Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism

Circadian clock genes are emerging targets in many types of cancer, but their mechanistic contributions to tumor progression are still largely unknown. This makes it challenging to stratify patient populations and develop corresponding treatments. In this work, we show that in breast cancer, the disrupted expression of circadian genes has the potential to serve as biomarkers. We also show that the master circadian transcription factors (TFs) BMAL1 and CLOCK are required for the proliferation of metastatic mesenchymal stem-like (mMSL) triple-negative breast cancer (TNBC) cells. Using currently available small molecule modulators, we found that a stabilizer of cryptochrome 2 (CRY2), the direct repressor of BMAL1 and CLOCK transcriptional activity, synergizes with inhibitors of proteasome, which is required for BMAL1 and CLOCK function, to repress a transcriptional program comprising circadian cycling genes in mMSL TNBC cells. Omics analyses on drug-treated cells implied that this repression of transcription is mediated by the transcription factor binding sites (TFBSs) features in the cis-regulatory elements (CRE) of clock-controlled genes. Through a massive parallel reporter assay, we defined a set of CRE features that are potentially repressed by the specific drug combination. The identification of cis -element enrichment may serve as a new way of defining and targeting tumor types through the modulation of cis -regulatory programs, and ultimately provide a new paradigm of therapy design for cancer types with unclear drivers like TNBC.

Predictive value of CDC37 gene expression for targeted therapy in metastatic colorectal cancer

BACKGROUND

CDC37 is a key determinant of client kinase recruitment to the HSP90 chaperoning system. We hypothesized that kinase-specific dependency on CDC37 alters the efficacy of targeted therapies for metastatic colorectal cancer (mCRC).

MATERIAL AND METHODS

Two independent mCRC cohorts were analyzed to compare the survival outcomes between CDC37-high and CDC37-low patients (stratified by the median cutoff values): the CALGB/SWOG 80405 trial (226 and 207 patients receiving first-line bevacizumab- and cetuximab-containing chemotherapies, respectively) and Japanese retrospective (50 refractory patients receiving regorafenib) cohorts. A dataset of specimens submitted to a commercial CLIA-certified laboratory was utilized to characterize molecular profiles of CDC37-high (top quartile, N = 5055) and CDC37-low (bottom quartile, N = 5055) CRCs.

RESULTS

In the bevacizumab-treated group, CDC37-high patients showed significantly better progression-free survival (PFS) (median 13.3 vs 9.6 months, hazard ratio [HR] 0.59, 95% confidence interval [CI] 0.44-0.79, p < 0.01) than CDC37-low patients. In the cetuximab-treated group, CDC37-high and CDC37-low patients had similar outcomes. In the regorafenib-treated group, CDC37-high patients showed significantly better overall survival (median 11.3 vs 6.0 months, HR 0.24, 95% CI 0.11-0.54, p < 0.01) and PFS (median 3.5 vs 1.9 months, HR 0.51, 95% CI 0.28-0.94, p = 0.03). Comprehensive molecular profiling revealed that CDC37-high CRCs were associated with higher VEGFA, FLT1, and KDR expressions and activated hypoxia signature.

CONCLUSIONS

CDC37-high mCRC patients derived more benefit from anti-VEGF therapies, including bevacizumab and regorafenib, but not from cetuximab. Molecular profiles suggested that such tumors were dependent on angiogenesis-relating pathways.

Recent Developments in the Regulation of Heritable Human Genome Editing

In 2018, the Chinese scientist He Jiankui presented his research at the Second International Summit on Human Genome Editing in Hong Kong. While it was intended that he facilitate a workshop, he was instead called on to present his research in heritable human genome editing, where he made the announcement that he had taken great strides in advancement of his research, to the extent that he had gene-edited human embryos and that this had resulted in the live births of two children. While his research ethic and methodology was interrogated, he insisted that two children, twin girls, had been born healthy and that there was another pregnancy (at the time) where birth of a third gene edited child would be imminent. This announcement generated a ripple effect in the scientific community and exposed the gaps in regulation and absence of law relating to the technology. This resulted in a flurry of activity and conversation around regulation of the technology, which scientists stated was not ready for human trials. This article reviews the Third Summit which was held in London in March 2023 and comments on the latest developments in the regulation of heritable human genome editing.

Unlocking Diversity: From Simple to Cutting-Edge Synthetic Methodologies of Bis(indolyl)methanes

From a synthetic perspective, bis(indolyl)methanes have undergone extensive investigation over the past two to three decades owing to their remarkable pharmacological activities, encompassing anticancer, antimicrobial, antioxidant, and antiinflammatory properties. These highly desirable attributes have spurred significant interest within the scientific community, leading to the development of various synthetic strategies that are not only more efficient but also ecofriendly. This synthesis-based literature review delves into the advancements made in the past 5 years, focusing on the synthesis of symmetrical as well as unsymmetrical bis(indolyl)methanes. The review encompasses a wide array of methods, ranging from well-established techniques to more unconventional and innovative approaches. Furthermore, it highlights the exploration of various substrates, encompassing readily available chemicals such as indole, aldehydes/ketones, indolyl methanols, etc. as well as the use of some specific compounds as starting materials to achieve the synthesis of this invaluable molecule. By encapsulating the latest developments in this field, this review provides insights into the expanding horizons of bis(indolyl)methane synthesis.

CCR5 and CCL5 gene expression in colorectal cancer: comprehensive profiling and clinical value

BACKGROUND

The C-C motif chemokine receptor 5 (CCR5)/C-C motif chemokine ligand 5 (CCL5) axis plays a major role in colorectal cancer (CRC). We aimed to characterize the molecular features associated with CCR5/CCL5 expression in CRC and to determine whether CCR5/CCL5 levels could impact treatment outcomes.

METHODS

7604 CRCs tested with NextGen Sequencing on DNA and RNA were analyzed. Molecular features were evaluated according to CCR5 and CCL5 tumor gene expression quartiles. The impact on treatment outcomes was assessed in two cohorts, including 6341 real-world patients and 429 patients from the Cancer and Leukemia Group B (CALGB)/SWOG 80405 trial.

RESULTS

CCR5/CCL5 expression was higher in right-sided versus left-sided tumors, and positively associated with consensus molecular subtypes 1 and 4. Higher CCR5/CCL5 expression was associated with higher tumor mutational burden, deficiency in mismatch repair and programmed cell death ligand 1 (PD-L1) levels. Additionally, high CCR5/CCL5 were associated with higher immune cell infiltration in the tumor microenvironment (TME) of MMR proficient tumors. Ingenuity pathway analysis revealed upregulation of the programmed cell death protein 1 (PD-1)/PD-L1 cancer immunotherapy pathway, phosphatase and tensin homolog (PTEN) and peroxisome proliferator-activated receptors (PPAR) signaling, and cytotoxic T-lymphocyte antigen 4 (CTLA-4) signaling in cytotoxic T lymphocytes, whereas several inflammation-related pathways were downregulated. Low CCR5/CCL5 expression was associated with increased benefit from cetuximab-FOLFOX treatment in the CALGB/SWOG 80405 trial, where significant treatment interaction was observed with biologic agents and chemotherapy backbone.

CONCLUSIONS

Our data show a strong association between CCR5/CCL5 gene expression and distinct molecular features, gene expression profiles, TME cell infiltration, and treatment benefit in CRC. Targeting the CCR5/CCL5 axis may have clinical applications in selected CRC subgroups and may play a key role in developing and deploying strategies to modulate the immune TME for CRC treatment.

Steinernema shori n. sp., a new entomopathogenic nematode (Nematoda: Steinernematidae) from India

In this study, morphological and molecular features were used to identify a new Steinernema sp. from Chhattisgarh, India. Morphological and molecular features provide evidence for placing the new species into the "bicornutum" clade. The new species is characterized by the following morphological features: infective juveniles with a body length of 587 (494-671) μm; a distance from the anterior end to excretory pore of 46 (43-50) μm; a distance from anterior end to nerve ring of 72 μm (61-85 μm); and E% of 88 (77-97). The first-generation males are characterised by 27 genital papillae and very short spicules, with a length of 61 μm (53-67) μm. The SW% and GS% ratio of S. shori n. sp. are 139 (107-190) and 75 (62-90), respectively. The new species is further characterized by sequences of the internal transcribed spacer and partial 28S regions of the ribosomal DNA. Phylogenetic analyses show that S. shori n. sp. is most closely related to S. abbasi, S. kandii, and S. yirgalemense.

