Abstract 3478: Feasibility of single-cell transcriptomic profiling of pleural effusions from advanced-stage cancer patients

The pleura is a frequent metastatic site during the evolution of cancers, which can lead to a symptomatic accumulation of pleural fluid that contains tumor and immune cells. To improve patients’ comfort this fluid is removed via chest draining, and the recovered liquid is generally considered as biological waste. Here, we aim to develop an optimized protocol for single-cell sequencing of floating cells in pleural effusion from advanced-stage cancer patients. To date, pleural effusion samples have been obtained from treatment-naïve, advanced-stage cancer patients (lung n= 8, breast n= 3; ovary n=4, others n=4). After red blood cell lysis, 768 cells/sample were isolated using the image-based cellenONE technology. Single-cell RNA sequencing was performed using SORT-seq. Bioinformatic analysis was done using an in-house pipeline on cells passing these filters: >200 detected genes per cell, >500 UMIs per cell, <25% of UMIs mapping on mitochondrial genes and <20% of spike-in reads. Pleural samples exhibited very heterogeneous data quality, which was reflected in a marked difference in the quality control (Qc) metrics between the samples but was not influenced by tumor type. After Qc filtering, the median number of analyzable cells/sample (mNAC) was 153 [5 - 460], for which the median number of expressed genes/cell per sample (mNEG) was 2,431 [1,022 - 4,026]. The time elapsed between patient sample collection and the initiation of single-cell sorting likely impacted data quality (>3h: mNAC: 99; mNEG: 1,553) compared to samples processed more rapidly (<3h: mNAC: 169; mNEG: 2,492), although not reaching statistical significance. A higher isolation frequency and recovery rate during single-cell sorting resulted in the capture of higher quality cells. The duration of single-cell isolation varied between 11’ and 100’ (median: 21’) and was dependent on the initial cell concentration. No significant differences were observed in terms of cell diameter or elongation with regards to cancer type. However, cell diameter was correlated with mNAC. For cell type inference, we used SingleR with the Human Pan-Cancer Atlas database as reference. Epithelial cells were the most predominant cell type in these samples, followed by subpopulations of monocytes and macrophages. A combination of the “mean variance” and “rank based” methods was used to obtain the list of the most variable genes, to define expression clusters and discern samples by cancer type. Calculation of the enrichment of transcriptomic signatures and therapy response signatures (i.e., IFN-gamma) was used to apprehend the potential biological differences between samples and cell subpopulations. Results will be presented at the conference. This protocol is currently applicable to analyze floating cells from pleural effusions and is expected to provide a complementary source for the molecular profiling of advanced-stage cancers.

Citation Format: Sandra Ortiz-Cuaran, Lucas Michon, Marion Godefroy, Joyce Levy, Osman Osman, Maxime Boussageon, Aurélie Swalduz, Maurice Pérol, Bruno Russias, François Monjaret, Pierre Saintigny. Feasibility of single-cell transcriptomic profiling of pleural effusions from advanced-stage cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3478.

Survival and risk of COVID-19 after SARS-COV-2 vaccination in a series of 2391 cancer patients

BACKGROUND

Patients with cancer are at high risk of severe or lethal COVID-19. The impact of SARS-COV-2 vaccination on the risk of developing COVID-19 was investigated in an exhaustive series of patients from a comprehensive cancer center.

METHODS

This is a study of the exhaustive population of 2391 cancer patients who were prescribed SARS-COV-2 vaccination until 09/21. Patient characteristics, documented SARS-COV-2 infection with RT-PCR, and survival were collected. The primary endpoint was the rate of COVID-19 after vaccination. Secondary endpoints included risk factors to develop COVID-19 after vaccination, with a comparison with the cohort of vaccinated health care workers (HCW), and risk factors for death.

RESULTS

From January to September 2021, among 2391 patients with cancer under active treatment in whom a SARS-COV-2 vaccine was prescribed, 659 (28%), 1498 (63%) and 139 (6%) received 1, 2, and 3 doses, respectively. Ninety five patients received a single dose of vaccine after a previous COVID-19. Two thousand two hundred eighty five health care workers (HCW) received one (N = 17, 0.7%), 2-3 (N = 2026, 88.7%) vaccine doses and one dose after COVID-19 (N = 242, 10.6%). With a median follow-up of 142 and 199 days for patients and HCW, respectively. Thirty nine (1.6%) patients and 35 (1.5%) HCW developed COVID-19 after vaccination. Six of 39 cancer patients and no HCW died because ofCOVID-19 within 50 days after diagnosis. Independent risk factors for COVID-19 in vaccinated patients were age, single dose of vaccine without previous COVID-19 and anti-CD20 treatment in the last three months. Independent risk factors for death included metastatic disease, gender, cancer type, but also documented COVID-19 before vaccination.

CONCLUSIONS

Patients receiving two or more doses of COVID-19 vaccine have reduced risk of COVID-19. The risk of death of vaccinated cancer patients presenting COVID-19 remains high. COVID-19 before vaccination is associated with an increased overall risk of death.

