Abstract C012: Dissecting the reorganization of pancreatic tumor microenvironments after radiation and immunotherapy reveals insights into immunotherapy resistance

Immune checkpoint blockade (ICB) has revolutionized the treatment of many cancers but has been ineffective for the treatment of microsatellite stable (MSS) PDAC. The lack of efficacy of immunotherapies in PDAC is due to: 1) a desmoplastic tumor microenvironment (TME); 2) the presence of suppressive cells, including myeloid derived suppressor cells and regulatory T cells; and 3) the lack of antigen-presenting dendritic cells (DCs) that are important in priming an effective immune response to generate functionally effective tumor antigen-specific T cells. We recently completed a pilot study of dual ICB (Ipilumamab and Nivolumab) with radiation therapy (SBRT 8Gy for 3 fractions) in a cohort of 25 metastatic PDAC patients that had progressed on conventional chemotherapy; this combination conferred an impressive 18% ORR and 29% disease control rate measured on non-irradiated lesions (historical 0% ORR with ICB in PDAC). This led to a phase 2 study in 30 metastatic PDAC patients using this dual modality treatment paradigm. To understand the role of radiation and ICB in altering the PDAC tumor microenvironment we performed single-cell RNA-sequencing and TCR-sequencing (>180k cells), and single-nucleus RNA-sequencing (>300k cells) on 36 tumor biopsies (23 pre-treatment, 13 paired on-treatment between day 10 and 21) from patients undergoing treatment in our phase 2 study. Tumor tissue was taken from distinct tissue sites, including primary tumors in the pancreas, and liver and abdominal wall metastases. We identified distinct tumor cell state distributions within different tissues, and a redistribution of cells from basal/mesenchymal states to classical states after radiation. We identified several state-specific interferon stimulated gene programs thus cataloging distinct responses of epithelial cells with different transcriptional states. Importantly, we found a redistribution of T cells states towards proliferating and exhausted T cells with unique clonality after radiation. Additionally, the myeloid compartment after radiation was enriched for C1QC+ and MHCII+ macrophage subsets, as well as infiltrating CD16/CD16 monocytes and CD14 monocytes, each showing induction of unique sets of interferon stimulated genes (ISGs). We next sought to better understand immunotherapy resistance mechanisms within these PDAC patients despite finding strong ISG induction in several subsets. We analyzed covarying gene programs and identified multicellular communities of cells before and after radiation that underlie interaction networks associated with radiation. Together our data provides the most comprehensive single-cell atlas of paired biopsies to study tumor and immune cell states in the context of radiation and ICB response.

Citation Format: Arnav Mehta, Aparna Parikh, Milan Parikh, Ryan Park, Moshe Sade-Feldman, Lynn Bi, Nicole Carzo, Tarin M. Grillo, Islam Baiev, Olanike Asupoto, Irena Gushterova, Tom LaSalle, Anna Gonye, Emily Blaum, Sebastien Vigneau, Ronan Chaligne, Ana Lako, Thomas Lila, David Nelson, Caroline Porter, Orr Ashenberg, Karthik Jagadesh, William L. Hwang, Christopher Smillie, David P. Ryan, David T. Ting, Theodore Hong, Dana Pe'er, Nir Hacohen. Dissecting the reorganization of pancreatic tumor microenvironments after radiation and immunotherapy reveals insights into immunotherapy resistance [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C012.

GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome

Gut dysmotility is associated with constipation, diarrhea, and functional gastrointestinal disorders like irritable bowel syndrome (IBS), although its molecular underpinnings are poorly characterized. We studied stool frequency (defined by the number of bowel movements per day, based on questionnaire data) as a proxy for gut motility in a GWAS meta-analysis including 167,875 individuals from UK Biobank and four smaller population-based cohorts. We identify 14 loci associated with stool frequency (p ≤ 5.0 × 10^-8). Gene set and pathway analyses detected enrichment for genes involved in neurotransmitter/neuropeptide signaling and preferentially expressed in enteric motor neurons controlling peristalsis. PheWAS identified pleiotropic associations with dysmotility syndromes and the response to their pharmacological treatment. The genetic architecture of stool frequency correlates with that of IBS, and UK Biobank participants from the top 1% of stool frequency polygenic score distribution were associated with 5× higher risk of IBS with diarrhea. These findings pave the way for the identification of actionable pathological mechanisms in IBS and the dysmotility syndromes.

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.

Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC fate or the balance between self-renewal and differentiation. Here, we use single-cell RNA sequencing (scRNA-seq) to identify MHC class II (MHCII) machinery enrichment in two subsets of Lgr5⁺ ISCs. We show that MHCII⁺ Lgr5⁺ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4⁺ T helper (Th) cells. Stimulation of intestinal organoids with key Th cytokines affects Lgr5⁺ ISC renewal and differentiation in opposing ways: pro-inflammatory signals promote differentiation, while regulatory cells and cytokines reduce it. In vivo genetic perturbation of Th cells or MHCII expression on Lgr5⁺ ISCs impacts epithelial cell differentiation and IEC fate during infection. These interactions between Th cells and Lgr5⁺ ISCs, thus, orchestrate tissue-wide responses to external signals.