Advances in the synthetic strategies of benzoxazoles using 2-aminophenol as a precursor: an up-to-date review

Benzoxazole is a resourceful and important member of the heteroarenes that connects synthetic organic chemistry to medicinal, pharmaceutical, and industrial areas. It is a bicyclic planar molecule and is the most favorable moiety for researchers because it has been extensively used as a starting material for different mechanistic approaches in drug discovery. The motif exhibits a high possibility of broad substrate scope and functionalization to offer several biological activities like anti-microbial, anti-fungal, anti-cancer, anti-oxidant, anti-inflammatory effects, and so on. There has been a large upsurge in the synthesis of benzoxazole via different pathways. The present article presents recent advances in synthetic strategies for benzoxazole derivatives since 2018. A variety of well-organized synthetic methodologies for benzoxazole using 2-aminophenol with aldehydes, ketones, acids, alcohols, isothiocyanates, ortho-esters, and alkynones under different reaction conditions and catalysts, viz. nanocatalysts, metal catalysts, and ionic liquid catalysts, with other miscellaneous techniques has been summarized.

Exploring the synthetic potential of a g-C3N4·SO3H ionic liquid catalyst for one-pot synthesis of 1,1-dihomoarylmethane scaffolds via Knoevenagel-Michael reaction

A highly promising approach for the synthesis of functionalized 1,1-dihomoarylmethane scaffolds (bis-dimedones, bis-cyclohexanediones, bis-pyrazoles, and bis-coumarins) using g-C₃N₄·SO₃H ionic liquid via Knoevenagel-Michael reaction has been developed and the synthesized derivatives were well characterized using spectral studies. The method involved the reaction of C-H activated acids with a range of aromatic aldehydes, in a 2 : 1 ratio catalyzed by a g-C₃N₄·SO₃H ionic liquid catalyst. The use of g-C₃N₄·SO₃H as a catalyst has several benefits, such as low cost, easy preparation, and high stability. It was synthesized from urea powder and chloro-sulfonic acid and was thoroughly characterized using FT-IR, XRD, SEM, and HRTEM. The present work unveils a promising and environmentally friendly method for synthesizing 1,1-dihomoarylmethane scaffolds with high yield, selectivity, and efficiency, using mild reaction conditions, no need for chromatographic separation, and short reaction times. The approach adheres to green chemistry principles and offers a viable alternative to the previously reported methods.

Effects of oral probiotic and lactoferrin interventions on iron-zinc homeostasis, oxidant/antioxidant equilibrium and diarrhoea incidence of neonatal piglets

The objective of this study was to examine the effects of early-life host specific probiotic and lactoferrin (LF) supplementations on diarrhoea incidence, iron (Fe)-zinc (Zn) balance and antioxidant capabilities in serum of neonatal piglets. A total of eight sow litters obtained from parity matched sows were randomly divided into four groups and assigned to one of the four interventions: control (2.0 ml normal saline), bovine lactoferrin (bLF) (100 mg bLF in normal saline), probiotic (Pb) (1×10⁹ cfu of swine origin Pediococcus acidilactici FT28 strain) and bLF+Pb (both 100 mg bLF and 1×10⁹ cfu of P. acidilactici FT28). All the piglets received supplementations once daily orally for first 7 days of life. The incidence of diarrhoea markedly decreased in bLF group compared to control group. Notably, no incidences of diarrhoea were recorded in Pb and bLF+Pb groups. The Zn and Fe concentrations were significantly increased from day 7 to 21 in bLF and on day 21 in bLF+Pb group. No such changes were noted in Pb group. Total antioxidant capacity (TAC) in serum was significantly increased on days 7 and 15 in bLF group and on days 7 and 21 in bLF+Pb group. Malonaldehyde concentration was markedly reduced from day 7 to 21 in bLF and bLF+Pb groups. The concentrations of nitrate on days 15 and 21 and malonaldehyde on day 7 were significantly higher in Pb group, but mean TAC was unaltered from day 0 to 21. Although no correlation between the incidence of diarrhoea and Zn/Fe and oxidant/antioxidant homeostasis was noted in the Pb group, the supplementation of P. acidilactici FT28 alone was sufficient to prevent the incidence of diarrhoea in neonatal piglets. Taken together, it is concluded that strategic supplementation of P. acidilactici FT28 in early life could help in preventing diarrhoea until weaning of piglets.

Abstract 4234: Effects of age-diet interactions on colorectal cancer (CRC) progression in mice

Background. CRC is the third leading cause of cancer related deaths worldwide with age and diet are among the strongest risk factors. CRC characteristics appear to be distinct between younger and older patients. We evaluated the effects of age on CRC tumor biology using syngeneic mice models with a focus on a) specific differences in tumor growth patterns and the role of the tumor microenvironment (TME) in young versus old mice harboring CRC allografts; b) differential dietary effects in young versus old hosts.

Methods. 1 × 106 MC38 cells were subcutaneously implanted into the right flank of young (6 weeks) or old (24 months) C57BL/6 male mice. Mice were randomized into 3 diet groups: A. Standard Chow (SC); B. Calorie Restriction (CR: 30% reduction in total calories); C. High Fat (HF). Parameters studied were daily food intake, body weight, tumor growth and survival. Once endpoint reached, tumors were isolated and processed for RNA sequencing. Cytokine analysis was done on plasma using multiplex immunoassays on the Meso Scale Discovery platform.

Results. Both old and young mice showed significant reduction in tumor growth while on the CR protocol when compared to other dietary groups. Young mice fed with HF diet had increased tumor growth as compared to old. Cytokine analysis showed that the pro tumorigenic IFNγ, TNF α, IL10, IL-12p70, and 1L6 were higher in old mice relative to young. Caloric restriction irrespective of age led to significant reductions in IFNγ, TNFα, and 1L6 compared to other diets. Irrespective of diet, IL10, known for its immunosuppressive role in CRC, was significantly lower in young versus old mice. Proinflammatory IL-5 was significantly higher in young fed a HF diet compared to the other groups. RNA sequencing of the allograft tumors at the end of the study revealed that differentially expressed genes (DEGs) between young and old mice tumors were dramatically influenced by diet. The most affected gene expression pathways were antigen processing and presentation, MHC-II complex assembly and T cell activation. Diet affected the tumor expression of key oncogenes associated with immune escape, cell proliferation, invasion, metastasis, chemotaxis, ECM remodeling and chemosensitivity which were upregulated in old mice and HF diet.

Conclusion. Based on transcriptomic profiles and comprehensive cytokine analysis, our data shows that age-diet interactions significantly influence the host TME leading to differential gene expression in the tumor. Our findings will advance current understanding of the mechanisms by which aging and diet impact CRC onset, progression, metastasis, and therapeutic response but warrants further investigation.

Citation Format: Jae Ho Lo, Shivani Soni, Yan Yang, Goar Smbatyan, Junxiang Wan, Joshua Millstein, Kelvin Yen, Hemal H. Mehta, Brendan Miller, Francesca Battaglin, Pooja Mittal, Lesly Torres Gonzalez, Wu Zhang, Pinchas Cohen, Heinz Josef Lenz. Effects of age-diet interactions on colorectal cancer (CRC) progression in mice. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4234.

Abstract 4671: MAO A, MAO B inhibitors and NMI for colon cancer therapy

Background: Mitochondrial MAO A and MAO B isoenzymes catalyze oxidative deamination of neuroactive and vasoactive monoamines in CNS and peripheral tissues. MAO A inhibitors have been used as antidepressants; MAO B inhibitors have been used for Parkinson’s disease. Recently, we and others have shown MAO inhibitors can be repurposed for cancer therapy. This study focused on the MAO inhibitors as a novel therapeutic strategy for CRC utilizing patient derived xenograft (PDX) platform which recapitulates the patient’s molecular characteristics.

Methods and Results: CRC PDX models were selected from our repository based on MAO A and B expression and activity. To establish two PDX models with high or low MAO A/B activity we implanted patient’s tumor samples (F0 generation) with high MAO A/B activity (MAO high) or low MAO A/B activity (MAO low) in 8 weeks NSG mice (F1 generation). F1 MAO low PDX model showed substantially slower tumor growth rates as compared to MAO high PDX model (200 days vs 65 days), suggesting the role of MAOs in CRC growth. For each PDX model trial, tumors were pooled from 6 F1 PDX mice and implanted in 30 NSG mice (F2 generation). There were five mice in each of experimental groups: one control arm (vehicle: 67% PEG 400, 33% saline) and treatment arms (i.p. for 21 days): 1. MAO A inhibitors: clorygyline: 50mg/kg; 2. Near infrared dye conjugated MAO A inhibitor (NMI): 5 mg/kg; 3. MAO B inhibitor: deprenyl 10mg/kg;4. MAO A & B inhibitor: phenelzine (30mg/kg). MAO high PDX cohort showed significant reduction in tumor volume in mice treated with MAO A inhibitors clorygyline (p=0.009); NMI (p=0.053) and MAO B inhibitor deprenyl (p=0.022), phenelzine (p= 0.097) when compared to control. Angiogenesis marker CD31 staining of tumor tissues showed significant reduction in mice treated with clorygyline and NMI. Additionally, Ki 67 staining demonstrated considerable decrease in cell proliferation and TUNEL assay exhibited increase in apoptosis in tumor treated with clorygyline and NMI. RNA sequencing revealed 50 differentially expressed genes (DEGs) between clorygyline treated tumors and control, 171 between NMI treated and control group (padj &lt;0.05, |fold change| &gt;=1.5). Ingenuity Pathway Analysis showed alterations in pathways including oxidative phosphorylation, sirtuin pathway, estrogen receptor signaling, and mitochondrial dysfunction. NMI showed same efficacy with no toxicity compared to clorygyline even at 10 times lower dose in MAO high PDX model. No significant difference in tumor size was found among treatment groups in MAO low PDX cohort.

