Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

Immune checkpoint blockade (CPB) improves melanoma outcomes, but many patients still do not respond. Tumor mutational burden (TMB) and tumor-infiltrating T cells are associated with response, and integrative models improve survival prediction. However, integrating immune/tumor-intrinsic features using data from a single assay (DNA/RNA) remains underexplored. Here, we analyze whole-exome and bulk RNA sequencing of tumors from new and published cohorts of 189 and 178 patients with melanoma receiving CPB, respectively. Using DNA, we calculate T cell and B cell burdens (TCB/BCB) from rearranged TCR/Ig sequences and find that patients with TMBhigh and TCBhigh or BCBhigh have improved outcomes compared to other patients. By combining pairs of immune- and tumor-expressed genes, we identify three gene pairs associated with response and survival, which validate in independent cohorts. The top model includes lymphocyte-expressed MAP4K1 and tumor-expressed TBX3. Overall, RNA or DNA-based models combining immune and tumor measures improve predictions of melanoma CPB outcomes.

[Perinatal outcomes of dichorionic triamniotic triplet pregnancy]

Objective: To analyze the perinatal outcomes in different methods of multifetal pregnancy reduction in dichorionic triamniotic (DCTA) triplet pregnancy. Methods: A retrospective analysis was performed on 57 cases of DCTA triplets in Peking University Third Hospital from January 1, 2010 to January 1, 2020, including 27 cases in expectant pregnancy group and 30 cases in selective fetal reduction (FR) group. The selective FR group was further divided into 3 subgroups according to different FR methods:retaining monochorionic dichorionic (MCDA) group, retaining dichorionic dichorionic (DCDA) group, and retaining singleton group. The perinatal outcomes of expectant pregnancy group and 3 subgroups of selective FR group were compared. Results: The gestational weeks in selective FR group was (34.5±5.7) weeks, and full-term delivery rate was 53% (16/30), respectively higher than those of the expectant pregnancy group (29.9±6.0) weeks and 7% (2/27). The miscarriage rate of the selective FR group was 10% (3/30), lower than that of the expectant pregnancy group (33%, 9/27). The differences between the two groups were statistically significant (all P<0.05). The ratios of pregnancy complications and newborn admission to neonatal ICU (NICU) in the selective FR group were lower than those of the expectant pregnancy group (all P<0.05). In the selective FR group, the gestational weeks in retaining MCDA group (6 cases), retaining DCDA group (13 cases), and retaining singleton group (11 cases) were (32.2±4.3), (33.0±6.3), and (37.4±4.7) weeks; the miscarriage rates were 1/6, 1/13, and 1/11; the premature delivery rates were 4/6, 7/13, and 0/11; the full-term delivery rates were 1/6, 5/13, and 10/11; pregnancies with at least 1 survivor rates were 5/6, 12/13, and 10/11; NICU occupancy rates were 6/8, 9/18 and 0/10, respectively. The retaining singleton group had the highest rate of full-term delivery and the lowest rate of NICU occupancy. Compared with other groups, the differences were statistically significant (all P<0.05). The full-term delivery rate was significantly higher in the retaining DCDA group than that of the expectant pregnancy group (P<0.05). Conclusions: The risk of DCTA triplet pregnancy is high. Reduction of the MCDA pair to singleton has the highest rate of full-term delivery and the lowest rate of NICU occupancy. For pregnant women who wish to retain twin pregnancy, the risk should be fully informed, and consider reduction of one fetus of the MCDA and retaining DCDA twins to continue pregnancy.

Abstract 6670: Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma

Cancer immunotherapy with checkpoint blockade has improved survival and outcomes in melanoma, but still a majority of patients do not respond. Both high tumor mutation burden (TMB) and high T cell infiltration have been associated with response, but integrative models based on DNA or RNA assays have not been comprehensively explored and validated. Focusing on melanomas from patients receiving checkpoint blockade, we generated new and aggregated existing datasets of whole exome sequencing (WES) (n = 189 total) and bulk RNA sequencing (n = 154 total) to derive genomic and transcriptomic factors that predict survival and response to immunotherapy in melanoma.

We quantified T and B cell infiltrates using rearranged T cell receptor (TCR) and immunoglobulin (Ig) sequences, respectively, from DNA or RNA sequencing. High levels of rearranged TCR reads or rearranged Ig reads in RNA-seq were associated with survival (P = 0.0046, P = 0.015) and response (P = 0.0034, P = 0.047). We created RNA-based metrics of T and B cell burden (TCBRNA or BCBRNA) by normalizing the number of rearranged TCR reads by the total number of mapped reads. When we analyzed WES data in patients for whom DNA and RNA were extracted from the same region, we found that the TCBDNA correlated with TCBRNA (rho = 0.73) and BCBDNA with BCBRNA (rho = 0.41), demonstrating that the level of lymphocyte infiltration can be estimated using rearranged TCR or Ig reads from tumor WES alone.

We found that TCBDNA and BCBDNA both associated with survival (P = 0.0023 and 0.0089). In a combined model, patients with high TMB and high TCB DNA survived longer (P = 2.4e-4, HR = 2.68) and had a higher response rate (Fisher P = 0.028). This combined model was superior to models with TMB or TCBDNA alone. Similarly, patients with high TMB and high BCBDNA had longer survival and higher response rates (log-rank P = 0.0029, HR = 2.64, Fisher P = 0.015). We reanalyzed stage III/IV melanomas from TCGA and found that the TMB high, TCBDNA high subgroup had increased survival (P = 0.007).