Improving the diagnosis of LV non-compaction with cardiac magnetic resonance imaging

BACKGROUND

Current diagnostic criteria for left ventricular non-compaction (LVNC) poorly correlate with clinical outcomes. We aimed to develop a cardiac magnetic resonance (CMR) based semi-automated technique for quantification of non-compacted (NC) and compacted (C) masses and to ascertain their relationships to global and regional LV function.

METHODS

We analysed CMR data from 30 adults with isolated LVNC and 20 controls. NC and C masses were measured using relative signal intensities of myocardium and blood pool. Global and regional LVNC masses was calculated and correlated with both global and regional LV systolic function as well as occurrence of arrhythmia.

RESULTS

LVNC patients had significantly higher end-systolic (ES) and end-diastolic (ED) NC:C ratios compared to controls (ES 0.21 [SD 0.09] vs. 0.12 [SD 0.02], p<0.001; ED 0.39 [SD 0.08] vs. 0.26 [SD 0.05], p<0.001). NC:C ratios correlated inversely with global ejection fraction, with a stronger correlation in ES vs. ED (r=-0.58, p<0.001 vs. r=-0.30, p=0.03). ES basal, mid and apical NC:C ratios also showed a significant inverse correlation with global LV ejection fraction (ES basal r=-0.29, p=0.04; mid-ventricular r=-0.50, p<0.001 and apical r=-0.71, p<0.001). Upon ROC testing, an ES NC:C ratio of 0.16 had a sensitivity of 70% and a specificity of 95% for detection of significant LVNC. Patients with sustained ventricular tachycardia had a significantly higher ES NC:C ratio (0.31 [SD 0.18] vs. 0.20 [SD 0.06], p=0.02).

CONCLUSIONS

The NC:C ratio derived from relative signal intensities of myocardium and blood pool improves the ability to detect clinically relevant NC compared to previous CMR techniques.

Microbial reprogramming inhibits Western diet-associated obesity

A recent epidemiological study showed that eating ‘fast food’ items such as potato chips increased likelihood of obesity, whereas eating yogurt prevented age-associated weight gain in humans. It was demonstrated previously in animal models of obesity that the immune system plays a critical role in this process. Here we examined human subjects and mouse models consuming Westernized ‘fast food’ diet, and found CD4⁺ T helper (Th)17-biased immunity and changes in microbial communities and abdominal fat with obesity after eating the Western chow. In striking contrast, eating probiotic yogurt together with Western chow inhibited age-associated weight gain. We went on to test whether a bacteria found in yogurt may serve to lessen fat pathology by using purified Lactobacillus reuteri ATCC 6475 in drinking water. Surprisingly, we discovered that oral L. reuteri therapy alone was sufficient to change the pro-inflammatory immune cell profile and prevent abdominal fat pathology and age-associated weight gain in mice regardless of their baseline diet. These beneficial microbe effects were transferable into naïve recipient animals by purified CD4⁺ T cells alone. Specifically, bacterial effects depended upon active immune tolerance by induction of Foxp3⁺ regulatory T cells (Treg) and interleukin (Il)-10, without significantly changing the gut microbial ecology or reducing ad libitum caloric intake. Our finding that microbial targeting restored CD4⁺ T cell balance and yielded significantly leaner animals regardless of their dietary ‘fast food’ indiscretions suggests population-based approaches for weight management and enhancing public health in industrialized societies.

Probiotic bacteria induce a 'glow of health'

Radiant skin and hair are universally recognized as indications of good health. However, this 'glow of health' display remains poorly understood. We found that feeding of probiotic bacteria to aged mice induced integumentary changes mimicking peak health and reproductive fitness characteristic of much younger animals. Eating probiotic yogurt triggered epithelial follicular anagen-phase shift with sebocytogenesis resulting in thick lustrous fur due to a bacteria-triggered interleukin-10-dependent mechanism. Aged male animals eating probiotics exhibited increased subcuticular folliculogenesis, when compared with matched controls, yielding luxuriant fur only in probiotic-fed subjects. Female animals displayed probiotic-induced hyperacidity coinciding with shinier hair, a feature that also aligns with fertility in human females. Together these data provide insights into mammalian evolution and novel strategies for integumentary health.

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease

BACKGROUND

Pediatric inflammatory bowel disease (IBD) is challenging to diagnose because of the non-specificity of symptoms; an unequivocal diagnosis can only be made using colonoscopy, which clinicians are reluctant to recommend for children. Diagnosis of pediatric IBD is therefore frequently delayed, leading to inappropriate treatment plans and poor outcomes. We investigated the use of 16S rRNA sequencing of fecal samples and new analytical methods to assess differences in the microbiota of children with IBD and other gastrointestinal disorders.