Conclusion: Our CRC PDX studies showed both MAO A and B are important for tumor growth and are potential target for therapy. Both MAO A and B inhibitors and NMI (NIR-conjugated MAO an inhibitor, clorgyline) reduced tumor growth. IHC and RNA seq data shows MAO A inhibitor and NMI has similar mechanisms, though NMI is more effective than clorygyline and also can be used for diagnosis.

Citation Format: Shivani Soni, Hui Ju Tseng, Yan Yang, Goar Smbatayan, Unnati Hemant Shah, Jae Ho Lo, Joshua Millstein, Francesca Battaglin, Pooja Mittal, Lesly Torres Gonzalez, Wu Zhang, Jean Chen Shih, Heinz Josef Lenz. MAO A, MAO B inhibitors and NMI for colon cancer therapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4671.

Impact of genetic variants involved in the lipid metabolism pathway on progression free survival in patients receiving bevacizumab-based chemotherapy in metastatic colorectal cancer: a retrospective analysis of FIRE-3 and MAVERICC trials

BACKGROUND

Antiangiogenic drug (AAD)-triggered oxygen and nutrient depletion through suppression of angiogenesis switches glucose-dependent to lipid-dependent metabolism. Blocking fatty acid oxidation can enhance AAD-mediated anti-tumor effects in colorectal cancer (CRC). Therefore, we hypothesised that genetic variants in the lipid metabolism pathway may predict clinical outcomes [overall response rate (ORR), overall survival (OS) and progression-free survival (PFS)] in metastatic CRC (mCRC) patients receiving bevacizumab-based first-line treatment.

METHODS

Genomic DNA from blood samples of patients enrolled in FIRE-3 (a global, randomised, open-label, phase 3 trial, between 2007-6-23 and 2012-9-19, discovery cohort: FOLFIRI/bevacizumab arm, n = 107; control cohort: FOLFIRI/cetuximab arm, n = 129) and MAVERICC (a global, randomised, open-label, phase II study, between 2011-8 and 2015-7, in United States, Canada, Estonia, Ireland, Switzerland, Norway, and Portugal. Validation cohort: FOLFIRI/bevacizumab arm, n = 163) trials, was genotyped using the OncoArray-500 K beadchip panel. The impact on OS and PFS of 17 selected SNPs in 7 genes involved in the lipid metabolism pathway (CD36, FABP4, LPCAT1/2, CPT1A, FASN, ACACA) was analysed using Kaplan-Meier curves, the log-rank test for univariate analyses and likelihood ratio tests of Cox proportional hazards regression parameters for multivariable analyses. ORR and SNP associations were evaluated using Chi-square or Fisher's exact tests.

FINDINGS

In the discovery cohort, patients with FASN rs4485435 any C allele (n = 21) showed significantly shorter PFS (median PFS: 8.69 vs 13.48 months) compared to carriers of G/G (n = 62) in multivariable (HR = 2.87; 95%CI 1.4-5.9; p = 0.00675) analysis. These data were confirmed in the validation cohort in multivariable analysis (HR = 2.07, 95%CI: 1.15-3.74; p = 0.02), but no association was observed in the cetuximab cohort of FIRE-3. In the comparison of bevacizumab vs cetuximab arm in FIRE-3, a significant interaction was shown with FASN rs4485435 (p = 0.017) on PFS.

INTERPRETATION

Our study demonstrates for the first time, to our knowledge, that FASN polymorphisms may predict outcome of bevacizumab-based treatment in patients with mCRC. These findings support a possible role of the lipid metabolism pathway in contributing to resistance to anti-VEGF treatment.

FUNDING

This work was supported by the National Cancer Institute [P30CA 014089 to H.-J.L.], Gloria Borges WunderGlo Foundation, Dhont Family Foundation, Victoria and Philip Wilson Research Fund, San Pedro Peninsula Cancer Guild, Ming Hsieh Research Fund, Eddie Mahoney Memorial Research Fund, Shanghai Sailing Program (22YF1407000), China National Postdoctoral Program for Innovative Talents (BX20220084), China Postdoctoral Science Foundation (2022M710768), National Natural Science Foundation of China (82202892).

SETD2 gene expression and the molecular landscape of colorectal cancer (CRC)

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Background: SETD2, a key methyltransferase modulating histone 3 gene transcription, has been shown to act as a tumor suppressor gene by reducing oxidative stress, colonic inflammation and tumorigenesis in animal models. SETD2 gene expression has been reported to be significantly downregulated in CRC and linked with poorer patient survival. Additionally, SETD2 plays an important role in DNA repair and loss of function mutations have been associated with increased tumor mutational burden (TMB), mismatch repair (MMR) deficiency, and benefit from immunotherapy. Hence, we aimed to characterize the molecular features associated with SETD2 gene expression in CRC. Methods: 15,425 CRC tumors tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (592 genes or whole exome sequencing), RNA (whole transcriptome sequencing), and IHC were analyzed. SETD2-high and -low expression were defined as ≥ top and < bottom quartile of SETD2 transcripts per million (TPM), respectively. Cell infiltration in the tumor microenvironment (TME) was estimated by QuantiSEQ. Mann-Whitney U and X2/Fisher-Exact tests were applied where appropriate, with P-values adjusted for multiple comparisons ( q < .05). Gene expression profiles were analyzed for transcriptional signatures predictive of response to immunotherapy (T cell-inflamed) and MAPK pathway activation (MPAS). Real-world overall survival information was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined patients. Results: SETD2 expression was significantly increased in left-sided/rectal compared to right-sided tumors (median TPM [mTPM] 55.8 vs 51.1, q < .001). SETD2 mutations were associated with reduced SETD2 expression in pMMR/MSS CRC (mTPM 37.9 vs 54.3 in WT, q < .001), although not statistically significant in dMMR/MSI-H CRC (mTPM 43.6 vs 51.7 in WT, P = .17). Compared to SETD2-high tumors, SETD2-low was associated with increased rates of TMB-high (10.4% vs 8.2%, P = .009), dMMR/MSI-H (7.3% vs 5.6%, P = .02), and PD-L1 IHC levels (4.4% vs 2.5%, q < .002). Only minor differences in gene mutation and copy number rates were observed between SETD2-high and -low tumors , whereas SETD2-high TME was associated with increased immune cell infiltration, including neutrophils, B cells, NK cells, M2 macrophages, and dendritic cells ( q < .05). SETD2-high was also associated with increased T cell-inflamed and MPAS signatures (152% and 159% median increase, respectively, q < .001), regardless of tumor MMR status. Among dMMR/MSI-H CRC, SETD2-high tumors receiving immune checkpoint inhibitors had longer time-on-treatment (HR: 0.39, 95% CI: 0.2-0.76, P = .005) and a trend towards longer OS (HR: 0.29, 95% CI: 0.07-1.2, P = .069). Conclusions: Our data show distinct immune biomarkers and TME cell infiltration associated with SETD2 gene expression in CRC. These findings support a key role for SETD2 in modulating anti-tumor immunity and TME.

Mutational analysis of microsatellite-stable gastrointestinal cancer with high tumour mutational burden: a retrospective cohort study

BACKGROUND

Genomic signatures contributing to high tumour mutational burden (TMB-H) independent from mismatch-repair deficiency (dMMR) or microsatellite instability-high (MSI-H) status are not well studied. We aimed to characterise molecular features of microsatellite stable (MSS) TMB-H gastrointestinal tumours.

METHODS

Molecular alterations of 48 606 gastrointestinal tumours from Caris Life Sciences (CARIS) identified with next-generation sequencing were compared among MSS-TMB-H, dMMR/MSI-H, and MSS-TMB-low (L) tumours, using χ2 or Fisher's exact tests. Antitumour immune response within the tumour environment was predicted by analysing the infiltration of immune cells and immune signatures using The Cancer Genome Atlas database. The Kaplan-Meier method and the log-rank test were used to evaluate the impact of gene alterations on the efficacy of immune checkpoint inhibitors in MSS gastrointestinal cancers from the CARIS database, a Memorial Sloan Kettering Cancer Center cohort, and a Peking University Cancer Hospital cohort.