Next, clustering of tumor transcriptomes identified 5 tumor subtypes based on melanocyte differentiation, immune infiltration and keratin levels. These melanoma subtypes were associated with survival outcomes after immunotherapy (P = 0.019). We found that TBX3, a tumor-expressed transcription factor enriched in poorly differentiated melanomas, was over-expressed among non-responders within the immune-infiltrated subtype and among all patients (P = 3.9e-4, P = 8.7e-5). Patients whose tumors had high immune infiltrate and low expression of TBX3 had longer survival (P = 1.6e-5, HR = 3.39), however this subgroup did not have longer survival in an independent cohort (n = 73, P = 0.10, HR = 2.63). In conclusion, we demonstrate both RNA-based (immune infiltrate and tumor subtype) and DNA-based metrics (TMB/TCB or TMB/BCB) can be used as pre-treatment predictors of survival after checkpoint blockade in melanoma.

Citation Format: Samuel S. Freeman, Moshe Sade-Feldman, Jaegil Kim, Chip Stewart, Arvind Ravi, Monica Arniella, Keren Yizhak, Ignaty Leshchiner, Liudmila Elagina, Oliver Spiro, Dimitri Livitz, Daniel Rosebrock, François Aguet, Jian Carrot-Zhang, Anna Gonye, Gavin Ha, Ziao Lin, Jonathan H. Chen, Dennie T. Frederick, Michal Barzily-Rokni, Marc R. Hammond, Hans Vitzthum, Shauna M. Blackmon, Yunxin J. Jiao, Donald P. Lawrence, Lyn M. Duncan, Anat Stemmer-Rachamimov, Jennifer A. Wargo, Keith T. Flaherty, Genevieve M. Boland, Ryan J. Sullivan, Matthew Meyerson, Gad Getz, Nir Hacohen. Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma [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 6670.

[Sero-prevalence of Babesia infection among voluntary blood donors in Jiangsu Province]

OBJECTIVE

To evaluate the sero-positivity of Babesia infection in voluntary blood donors in Jiangsu region, so as to provide the evidence for transfusion safety.

METHODS

A total of 950 blood samples were collected from voluntary blood donors in Jiangsu Provincial Blood Center from February to May, 2017, and detected by double antigen sandwich ELISA targeting peptides derived from B. microti-secreted antigen 1 (BmSA1). The positive samples were confirmed by microscopy and nested-PCR to determine parasitemia. The prevalence of anti-BmSA1 was analyzed between/among different genders, ages and occupations of the blood donors.

RESULTS

Of the 950 blood screened samples, 5 were positive for anti-BmSA1, and the sero-prevalence of Babesia infection was 0.53%. The 5 samples were all negative by microscopy and nested-PCR. There were no gender- (χ² = 0.01, P =0.92) or age-specific differences (χ² = 0.11, P = 0.95) in the sero-prevalence of Babesia infection; however, there was an occupation-specific difference detected in the sero-prevalence of Babesia infection (χ² = 11.93, P < 0.05).

CONCLUSIONS

Babesia infection is detected in voluntary blood donors in Jiangsu region, which should be paid much attention.

Unveiling the Superconducting Mechanism of Ba_{0.51}K_{0.49}BiO_{3}

The mechanism of high superconducting transition temperatures (T_{c}) in bismuthates remains under debate despite more than 30 years of extensive research. Our angle-resolved photoemission spectroscopy studies on Ba_{0.51}K_{0.49}BiO_{3} reveal an unexpectedly 34% larger bandwidth than in conventional density functional theory calculations. This can be reproduced by calculations that fully account for long-range Coulomb interactions-the first direct demonstration of bandwidth expansion due to the Fock exchange term, a long-accepted and yet uncorroborated fundamental effect in many body physics.Furthermore, we observe an isotropic superconducting gap with 2Δ_{0}/k_{B}T_{c}=3.51±0.05, and strong electron-phonon interactions with a coupling constant λ∼1.3±0.2. These findings solve a long-standing mystery-Ba_{0.51}K_{0.49}BiO_{3} is an extraordinary Bardeen-Cooper-Schrieffer superconductor, where long-range Coulomb interactions expand the bandwidth, enhance electron-phonon coupling, and generate the high T_{c}. Such effects will also be critical for finding new superconductors.

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Treatment with immune checkpoint blockade (CPB) therapies often leads to prolonged responses in patients with metastatic melanoma, but the common mechanisms of primary and acquired resistance to these agents remain incompletely characterized and have yet to be validated in large cohorts. By analyzing longitudinal tumor biopsies from 17 metastatic melanoma patients treated with CPB therapies, we observed point mutations, deletions or loss of heterozygosity (LOH) in beta-2-microglobulin (B2M), an essential component of MHC class I antigen presentation, in 29.4% of patients with progressing disease. In two independent cohorts of melanoma patients treated with anti-CTLA4 and anti-PD1, respectively, we find that B2M LOH is enriched threefold in non-responders (~30%) compared to responders (~10%) and associated with poorer overall survival. Loss of both copies of B2M is found only in non-responders. B2M loss is likely a common mechanism of resistance to therapies targeting CTLA4 or PD1.

[Mast cell in the gingival cancer: histochemical and electron microscopical study]

OBJECTIVE

To observe the relation between mast cells and gingival cancer.

METHODS

The gingival cancer tissue of 24 cases and normal gingival tissue of 7 cases were studied with histochemical and electron microscopical methods.

RESULTS

The results showed that the number of mast cells around the periphery of gingival cancer tissue increased significantly. The histochemical properties of these mast cells differed from the normal gingival tissue. The former did not contain heparin which was present normally. Under electron microscope, according to the characteristic ultrastructure, the mast cells around the gingival cancer were TC mast cells. Some of them showed the appearance of degranulation, and contacted intimately with cancer cells, lymphocytes and macrophages.

CONCLUSION

These results suggested that together with lymphocytes, macrophages, the mast cell contributed to the defense reaction to the cancer tissue.