Immune checkpoint inhibitor treatment of a first cancer is associated with a decreased incidence of second primary cancer

Background

Second primary cancers (SPCs) are diagnosed in over 5% of patients after a first primary cancer (FPC). We explore here the impact of immune checkpoint inhibitors (ICIs) given for an FPC on the risk of SPC in different age groups, cancer types and treatments.

Patients and methods

The files of the 46 829 patients diagnosed with an FPC in the Centre Léon Bérard from 2013 to 2018 were analyzed. Structured data were extracted and electronic patient records were screened using a natural language processing tool, with validation using manual screening of 2818 files of patients. Univariate and multivariate analyses of the incidence of SPC according to patient characteristics and treatment were conducted.

Results

Among the 46 829 patients, 1830 (3.9%) had a diagnosis of SPC with a median interval of 11.1 months (range 0-78 months); 18 128 (38.7%) received cytotoxic chemotherapy (CC) and 1163 (2.5%) received ICIs for the treatment of the FPC in this period. SPCs were observed in 7/1163 (0.6%) patients who had received ICIs for their FPC versus 437/16 997 (2.6%) patients receiving CC and no ICIs for the FPC versus 1386/28 669 (4.8%) for patients receiving neither CC nor ICIs for the FPC. This reduction was observed at all ages and for all histotypes analyzed. Treatment with ICIs and/or CC for the FPC are associated with a reduced risk of SPC in multivariate analysis.

Conclusion

Immunotherapy with ICIs alone and in combination with CC was found to be associated with a reduced incidence of SPC for all ages and cancer types.

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From 2013 to 2018, 3.9% of the 46 829 patients diagnosed with a first cancer presented with an SPC.

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Treatment of the first cancer with ICIs was associated with a major reduction of SPC.

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CC given for an FPC was also associated with a lower magnitude of reduction of SPC.

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There were no SPC in cancer patients treated with ICIs in the localized phase of their first cancer.

High mortality rate in cancer patients with symptoms of COVID-19 with or without detectable SARS-COV-2 on RT-PCR

Background

Cancer patients presenting with COVID-19 have a high risk of death. In this work, predictive factors for survival in cancer patients with suspected SARS-COV-2 infection were investigated.

Methods

PRE-COVID-19 is a retrospective study of all 302 cancer patients presenting to this institute with a suspicion of COVID-19 from March 1st to April 25th 2020. Data were collected using a web-based tool within electronic patient record approved by the Institutional Review Board. Patient characteristics symptoms and survival were collected and compared in SARS-COV-2 real-time or reverse-transcriptase PCR (RT-PCR)–positive and RT-PCR–negative patients.

Results

Fifty-five of the 302 (18.2%) patients with suspected COVID-19 had detectable SARS-COV-2 with RT-PCR in nasopharyngeal samples. RT-PCR–positive patients were older, had more frequently haematological malignancies, respiratory symptoms and suspected COVID-19 pneumonia of computed tomography (CT) scan. However, respectively, 38% and 20% of SARS-COV-2 RT-PCR–negative patients presented similar respiratory symptoms and CT scan images. Thirty of the 302 (9.9%) patients died during the observation period, including 24 (80%) with advanced disease. At the median follow-up of 25 days after the first symptoms, the death rate in RT-PCR–positive and RT-PCR–negative patients were 21% and 10%, respectively. In both groups, independent risk factors for death were male gender, Karnofsky performance status <60, cancer in relapse and respiratory symptoms. Detection of SARS-COV-2 on RT-PCR was not associated with an increased death rate (p = 0.10). None of the treatment given in the previous month (including cytotoxics, PD1 Ab, anti-CD20, VEGFR2…) correlated with survival. The survival of RT-PCR–positive and –negative patients with respiratory symptoms and/or COVID-19 type pneumonia on CT scan was similar with a 18.4% and 19.7% death rate at day 25. Most (22/30, 73%) cancer patients dying during this period were RT-PCR negative.

Conclusion

The 30-day death rate of cancer patients with or without documented SARS-COV-2 infection is poor, but the majority of deaths occur in RT-PCR–negative patients.

[Value of percutaneous core needle biopsy in the investigation of a suspected bone tumor]

PURPOSE

To Determine the value of percutaneous core needle biopsy in the investigation of a suspected bone neoplasm.

MATERIAL AND METHODS

We performed a retrospective study of 91 core needle biopsies performed between May 1995 and October 2001. Patients were excluded if they had a known primary carcinoma or if an infection was suspected by clinical, physical or laboratory findings. The results were correlated to the analysis of the surgical piece or, for the 28 patients who did not undergo surgery, to the clinical evolution over more than 12 months.

RESULTS

The final diagnosis was metastasis in 29 cases, primary bone tumor in 36 cases and benign lesions in 25 cases. Sensitivity was 92.3% and specificity was 97.4%. For primary malignant bone tumors, results respected histology features and grade in 79.2%. In cases of mistake, because of the correlation of these results to the clinical and radiological context, the treatment of the bony malignant lesions were adapted in 95.8% of cases. Only one major complication was reported in these 91 biopsies.

CONCLUSION

First intention core needle biopsy, confronted with radio-clinical context seems to have a place in the evaluation of bone lesions when a tumor is suspected. This technique, less expensive than an open biopsy and with fewer complications, is best performed as part of a multidisciplinary approach with the surgeon's collaboration.