FINDINGS

MSS-TMB-H was observed in 1600 (3·29%) of 48 606 tumours, dMMR/MSI-H in 2272 (4·67%), and MSS-TMB-L in 44 734 (92·03%). Gene mutations in SMAD2, MTOR, NFE2L2, RB1, KEAP1, TERT, and RASA1 might impair antitumour immune response despite TMB-H, while mutations in 16 other genes (CDC73, CTNNA1, ERBB4, EZH2, JAK2, MAP2K1, MAP2K4, PIK3R1, POLE, PPP2R1A, PPP2R2A, PTPN11, RAF1, RUNX1, STAG2, and XPO1) were related to TMB-H with enhanced antitumour immune response independent of dMMR/MSI-H, constructing a predictive model (modified TMB [mTMB]) for immune checkpoint inhibitor efficacy. Patients with any mutation in the mTMB gene signature, in comparison with patients with mTMB wildtype tumours, showed a superior survival benefit from immune checkpoint inhibitors in MSS gastrointestinal cancers in the CARIS cohort (n=95, median overall survival 18·77 months [95% CI 17·30-20·23] vs 7·03 months [5·73-8·34]; hazard ratio 0·55 [95% CI 0·31-0·99], p=0·044). In addition, copy number amplification in chromosome 11q13 (eg, CCND1, FGF genes) was more prevalent in MSS-TMB-H tumours than in the dMMR/MSI-H or MSS-TMB-L subgroups.

INTERPRETATION

Not all mutations related to TMB-H can enhance antitumour immune response. More composite biomarkers should be investigated (eg, mTMB signature) to tailor treatment with immune checkpoint inhibitors. Our data also provide novel insights for the combination of immune checkpoint inhibitors and drugs targeting cyclin D1 or FGFs.

FUNDING

US National Cancer Institute, Gloria Borges WunderGlo Foundation, Dhont Family Foundation, Gene Gregg Pancreas Research Fund, San Pedro Peninsula Cancer Guild, Daniel Butler Research Fund, Victoria and Philip Wilson Research Fund, Fong Research Project, Ming Hsieh Research Fund, Shanghai Sailing Program, China National Postdoctoral Program for Innovative Talents, China Postdoctoral Science Foundation, National Natural Science Foundation of China.

Molecular correlates of DSCR1 expression in colorectal cancer (CRC)

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Background: Down syndrome (DS), a genetic disorder caused by trisomy of chr 21, is associated with a considerably lower risk for solid tumors and other angiogenesis related diseases. DSCR1 belongs to a family of evolutionary conserved protein-coding genes located on chr 21 and is highly upregulated in DS patients. Its product, calcipressin-1, has been shown to reduce cancer risk by suppressing angiogenesis. We previously reported that a germline polymorphism in DSCR1 was associated with time to recurrence in resected CRC and anti-VEGF treatment outcomes in metastatic CRC. Here, we analyzed the molecular landscape of CRC according to DSCR1 expression levels. Methods: 20,237 samples from CRC tested at Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES) were analyzed. Top quartile transcripts per million (TPM) for DSCR1 expression were considered high (Q4) while bottom quartile low (Q1). Cell infiltration (CI) in the tumor microenvironment (TME) was estimated by RNA deconvolution analysis using QuantiSEQ. Interferon-gamma and T-cell inflamed signatures were also calculated from RNA data. X2 and Fisher-Exact tests were used and statistical significance was determined as P-value adjusted for multiple comparisons ( q < 0.05). Results: DSCR1 expression was higher in primary tumors than metastases (10.5 vs 8.1 median TPM, q < 0.05). No significant difference was observed in right- versus left-sided tumors, however rectal tumors showed the highest DSCR1 expression ( P < 0.05). Overall, high DSCR1 TPM were associated with TMB-high (11.3% vs 9.3%), dMMR/MSI-H (7.9% vs 5.9%), and PD-L1 (4.7% vs 3.1%) ( q < 0.01); the association with TMB-H was not significant in pMMR/MSS. DSCR1 high was associated with lower mutation rates of APC, KRAS, TP53 and amplification of FLT1/ FLT3, while higher mutation rates of KMT2C/D, BRAF, PTEN, RNF43, and RSPO3 fusions ( q < 0.0001). Gene set enrichment analysis showed that high DSCR1 expressing tumors were enriched in alterations of several pathways including hypoxia, apoptosis, DNA repair, KRAS signaling, inflammatory response, and oxidative stress-related pathways (all P < 0.05, FDR < 0.25). B cells, macrophages, neutrophils, NK cells, Tregs, cancer associated fibroblasts and endothelial cells were more abundant in the TME of tumors with high DSCR1 while myeloid dendritic cells were lower, regardless of MMR status (all q < 0.001). DSCR1 expression was associated with a higher T-cell inflamed signature and IFN score ( q < 0.05). Conclusions: This is the first and most extensive profiling study to investigate DSCR1 expression in CRC. Our data show a strong association between tumor DSCR1 gene expression and distinct molecular features and TME cell infiltration. These findings suggest that DSCR1 holds potential as a novel therapeutic target for CRC and may be an important player in TME modulation.

Breast cancer and neurotransmitters: emerging insights on mechanisms and therapeutic directions

Exploring the relationship between various neurotransmitters and breast cancer cell growth has revealed their likely centrality to improving breast cancer treatment. Neurotransmitters play a key role in breast cancer biology through their effects on the cell cycle, epithelial mesenchymal transition, angiogenesis, inflammation, the tumor microenvironment and other pathways. Neurotransmitters and their receptors are vital to the initiation, progression and drug resistance of cancer and progress in our biological understanding may point the way to lower-cost and lower-risk antitumor therapeutic strategies. This review discusses multiple neurotransmitters in the context of breast cancer. It also discusses risk factors, repurposing of pharmaceuticals impacting neurotransmitter pathways, and the opportunity for better integrated models that encompass exercise, the intestinal microbiome, and other non-pharmacologic considerations. Neurotransmitters' role in breast cancer should no longer be ignored; it may appear to complicate the molecular picture but the ubiquity of neurotransmitters and their wide-ranging impacts provide an organizing framework upon which further understanding and progress against breast cancer can be based.

Tissue factor expression in colorectal cancer

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Background: Tissue factor (TF), a component of the coagulation cascade, transmembrane receptor, and cofactor for factor VII/VIIa is expressed by subendothelial cells and critical to hemostasis, thrombosis, cell proliferation, angiogenesis, and metastasis. TF is suggested to have a critical role in colorectal cancer (CRC). Here we assessed the clinico-molecular features associated with TF expression (exp) in CRC. Methods: Tumor molecular profiling was performed for 14,0786 samples by NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) and immunohistochemistry (IHC) at Caris Life Sciences (Phoenix, AZ). TF-high (TF-H) and TF-low (TF-L) RNA exp were defined as ≥ 75th- and < 25th-percetile of TF transcripts per million (TPM), respectively. X2/Fisher-exact and Mann Whitney U tests were used for comparison, and P-values were adjusted for multiple comparisons. Cell infiltration in the tumor microenvironment (TME) was estimated by quanTIseq. Real-world overall survival (OS) information was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined patients (pts). Results: TF exp was higher in primary tumors compared to metastatic sites (2.3-fold, P < 0.001); higher in lung vs. liver metastases (0.6-fold and 0.3-fold, p < 0.001); higher in rectal (1.4-fold), right-sided (1.3-fold), and transverse (1.2-fold) compared to left-sided (P < 0.001); and highest in CMS1 tumors (CMS2 0.4-fold, CMS3 0.7-fold, CMS4 0.8-fold, P < 0.001). TF exp was higher in tumors with high TMB (TMB ≥ 10 Mut/Mb) (1.6-fold), dMMR/MSI-H (1.9-fold), and PD-L1 exp (1.8-fold) (P < 0.001 each). Compared to WT tumors, mutations in KRAS (1.2-fold, P < 0.001), BRAF (1.5-fold, P < 0.001) and ERBB2 (1.2-fold, P < 0.01) were associated with higher TF exp. In pMMR/MSS CRC, TF-L tumors were associated with TP53, APC, and NRAS mutations, and TF-H was associated with KRAS, PIK3CA, SMAD4, FBXW7, BRAF, ARID1A, GNAS, SMAD2, RNF43, KMT2D and BRCA1 mutations. TF exp was positively associated with most immune cell populations, most strongly with endothelial cells. In pMMR/MSS KRAS WT CRC, TF-H was associated with worse OS than TF-L. TF-H was also associated with worse OS for pMMR/MSS CRC pts treated with FOLFOX (HR: 1.5, CI:1.2-1.8, p < 0.0001), FOLFIRI (HR:1.7, CI:1.3-2.1, p < 0.0001), VEGF (HR:1.3, CI:1.1-1.6, p = 0.002) and EGFR inhibitors (HR:1.6, CI:1.1-2.3, p = 0.009) than TF-L. TF-H was associated with greater median days on pembrolizumab compared to TF-L in dMMR/MSI-H CRC (HR: 0.6, CI: 0.4-0.9, p = 0.018). Conclusions: Our data show TF exp is associated with distinct clinical and molecular features, including tumor sidedness and metastatic pattern, as well as CMS subtype and KRAS, BRAF and ERBB2 mutations. TME cell infiltration and IO-related biomarkers were enriched in TF-H, with TF exp correlating with endothelial cell abundance. These findings and associations with patient outcomes suggest that TF may be a relevant biomarker and target in CRC.