METHODOLOGY/PRINCIPAL FINDINGS

We applied synthetic learning in microbial ecology (SLiME) analysis to 16S sequencing data obtained from i) published surveys of microbiota diversity in IBD and ii) fecal samples from 91 children and young adults who were treated in the gastroenterology program of Children's Hospital (Boston, USA). The developed method accurately distinguished control samples from those of patients with IBD; the area under the receiver-operating-characteristic curve (AUC) value was 0.83 (corresponding to 80.3% sensitivity and 69.7% specificity at a set threshold). The accuracy was maintained among data sets collected by different sampling and sequencing methods. The method identified taxa associated with disease states and distinguished patients with Crohn's disease from those with ulcerative colitis with reasonable accuracy. The findings were validated using samples from an additional group of 68 patients; the validation test identified patients with IBD with an AUC value of 0.84 (e.g. 92% sensitivity, 58.5% specificity).

CONCLUSIONS/SIGNIFICANCE

Microbiome-based diagnostics can distinguish pediatric patients with IBD from patients with similar symptoms. Although this test can not replace endoscopy and histological examination as diagnostic tools, classification based on microbial diversity is an effective complementary technique for IBD detection in pediatric patients.

Evaluating the graduates of the Dalhousie University School of Nursing baccalaureate programme: a quantitative/qualitative responsive model

The purpose of this study was to determine if the Dalhousie University School of Nursing's curriculum enabled its graduates to meet the terminal objectives of the programme and to determine if these objectives were consistent with the requirements of their employers. An explorative, descriptive design using qualitative and quantitative data were employed through a mailed survey and employer focus groups. Stufflebeam's model served as the conceptual framework to guide this product evaluation. The setting for this study was a baccalaureate school of nursing and eight employing agencies in eastern Canada. A total of 190 graduates were sampled comprising basic and post-RN graduates from the class of 1989 to 1991 inclusive. The response rate was 40.5% (n = 77). Analysis of data included frequency and percentage calculations and thematic descriptions of employer and graduate responses. Findings of this study indicated that the graduates and their respective employers rated the nursing programme to be very satisfactory. Implications for curriculum accountability are discussed.

Preparing health professionals for a collaborative health promotion role

Practitioners and educators must consider whether or not the curriculum offered in a university setting by our health professional schools prepares the potential practitioner for work in the multisectorial, interdisciplinary milieu that has been recommended by The Alma Ata Declaration, the Epp Health Promotion document and the Ottawa Charter. I describe a final-year course in Community Health Nursing that is being offered by Dalhousie University School of Nursing. The course is open to generic and post-registration nurses. The course, based on adult learning principles, used a collaborative community development approach. The curriculum was designed to give baccalaureate student nurses the experience of participating in collaborative health promotion directed towards the strengthening of a community. Student, faculty, preceptor and service-based coordinators' evaluation of the two-year implementation of the course is described in the paper.

Primary health care through a community based smoking-cessation program

The International Conference on Primary Health Care, meeting in Alma-Ata, in the Soviet Union, September 12, 1978, expressed the need for urgent action by all governments, all health and development workers and the world community, to protect and promote the health of all people of the world. The world was caught by the phrase which emerged from this conference, "Health For All by the Year 2000" and many have examined the articles of the Alma-Ata declaration and tried to implement them in their corner of the world. This paper describes a community-based smoking-cessation program which was implemented in the province of Nova Scotia, Canada, during the years 1980-1984. Primary to this project was the belief that people have the right and the duty to participate individually and collectively in planning and implementing their health care. This paper describes one community's effort in putting this belief into practice.

Planning and evaluation of cross-cultural health education activities

This paper was written to assist health professionals who are or who are planning to undertake health education activities with people of a different culture. The focus is on the educative function of health promotion. A short summary of relevant learning theory is presented. Some obstacles (pitfalls) encountered in cross-cultural transfer of information, knowledge and skills are presented and the effects of this learning process on the learner and teacher are explored. Examples of possible conflict situations drawn from the author's experiences and research are presented. Variables which influence planning and implementation of health education in cross-cultural settings are examined. A cyclical model which identifies critical questions to be asked and decisions to be made in a four-phased process of assessment, planning, implementation and evaluation is described for the use of health educators in transcultural settings. The need for systematic cultural assessment prior to planning is stressed to ensure relevancy, acceptance and positive outcome of programmes. Cooperative efforts of health educators with existing systems and traditional teachers and involvement of clients during all phases of the decision making process are suggested.

A proposed framework for evaluation of support courses in a nursing curriculum

Evaluation of nursing educational programmes has received increased attention since the early 1970s. Many evaluation models have been proposed; they are intended for evaluation of the total educational programme, but provide little evidence on the relevancy of the support courses to nursing practice. This paper describes one nursing school's experience in evaluation of a support course. The nature and sources of problems and difficulties encountered during the evaluation process are also discussed. The authors propose a framework for evaluation of support courses in a nursing curriculum. This framework is an application of the Glaser, Stufflebeam and Stake models of programme evaluation. It is designed to assist nurse educators to strive for sound curriculum decisions.