with the cutoff of 1/HPF; PD-L1 expression was measured on tumor cells with the cutoff of 2+, 5%. Biomarker association was tested with ANOVA test (SPSS v23, IBM). Results: As shown in table, cervical (CC) and endometrial cancers (EC) had the highest TML and squamous CC and triple negative BC (TNBC) tumors with highest PD-L1. In EC, MSI-H was associated with higher TML when compared to MSS (20.1 vs. 6.1, p<0.001); 4 POLE-mutated tumors all carried TML (36-678) higher than mean (11.5). TML was not associated with PD1 or PDL1 positivity in any of the diseases. BRCA1/2 mutations were associated with higher mean TML in ovarian cancer (OC) (6.8 vs. 5.4 in wild type, p<0.001) but not in BC (6.3 vs. 6.8 in wild type, p=0.48). Conclusions: In this sample of patients who underwent molecular profiling, there was no association between TML and PD1 or PD-L1 expression. Association between BRCA1/2 tumor mutations and TML in OC is worth exploring. High TML in CC and EC support the development of immunotherapy for these diseases. [Table: see text]
Characterization of potential predictive biomarkers of response to nivolumab in CheckMate-141 in patients with squamous cell carcinoma of the head and neck (SCCHN).
Authors: Ferris Robert L. , Concha-Benavente Fernando , Blumenschein George R. , Harrington Kevin J. , Fayette Jerome , Colevas A. Dimitrios , Licitra Lisa F. , Kasper Stefan , Even Caroline , Gillison Maura L. , Worden Francis , Saba Nabil F. , Haddad Robert I. , Tahara Makoto , Hasegawa Yasuhisa , Yen Chia-Jui , Lynch Mark John , Monga Manish , Geese William J. , Vokes Everett E. 
Published: November 2019

5 Background: Nivolumab, an anti-programmed death-1 (PD-1) monoclonal antibody, demonstrated longer median overall survival (7.5 vs. 5.1 months) and improved response (13.3% vs. 5.8%) versus investigator choice chemotherapy (ICC) in patients with recurrent SCCHN after platinum failure in CheckMate 141 (NCT02105636), a randomized, open-label Phase 3 trial. We screened peripheral blood lymphocytes (PBL) to identify biomarkers which may predict response to nivolumab. Methods: Paired baseline (day 1) and on treatment (day 43) PBL samples (n=36; 24 nivolumab; 12 ICC) were analyzed using multicolor flow cytometry and a non-competing anti-PD-1 antibody. Results were correlated with clinical outcome: responders (complete/partial response) and non-responders (stable or progressive disease). Results: Levels of CD8+ T cells at baseline and on treatment were higher in nivolumab responders compared to non-responders (23% vs. 13%; p<0.05). Interestingly, PD-1+ CD8+ and PD-1+ CTLA-4+ CD8+ effector T cells (likely exhausted T cells) decreased about 2-fold following nivolumab in both responders and non-responders (p<0.05), whereas, the decrease in CTLA-4+ CD8+ effector T cells following nivolumab was significant in responders only (8% vs. 5%; p<0.05). Levels of PD-1+ TIM-3+ CD8+ effector cells decreased following nivolumab in non-responders only (11% vs. 7%; p<0.05), a similar non-significant reduction was observed in responders. Levels of PD-1+Tregs were lower in responders than non-responders at baseline (19% vs. 33%; p<0.01), and following nivolumab (12% vs. 20%; p<0.001). As in T effector cell populations, PD-1+ Tregs decreased about 1.6-fold after nivolumab in both responders and non-responders (p<0.01). Interestingly, baseline Ki67+ Treg levels were lower in non-responders (28% vs. 17%; p<0.05). Conclusions: Response to nivolumab may be associated with higher levels of CD8+ T cells and CTLA-4+ CD8+ effector T cells, and lower PD-1+ CD8+ effector T cells and PD-1+ Tregs at baseline. Targeting both PD-1 and CTLA-4 axes is warranted in SCCHN to overcome suppressive signals in CD8+ effector T cells and in Treg cells expressing both checkpoint receptors. Clinical trial information: NCT02105636.
Feasibility of miR-9, miR-21, and miR-155 as alternative biomarkers in both HPV-positive and HPV-negative cervical cancers.
Authors: Chung Dawn , Park Sunyoung , Eom Kiyoon , Park Kwang Hwa , Lee Hyeyoung 
Published: November 2019