The role of gene expression of CD47 in colorectal cancer (CRC)

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Background: CD47 belongs to the immunoglobulin superfamily and is overexpressed in many tumor types. CD47 plays an important role in suppressing phagocytosis through binding to transmembrane protein SIRP-alpha on macrophages. Targeting CD47 is a novel strategy for cancer immunotherapy and is being evaluated in ongoing clinical trials. However, molecular characteristics of CD47-overexpressed colorectal cancer (CRC) are largely unknown. Methods: We retrospectively reviewed CRC patient samples (n = 14786) submitted to a commercial CLIA-certified laboratory (Caris Life Sciences, Phoenix AZ). Next-generation sequencing of DNA and RNA (whole-transcriptome sequencing) and immunohistochemistry were performed. Correlation of CD47 expression with danger-associated molecular pattern (DAMP)-related genes ( HMGB1, CALR, ANXA1, HSP90AA1, HSPA1A, and CXCL10) expressions was tested. DAMP signature calculated as composite z-score of the DAMP related genes was compared between CD47-high and -low patients classified according to the median level of CD47 expression. Distributions of KRAS and BRAF mutations, consensus molecular subtype (CMS), and signatures of oncogenic signaling pathways were compared between CD47-high and -low patients. In addition, overall survival (OS) was compared between CD47-high and -low patients available for survival data. Results: CD47 expression level was significantly higher in metastatic compared to primary lesions (1.07-fold, q < 0.05) and microsatellite instability high tumors compared to microsatellite stable tumors (1.15-fold, q < 0.05). CD47 expression was positively correlated with DAMP genes expression except for HSPA1A, and the DAMP signature (median score [MS]: 2.66 vs -2.29, q < 0.05) was significantly increased in CD47-high patients. KRAS mutations were less prevalent (45.87% vs 50.05%) and CMS1(17.72% vs 14.42%) and CMS4 (40.33% vs 27.28%) were more prevalent in CD47-high patients, while no difference was observed in the prevalence of BRAF mutations between CD47-high and -low patients. Signatures of EMT (MS:2.91 vs -3.19), TGF-beta (MS:3.72 vs -3.52), angiogenesis (MS:2.95 vs -2.78), MAPK (MS:4.99 vs -4.12), PI3K (MS:2.41 vs -2.03), and immune-related signaling pathways (MS:1.20 vs -2.51) were significantly enriched in CD47-high patients (all q < 0.05). CD47-high patients (n = 4873) showed significantly worse OS than CD47-low patients (n = 4898) (median OS, 32.4 vs 37.6 months; hazard ratio = 1.158, p< 0.01). Conclusions: Highly CD47-expressed CRC harbored activation of DAMPs and oncogenic signaling pathways that linked to aberrant tumor microenvironment and worse prognosis. Our results support intensive treatment strategies using CD47 inhibitors combined with cytotoxic agents and molecular targeted agents (such as anti-VEGF agents) in CD47-overexpressed CRC.

The role of gene expression of CDC37 in colorectal cancer (CRC)

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Background: CDC37-HSP90 axis is an essential chaperoning system for stabilization of kinases. CDC37 determines selectivity of client kinases recognized by HSP90. We previously showed patients with CDC37-dependent ( CDC37 high expression) colorectal cancer (CRC) derived more benefit from regorafenib and bevacizumab both of which target HSP90 client kinases or signaling pathway, but not from cetuximab which targets HSP90 non-client kinase. However, molecular characteristics and interaction with relevant signaling pathways in CDC37-dependent CRC are largely unknown. Methods: We retrospectively reviewed CRC patient samples submitted to a commercial CLIA-certified laboratory (Caris Life Sciences, Phoenix AZ). Next-generation sequencing of DNA and RNA (whole-transcriptome sequencing) and immunohistochemistry were performed. Molecular profiles between top quartile transcripts per million for CDC37 expression (Q4, CDC37-high: n = 5056) and bottom quartile (Q1, CDC37-low: n = 5056) were compared for gene mutations, microsatellite instability (MSI) status, PD-L1 expression, co-expression of HSP90 genes ( HSP90AA1 and HSP90AB1), MAPK pathway activity score (MPAS), T-cell inflamed signature, and cell infiltration in the tumor microenvironment (TME) assessed by QuantiSEQ. Gene set enrichment analysis (GSEA) was performed between CDC37-high (Q4) and CDC37-low (Q1) tumors. Results: KRAS mutations trended higher in CDC37-high tumors compared to CDC37-low tumors (49.5% vs 47.1%) while APC (76.9% vs 72.3%), TP53 (75.5% vs 71.8%) and TCF7L2 (5.0% vs 3.5%) mutations were significantly higher in CDC37-high tumors compared to CDC37-low tumors (q < 0.05). No significance in expression quartiles were observed for dMMR/MSI-H or PD-L1 expression. HSP90AA1 and HSP90AB1 expression levels were significantly higher in CDC37-high tumors (2.9-fold and 2.6-fold in median, respectively; both q< 0.05). Both MPAS and T-cell inflamed signatures were significantly higher in CDC37-high tumors ( q< 0.05). Infiltration of NK cells, Tregs, neutrophils, M1 macrophages, and B-cells were greater in CDC37-high tumors (q < 0.05). GSEA showed several signaling pathways, such as KRAS, TGF-beta, hypoxia, WNT-beta catenin, and PI3K-AKT-MTOR, were enriched in CDC37-high tumors. Conclusions: Highly CDC37-expressed (CDC37-dependent) CRC was associated with aberrant TME where abundance of immune cell infiltrate and broad activation of kinase-related signaling pathways were evident. Our results support the kinase-stabilizing function of CDC37 in CRC. Further investigations combined with survival data are warranted to address the prognostic and predictive values of CDC37 expression in targeted therapies of CRC.

Synthetic aspects of 1,4- and 1,5-benzodiazepines using o-phenylenediamine: a study of past quinquennial

Benzodiazepines, seven-membered heterocyclic compounds having two nitrogen atoms at different positions, are ruling scaffolds in the area of pharmaceutical industry. They act as cardinal moieties in organic synthesis as well as in medicinal chemistry. Among the different benzodiazepines, 1,4- and 1,5-benzodiazepines play a far-reaching role in the field of biological activities such as anticonvulsion, anti-anxiety, sedation, and hypnotics. In the past few decades, researchers have conducted a lot of work on these moieties and developed broad, valuable, and significant approaches for their synthesis. In this review article, we recapitulate the systematic synthetic strategies of 1,4- and 1,5-benzodiazepines using o-phenylenediamine as a precursor over the past five years (2018-2022). This article will be helpful for scientists and researchers to examine and explore novel and efficient methods for the synthesis of these biologically active moieties.

Neurotransmitter signaling: a new frontier in colorectal cancer biology and treatment

The brain-gut axis, a bidirectional network between the central and enteric nervous system, plays a critical role in modulating the gastrointestinal tract function and homeostasis. Recently, increasing evidence suggests that neuronal signaling molecules can promote gastrointestinal cancers, however, the mechanisms remain unclear. Aberrant expression of neurotransmitter signaling genes in colorectal cancer supports the role of neurotransmitters to stimulate tumor growth and metastatic spread by promoting cell proliferation, migration, invasion, and angiogenesis. In addition, neurotransmitters can interact with immune and endothelial cells in the tumor microenvironment to promote inflammation and tumor progression. As such, pharmacological targeting of neurotransmitter signaling represent a promising novel anticancer approach. Here, we present an overview of the current evidence supporting the role of neurotransmitters in colorectal cancer biology and treatment.

Age differences in the behavioural economics of cannabis use: Do adolescents and adults differ on demand for cannabis and discounting of future reward?

BACKGROUND

Adolescence is a period of psychological and neural development in which harms associated with cannabis use may be heightened. We hypothesised that adolescent who use cannabis (adolescentsWUC) would have steeper delay discounting (preference for immediate over future rewards) and greater demand (relative valuation) for cannabis than adults who use cannabis (adultsWUC).

METHODS

This cross-sectional study, part of the 'CannTeen' project, compared adultsWUC (n = 71, 26-29 years old) and adolescentsWUC (n = 76, 16-17 years old), and gender- and age-matched adolescent (n = 63) and adult (n = 64) controls. AdolescentsWUC and adultsWUC used cannabis 1-7 days/week and were matched on cannabis use frequency (4 days/week). The Monetary Choice Questionnaire assessed delay discounting. A modified Marijuana Purchase Task (MPT) assessed cannabis demand in adolescentsWUC and adultsWUC. The MPT yielded five indices: intensity (amount of cannabis used at zero cost), O_max (total peak expenditure), P_max (price at peak expenditure), breakpoint (cost at which cannabis demand is suppressed to zero) and elasticity (degree to which cannabis use decreases with increasing price). Analyses were adjusted for covariates of gender, socioeconomic status, other illicit drug use.

RESULTS

Both adolescentsWUC and adultsWUC had steeper delay discounting than controls (F, (1,254)= 9.13, p = 0.003, η_p²= 0.04), with no significant age effect or interaction. AdolescentsWUC showed higher intensity (F, (1,138)= 9.76, p = 0.002, η_p²= 0.07) and lower elasticity (F, (1,138)= 15.25, p < 0.001, η_p²= 0.10) than adultsWUC. There were no significant differences in P_max, O_max or breakpoint.

CONCLUSION

Individuals who use cannabis prefer immediate rewards more than controls. AdolescentsWUC, compared to adultsWUC, may be in a high-risk category with diminished sensitivity to cannabis price increases and a greater consumption of cannabis when it is free.

Search for Subsolar-Mass Binaries in the First Half of Advanced LIGO's and Advanced Virgo's Third Observing Run

We report on a search for compact binary coalescences where at least one binary component has a mass between 0.2  M_{⊙} and 1.0  M_{⊙} in Advanced LIGO and Advanced Virgo data collected between 1 April 2019 1500 UTC and 1 October 2019 1500 UTC. We extend our previous analyses in two main ways: we include data from the Virgo detector and we allow for more unequal mass systems, with mass ratio q≥0.1. We do not report any gravitational-wave candidates. The most significant trigger has a false alarm rate of 0.14  yr^{-1}. This implies an upper limit on the merger rate of subsolar binaries in the range [220-24200]  Gpc^{-3} yr^{-1}, depending on the chirp mass of the binary. We use this upper limit to derive astrophysical constraints on two phenomenological models that could produce subsolar-mass compact objects. One is an isotropic distribution of equal-mass primordial black holes. Using this model, we find that the fraction of dark matter in primordial black holes in the mass range 0.2  M_{⊙}<m_{PBH}<1.0  M_{⊙} is f_{PBH}≡Ω_{PBH}/Ω_{DM}≲6%. This improves existing constraints on primordial black hole abundance by a factor of ∼3. The other is a dissipative dark matter model, in which fermionic dark matter can collapse and form black holes. The upper limit on the fraction of dark matter black holes depends on the minimum mass of the black holes that can be formed: the most constraining result is obtained at M_{min}=1  M_{⊙}, where f_{DBH}≡Ω_{DBH}/Ω_{DM}≲0.003%. These are the first constraints placed on dissipative dark models by subsolar-mass analyses.

Genetic variants involved in the cGAS-STING pathway predict outcome in patients with metastatic colorectal cancer: Data from FIRE-3 and TRIBE trials

BACKGROUND

The activation of stimulator of interferon genes (STING) was reported to enhance cetuximab-mediated natural killer cell activation and dendritic cell maturation. Polymorphisms in genes in the cyclic GMP-AMP synthase (cGAS)-STING pathway may affect innate immune response. Therefore, we hypothesised that genetic variants in the cGAS-STING pathway may predict the efficacy of cetuximab-based treatment in patients with metastatic colorectal cancer.

METHODS

Genomic DNA from blood samples of patients enrolled in FIRE-3 (cetuximab arm, n = 129; bevacizumab arm, n = 107) and TRIBE (bevacizumab arm, n = 215) was genotyped using the OncoArray-500K bead chip panel. Seven selected single nucleotide polymorphisms in 3 genes (cGAS, STING and interferon B1 (IFNB1)) were analysed for the association with overall survival and progression-free survival.

RESULTS

In the cetuximab cohort, patients with STING rs1131769 any T allele showed significantly shorter overall survival (36.3 versus 56.1 months) than carriers of C/C in both univariate [hazard ratio (HR) = 2.08; 95% confidence interval (CI): 1.06-4.07; P = 0.03] and multivariate (HR = 2.98; 95% CI: 1.35-6.6; P = 0.0085) analyses; patients carrying IFNB1 rs1051922 G/A and A/A genotype showed a significantly shorter progression-free survival than carriers of G/G allele in both univariate (G/A versus G/G, 10.2 versus 14.1 months, HR = 1.84; 95% CI 1.23-2.76; A/A versus G/G, 10.7 versus 14.1 months, HR = 2.19; 95% CI 0.97-4.96; P = 0.0077) and multivariate analyses (G/A versus G/G, HR = 2; 95% CI 1.22-3.3; A/A versus G/G, HR = 2.19, 95% CI 0.92-5.26, P = 0.02). These associations were not observed in the bevacizumab arm of FIRE-3 or TRIBE.

CONCLUSION

These results suggest for the first time that germline polymorphisms in STING and IFNB1 genes may predict the outcomes of cetuximab-based treatment in patients with metastatic colorectal cancer.

fdrci: FDR confidence interval selection and adjustment for large-scale hypothesis testing

Motivation

Approaches that control error by applying a priori fixed discovery thresholds such as 0.05 limit the ability of investigators to identify and publish weak effects even when evidence suggests that such effects exist. However, current false discovery rate (FDR) estimation methods lack a principled approach for post hoc identification of discovery thresholds other than 0.05.

Results

We describe a flexible approach that hinges on the precision of a permutation-based FDR estimator. A series of discovery thresholds are proposed, and an FDR confidence interval selection and adjustment technique is used to identify intervals that do not cover one, implying that some discoveries are expected to be true. We report an application to a transcriptome-wide association study of the MAVERICC clinical trial involving patients with metastatic colorectal cancer. Several genes are identified whose predicted expression is associated with progression-free or overall survival.

Availability and implementation

Software is provided via the CRAN repository (https://cran.r-project.org/web/packages/fdrci/index.html).

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

DEFB1 gene expression and the molecular landscape of colorectal cancer (CRC)

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Background: Defensins are antimicrobial peptides that play important roles in innate immune response. Deregulation of beta-defensin-1 ( DEFB1) gene expression has been implicated in several cancers and we previously showed that single nucleotide polymorphisms in DEFB1 are associated with clinical outcomes in patients with metastatic CRC. Hence, we aimed to further characterize the molecular features associated with DEFB1 gene expression in CRC. Methods: 14416 CRC tumors tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (592 genes or WES), RNA (WTS) and IHC were analyzed. Top quartile transcripts per million (TPM) for DEFB1 expression were considered high (Q4) while bottom quartile low (Q1). Consensus molecular subtypes (CMS) were assessed using RNAseq. Cell infiltration in the tumor microenvironment (TME) was estimated by QuantiSEQ. X2/Fisher-Exact were used and significance was determined as P-value adjusted for multiple comparison ( Q <.05). Real-world overall survival information was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined patients. Results: DEFB1 expression was highest in left-sided and rectal tumors (median TPM 2.27) and lowest in right-sided tumors (median TPM 1.62). Overall, when compared to low expression, high DEFB1 was negatively associated with high TMB (≥ 10 Mut/Mb) (4.8% vs 17%), dMMR/MSI-H (2.2% vs 13.1%), and PD-L1 expression (3.1% vs 5.2%) (all Q <.05). Additionally, DEFB1 high was associated with higher expression of immune checkpoint genes CD274, CD80, CD86, HAVCR2, LAG3, PDCD1 and PDCD1LG2 (Fold Change/FC: 1.27-1.56) but lower IDO1 (FC: 0.89) (all Q <.05). Similar results were confirmed in MSS tumors only, but IDO1 was now positively associated with DEFB1 high (FC: 1.23). In the MSS cohort, DEFB1 expression was highest in CMS2 and lowest in CMS3 (2.84 vs 1.67 median TPM, Q <.05). In the MSS cohort, APC mutations were more frequent in DEFB1 high tumors (79% vs 72%) while BRAF (5.8% vs 9.4%), GNAS (1.1% vs 4.4%), FBXW7 (7.8% vs 10.5%), SMAD4 (12.3% vs 17%), RNF43 (2.2% vs 3.5%) and POLE (0.2% vs 0.7%) mutations as well as MYC (1.2% vs 2.6%) and MYB amplifications (0.1% vs 0.9%) were less frequent in DEFB1 high (all Q <.05). Higher neutrophils, NK cells, M2 macrophages, CD4+ T cells and myeloid dendritic cells but lower M1 macrophages, Tregs and CD8+ T cells in the TME were significantly associated with high DEFB1; both in the overall and MSS cohorts ( Q <.001). CRC patients with DEFB1 expression level above the median had worse OS compared to those below the median both in the overall cohort (HR: 1.18, 95% CI: 1.10-1.27) and in MSS tumors (HR: 1.18, 95% CI: 1.10-1.27). Conclusions: Our data show a distinct molecular landscape, including mutational profiles, CMS, immune biomarkers, and TME cell infiltration associated with DEF1B gene expression in CRC. These findings suggest a key role for DEF1B in modulating anti-tumor immunity and TME.