52 Background: Cervical cancer is the second leading cause of death among female patients with cancer in the world. High risk human papillomavirus has causal roles in cervical cancer initiation and progression by deregulating several cellular processes. However, HPV infection is not sufficient for cervical carcinoma development. Therefore, other genetic and epigenetic factors may be involved in this complex disease, and the identification of which may lead to better diagnosis and treatment. Our aim was to analyze the expression of microRNAs in cervical cancer cases positive or negative for HPV E6/E7 mRNA, and to assess their diagnostic usefulness and relevance. Methods: The expression of three different microRNAs (miR-9, miR-21, and miR-155) in 52 formalin-fixed paraffin-embedded (FFPE) primary cervical cancer tissue samples and 50 FFPE normal cervical tissue samples were evaluated. Results: MiR-9, miR-21, and miR-155 were significantly overexpressed in cervical cancer tissues compared to normal tissues ( P < 0.001). MiR-9, miR-21, and miR-155 expression combined with the HPV E6/E7 mRNA assay showed sensitivities of 82.7 %, 92.3 %, and 84.6 % respectively, demonstrating their potential as diagnostic tools. Moreover, miR-21 and miR-155 were predictors showing a 7 fold and 10.3 fold higher risk for HPV E6/E7 negative patients with cervical cancer ( P = 0.024 and P = 0.017, respectively) while miR-155 was a predictor showing a 27.9 fold higher risk for HPV E6/E7 positive patients with cervical cancer ( P < 0.0001). Conclusions: There is a strong demand for additional, alternative molecular biomarkers for diagnosis and management of precancer patients. MiR-9, miR-21, and miR-155 may be helpful in the prediction of both HPV positive and HPV negative cases of cervical cancer.
Flow cytometric detection of MDSC populations in unfractionated blood.
Authors: Diaz-Montero C. Marcela , Rayman Patricia A. , Kim Jin Sub , Pavicic Paul G , Tannenbaum Charles , Velcheti Vamsidhar , Funchain Pauline , Ko Jennifer S , Grivas Petros , Rini Brian I. , Montero Alberto J. , Finke James 
Published: November 2019

56 Background: MDSCs are a phenotypically diverse population of bone-marrow-derived cells that play an important role in tumor progression based on their immunosuppressive and pro-angiogenic properties. Mobilization of MDSCs from the bone marrow into the blood stream is dependent on tumor derived factors. Therefore, it is likely that levels of circulating MDSCs in cancer patients are reflective of tumor activity. However, the clinical applicability of MDSCs as a predictive biomarker in cancer has been hindered by a lack of consensus on the surface markers that defines them. Although there have been several attempts at harmonizing the nomenclature and characterization standards of MDSCs, there is still a lot of confusion particularly in the detection of MDSCs in unfractionated peripheral blood. To address this issue we have devised a simple flow cytometric test that reliably detects in whole blood the MDSCs subtypes that have been consistently reported to have clinical relevance in cancer. Methods: Whole blood from cancer patients and normal volunteers was stained with Lin cocktail, HLADR, CD33, CD15, CD14, and CD11b antibodies. After staining, red blood cells were lysed, samples were washed and analyzed by flow cytometry. Results: This approach identifies monocytic MDSCs (Linlo/CD33+/HLADR-/CD14+/CD15-), granulocytic or polymorphonucleated polymorphonuclear MDSCs (Linlo/CD33+/HLADR-/CD14-/CD15+), and promyelocytic or immature MDSCs (Linlo/CD33+/HLADR-/CD14-/CD15-), as well as Linlo/HLADR-/CD33+/CD11b+ MDSCs. This latter subpopulation has been reported by us and others to correlate with disease stage and tumor burden in several solid malignancies. This assay also allows the accurate determination of absolute numbers of each MDSC population when white blood cell counts are taken into consideration. Conclusions: Our proposed simple and rapid flow cytometry-based assay allows the measurement of frequency and absolute numbers of circulating MDSC subpopulations in unfractionated blood, and could provide a reference for their further characterization as predictive biomarkers for solid malignancies.
Neurological adverse events from checkpoint inhibition: A comprehensive review of literature.
Authors: Daher Ahmad , Sudhakar Tummala 
Published: November 2019

62 Background: Checkpoint (CTLA-4 & PD-1) inhibitors are the most commonly used anti-cancer immunotherapeutics. Their use is associated with well-documented immune-related adverse events (iAEs), but among those, neurological adverse events (nAEs) are rare. They have been described in multiple reports but detailed analysis of the spectrum of neurotoxicities, their relationship to the drug dose, and their time course is lacking. We provide a comprehensive review of all published checkpoint inhibitors-induced nAEs. Methods: PubMed and Ovid-MEDLINE databases were queried for all nAEs from checkpoint inhibition published cases. Three additional cases from our institution were included. Clinical, radiologic, and laboratory data was reviewed and analyzed. Results: 63 cases were identified, 57 of which were analyzed in Table 1. The remaining 6 cases included nAEs occurring > 6 months after initiation of therapy and were analyzed separately. Neurotoxicity occurred after a median of 3 doses with a range of 1 to 6. Neuropathy was the most common nAE from overall checkpoint inhibition (32%) or CTLA-4 inhibition (43%) but in PD-1 blockade cases, Myasthenia Gravis (44%) was more common than neuropathy (11%). CNS demyelination (11%), encephalopathy (10%), and meningitis (6%) were also reported. Peripheral nAEs outweighed central ones by about 2:1. Improvement was seen in 77% of the cases while systemic iAEs were seen in 25% only. The 6 cases with delayed nAEs analyzed occurred 31-76 weeks after therapy initiation. Conclusions: nAEs from checkpoint inhibition typically affect PNS > CNS, occur after a few doses of therapy, and are not commonly associated with systemic iAEs. Their profile varies by type of blockade (PD-1 vs. CTLA-4). Immunotherapy may unmask a subclinical previously undiagnosed neuromuscular disorder (ex: MG). Prompt recognition and relevant testing before and during therapy is of utmost importance as a majority of cases improve with discontinuation of the drug +/- immunosuppressive therapy. [Table: see text]