Landscape of endocytosis pathway in colorectal cancer (CRC)

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Background: Recent proteogenomic analyses of CRC revealed that driver gene alterations are enriched in the endocytosis pathway (Vasaikar S, et al. Cell 2019;177:1035-49). Endocytosis is a cellular system involving post-translational modification of plasma membrane proteins through internalization, intracellular trafficking, degradation, and recycling. Clathrin-mediated endocytosis (CME) is the main endocytic portal, and endosomal sorting complexes required for transport (ESCRT) play a critical role in the lysosomal degradation pathway. Besides the well-known function of endocytosis attenuating signaling pathways through receptor clearance from the cell surface, the opposite function contributing to signal maintenance has also been reported. However, the clinical implications of the endocytosis pathway alterations in CRC are largely unclear. Methods: We retrospectively reviewed CRC patient samples (n = 15025) submitted to a commercial CLIA-certified laboratory (Caris Life Sciences, Phoenix AZ). Next-generation sequencing of DNA and RNA (whole-transcriptome sequencing) and immunohistochemistry (IHC) were performed. CME-related (47 genes) and ESCRT-related (35 genes) expression signatures were calculated as composite z-scores and compared between subgroups stratified by RAS/ BRAF mutation status, MSS/MSI status, tumor sidedness, and consensus molecular subtype (CMS). VPS4A/ VPS4B expression correlation with major oncogenic pathway signatures (composite z-scores) and CMTM6/ CMTM4/ HIP1R expression association with PD-L1+ IHC were also assessed. Results: Among 17 endocytosis-related genes, no pathogenic/likely pathogenic mutations were identified. The CME-related signature was increased in RAS/ BRAF wild type vs. mutant (0.93 z-score difference, p= 0.04) and MSS vs. MSI-high (6.0 z-score difference, p< 0.01), while the ESCRT-related signature was higher in MSS compared to MSI-high (2.7 z-score difference; p< 0.01). No differences between tumor sidedness were observed in both CME- and ESCRT-related signatures (0.81 and 1.17 z-score differences, respectively). CMS4 had the highest expression of both signatures, while CMS3 had the lowest, of both CME- and ESCRT-related genes (each > 20 z-score difference, p< 0.01). VPS4A and VPS4B expression had a strong positive correlation with WNT, EGFR/MAPK, TGF-beta, and Notch pathway signatures (0.65-0.83 Spearman, all p< 0.01). CMTM6 expression was positively associated with PD-L1+ IHC (1.2-fold increase vs PD-L1-negative, p< 0.01), while CMTM4 and HIP1R expression showed a negative association (0.7- and 0.9-fold decrease, respectively, p< 0.01). Conclusions: This large study indicates endocytosis pathway expression is positively associated with oncogenic pathway signaling in CRC. Further analysis of RAS/ BRAF wild type, MSS, and CMS4 patient subgroups are warranted to determine the efficacy of targeting endocytosis pathways in CRC.

Characterization of TIM3 and its ligands in colorectal cancer

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Background: TIM-3 is an inhibitory checkpoint glycoprotein found on innate and adaptive immune cells and is highly expressed on tumor infiltrating lymphocytes. TIM-3 and its ligands, Galectin 9 (Gal9), HMGB1 and CEACAM1 play a critical role in immune regulation and preclinical data suggest a role in the pathogenesis of colorectal cancer (CRC). We aimed to characterize the molecular features and prognostic value of TIM3 and its ligands in CRC. Methods: Tumor molecular profiling was performed from 15,026 FFPE samples by NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) and immunohistochemistry (IHC) at Caris Life Sciences (Phoenix, AZ). Top quartile transcripts per million (TPMs) for TIM-3, Gal9, HMGB1 and CEACAM1 were considered high (Q4) while bottom quartile low (Q1) expression (exp). X2/Fisher-exact tests were used for comparison and significance was determined as P-value adjusted for multiple comparison and this was found for the results reported here ( Q < 0.05). Cell infiltration in the tumor microenvironment (TME) was estimated by quanTIseq. Real-world overall survival (OS) information was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined pts. Results: Gal 9/TIM3-high tumors had higher prevalence (prev) of high tumor mutational burden (TMB ≥ 10 Mut/Mb) (12% vs. 8%; 14% vs. 6%), deficiency in mismatch repair (dMMR) (9% vs. 5%; 10% vs. 4%), PD-L1 exp (5% vs. 3%; 7% vs. 2%), and was highest in transverse (Fold Change; FC: 1.05, 1.12) and right sided tumors (1.04, 1.10) compared to left sided tumors, and CMS4. In contrast, HMGB1 and CEACAM1-high tumors had lower prev of dMMR (5% vs. 8%, 3% vs. 12%), PD-L1 exp (3% vs. 5%, 3% vs. 6%) and TMB-H (8% vs. 11%, 6% vs. 16%), and was highest in CMS2. In MSS tumors, Gal9/TIM3-high tumors were associated (assoc) with lower frequency of TP53, amplifications (amp) of FLT1/3, CDX2, FOXO1, and CDK8 while CEACAM1 and HMGB1-high were assoc with higher mutation (mut) rates of TP53, APC, NRAS, amp of FLT1/3, CDX2, CDX8, and lower mut in GNAS, FBXW7 and RNF43. High Gal9 and TIM3 exp was assoc with higher infiltration of B cells, M1 and M2 macrophages, NK cells, CD4+ and C8+ T cells, and Tregs, while high HMGB1 and CEACAM1 exp was negatively assoc with Tregs, M1 macrophages, monocytes and CD8+ T cells. High exp of Gal9, TIM3, HMGB1, and CEACAM1 was assoc with worse OS in the entire cohort (HR 0.90, 95%CI, 0.84-0.97, P = 0.005, HR 0.81, 95% CI, 0.75-0.87, P< 0.00001; HR 0.88, 95% CI, 0.82-0.95, P < 0.001; HR 0.80; 95%CI, 0.74-0.86, P < 0.00003, respectively). Conclusions: Strong assoc were identified between Gal9/TIM3, HMGB1 and CEACAM1 gene exp and IO biomarkers, distinct molecular features, CMS, TME cell infiltration, and patient outcomes in CRC. Significantly different mut frequencies may signify unique subsets of CRC. These findings provide rationale for further evaluation of TIM3 and its ligands in CRC as prognostic biomarkers and potential therapeutic targets modifying the TME.

Predictive value of CDC37 gene expression for targeted therapy in metastatic colorectal cancer (mCRC)

3586

Background: HSP90 mediated chaperoning is a well-conserved biological mechanism for stabilization and activation of kinases. More than 60% of human kinases including VEGFR, CRAF, CSF1R, and FGFR are target of HSP90 (client kinases), whereas EGFR is non-client. CDC37 is a specific co-chaperone determining selectivity of client kinases recognized by HSP90. We hypothesized that gene expression levels of CDC37 have predictive values for anti-angiogenic therapies in mCRC. Methods: The subjects of this study were mCRC patients treated with regorafenib (REGO, Japanese retrospective cohort) and those treated with bevacizumab (BEV) or cetuximab (CET) in combination with first-line chemotherapy (CALGB/SWOG 80405 trial cohort). CDC37 expression levels were measured using RNA isolated from FFPE samples by nCounter gene expression profiling (Nanostring) and HiSeq 2500 (Illumina) in the Japanese and CALGB/SWOG 80405 cohorts, respectively. Overall survival (OS) and progression-free survival (PFS) were compared between patients with high CDC37 expression ( CDC37-H) and those with low expression ( CDC37-L), grouped by median cutoff value in each cohort. Results: In total, 484 patients were included (50 treated with REGO, 227 treated with BEV, and 207 treated with CET). In REGO-treated patients, CDC37-H showed significantly better OS (median 11.3 vs 6.0 months, adjusted hazard ratio [HR] 0.24, 95% confidence interval [CI] 0.11-0.54, p <0.01) and PFS (median 3.5 vs 1.9 months, adjusted HR 0.51, 95% CI 0.28-0.94, p = 0.03) compared to CDC37-L. Similarly, in BEV-treated patients, CDC37-H showed significantly better PFS (median 13.5 vs 9.6 months, adjusted HR 0.59, 95% CI 0.43-0.79, p <0.01) and numerically better OS (median 34.1 vs 29.4 months, adjusted HR 0.81, 95% CI 0.60-1.11, p = 0.20) compared to CDC37-L. However, in CET-treated patients, CDC37-H and CDC37-L patients showed similar OS (median 33.7 vs 26.1 months, adjusted HR 1.00, 95% CI 0.73-1.38, p = 0.98) and PFS (median 11.3 vs 11.0 months, adjusted HR 1.08, 95% CI 0.81-1.45, p = 0.60). Significant interaction was observed between CDC37 expression and treatment in terms of PFS in the CALGB/SWOG 80405 cohort ( p = 0.01). Conclusions: Our results suggest patients with CDC37-dependent ( CDC37-H) tumors may derive more benefit from REGO and BEV both of which target HSP90 client kinases or signaling pathways, but not from CET which target HSP90 non-client kinase. Further validation studies are warranted to develop a novel personalized approach for targeted therapies based on CDC37 expression in mCRC patients. Support: U10CA180821, U10CA180888; Pfizer, Genentech; https://acknowledgments.alliancefound.org. ClinicalTrials.gov Identifier: NCT00265850.

Characterization of NY-ESO-1 gene expression in gastric cancer (GC)

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Background: Tumor specific antigens, such as NY-ESO-1 , are emerging as key tumor immune modulating factors with great potential to be used as therapeutic targets to enhance immunotherapy efficacy and expand treatment options for GC. We sought to compare GC tumors expressing high vs low levels of NY-ESO-1 in terms of immune cell abundance in the tumor microenvironment (TME) as well as distinct molecular features and immune biomarkers. Methods: 1967 tumor samples tested with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) by Caris Life Sciences (Phoenix, AZ) were retrospectively reviewed. The top quartile of transcripts per million was considered high while the bottom quartile was considered low NY-ISO-1 expression. Tumor mutational burden (TMB) was calculated based on somatic nonsynonymous mutations. Mismatch repair deficiency/microsatellite instability (dMMR/MSI) status was evaluated by a combination of IHC, fragment analysis and NGS of known MSI loci. Gene fusions were detected based on WTS. X2, Fisher-exact, and Mann Whitney tests were used for comparison and significance adjusted for multiple testing by Benjamini-Hochberg correction ( q < 0.05). Cell infiltration in the TME was estimated by quanTIseq. Gene expression profiles were analyzed for a transcriptional signature predictive of response to immunotherapy (T cell-inflamed signature: TIS). Results: The analysis was focused on primary tumors (N = 1323) in this initial study. Expression of NY-ESO-1 was lower in primary/local than metastases (Fold Change FC met vs primary: 1.60, q < 0.05). NY-ESO-1 expression did not appear to be strongly associated with distinct gene mutation profiles in GC. There were no significant differences between low and high expression of NY-ESO-1 with regards to well established immuno-oncology markers (dMMR/MSI, TMB, PD-L1). However, high NY-ESO-1 expression was positively associated with immune related gene expression including CD274, CD80, CD86, CTLA4, HAVCR2, IDO1, IFNG, LAG3, PDCD1, and PDCD1LG2 (FC low vs high: 0.56 to 0.79, q < 0.0001). High NY-ESO-1 expression was also positively associated with cell abundance in the TME including NK cells (FC = 0.87, q < 0.0001), monocytes (FC = 0.29, q < 0.05), myeloid dendritic cells (FC = 0.66, q < 0.0001), CD4+ non-reg T cells (FC = 0.54, q < 0.0001), and CD8+ T cells (FC = 0.73, q < 0.05). Similarly, tumors with high NY-ESO-1 expression were associated with higher TIS scores ( q < 0.0001). Conclusions: In our large cohort of GC, tumors expressing high NY-ESO-1 displayed a distinct landscape of immune cells in the TME and were associated with high expression of immune related genes, as well as high TIS score, which has been reported to predict benefit from anti-PD-1 treatment. The results of our analysis support an association between a more immunologically active tumor microenvironment and NY-ESO-1 gene expression which may have relevant implications on immunotherapy treatment for GC.

Molecular correlates of MAEA expression in colorectal cancer (CRC)

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Background: Macrophage Erythroblast Attacher (MAEA) plays an important role in actin cytoskeleton rearrangement in macrophages and erythroid cells. We previously reported that MAEA suppresses migration, invasion and enhances chemosensitivity in CRC cell lines. Here we aimed to characterize the molecular features associated with MAEA gene expression in CRC. Methods: 14416 CRC were tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS). Top quartile transcripts per million (TPM) for MAEA expression were considered high (Q4) while bottom quartile low (Q1). Consensus molecular subtypes (CMS) were assessed using RNAseq. Cell infiltration (CI) in the tumor microenvironment (TME) was estimated by QuantiSEQ. X2 and Fisher-Exact tests were used and significance was determined as P-value adjusted for multiple comparisons ( Q < 0.05). Results: MAEA expression was highest in rectal tumors (13.6 median TPM) followed by transverse and right-sided tumors (13.0 and 12.8, respectively) and lowest in left-sided tumors (12.5). Overall, MAEA TPM were associated with higher tumor mutational burden (≥ 10 Mut/Mb) (11.8% vs. 8.2%) and dMMR/MSI-H (8.7% vs. 5.1%) ( Q < 0.0001); however, the association with TMB was not observed in MSS tumors. In the MSS cohort, MAEA expression was the highest in CMS4 (14.9 median TPM) followed by CMS1 (12.5), CMS2 (11.9), and the lowest in CMS3 (10.3, all intergroup Q < 0.05). MAEA high was associated with lower mutation rates of APC and amplification of FLT1/ FLT3 while higher mutation rates of ASXL1, KMT2A/C/D, SMARCA4, FBXW7, PTEN, RNF43, BRCA2, HNF1A in the overall cohort ( Q < 0.05). In the MSS cohort, FBXW7 mutation significance with MAEA high expression held true ( Q < 0.05) while MAEA high expression trended to associate with higher mutation rates of KMT2D, SMARCA4, PTEN, BRCA2 mutations, and a lower frequency of FLT1/ FLT3 CNA ( P < 0.05 but Q > 0.05). High MAEA was associated with higher immune CI in the TME, including B cells, macrophages (M1 and M2), neutrophils, NK cells, Tregs, CD4+ T cells and myeloid dendritic cells both in the overall cohort and in MSS tumors (fold change: 1.11-1.33, all Q < 0.001). Conclusions: Our data show a strong association between MAEA gene expression and distinct molecular features (including CMS and immune biomarkers) and TME cell infiltration in CRC. These findings suggest that targeting MAEA may have relevant clinical applications in selected CRC subgroups and MAEA may be an important player in determining the composition of the TME.

Comprehensive profiling of clock genes expression in colorectal cancer (CRC)

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Background: Disruption of the circadian clock has been linked to cancer risk, development and progression. Core clock proteins are emerging as novel therapeutic targets in cancer. We previously showed that polymorphisms in clock genes were associated with anti-VEGF treatment outcome in metastatic CRC. Here we further evaluated the molecular landscape of clock pathway alterations in CRC. Methods: 7591 CRC tested at Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES) were analyzed. Clock gene Score (CS) was determined using expression of core clock genes Z scores (positives of CLOCK, ARNTL, RORA/B/C and negatives of repressors CRY1/2, PER1/2/3, REVERBA/B) stratified by quartiles. xCell was used to quantify cell infiltration in the tumor microenvironment (TME). Consensus molecular subtypes (CMS) were assessed by RNAseq. Significance was determined as P-values adjusted for multiple testing ( q) of <.05. Real world survival was obtained from insurance claims data and Kaplan-Meier estimates were calculated for comparison. Results: CS was higher in primary tumors than metastases and in right- than left-sided CRC ( P <.001). Liver metastases were associated with lower CS (23% Q1 vs 19% Q4, P <.001). CS was positively associated with CMS1 and 3 (21 vs 11% and 23 vs 9%, respectively, Q4 vs Q1) and negatively correlated with CMS2 and 4 (22 vs 32% and 34 vs 48%) (all P <.001). These associations were confirmed in mismatch repair proficient (pMMR) tumors. Overall, TMB-H and dMMR/MSI-H were positively associated with CS (11 vs 6% and 8 vs 4%, Q4 vs Q1, q <.0001) and PD-L1 showed a similar trend ( P <.01, q =.06); the association with TMB-H was not significant in pMMR. High CS was associated with alterations of genes in WNT signaling, RAS, PI3K, TGF-β, and NOTCH pathways, while negatively associated with TP53 mutations, HER2 expression and CDX2 copy numbers, confirmed in pMMR (all q <.05). CS negatively correlated with the angiogenesis pathway signature (Q1 vs Q4 Z score: 6.6 vs -4.6, P <.001). B cells, M1 and M2 macrophages, neutrophils, NK, Tregs, CD4+ and CD8+ T cells, and myeloid dendritic cells were more abundant in the TME of tumors with high CS while cancer associated fibroblasts were lower, regardless of MMR status (all q <.001). Individually, ARNTL tumor expression below median was associated with better OS (overall: HR 0.88, 95% CI [0.82-0.94]; pMMR: HR 0.88 [0.81-0.94]) and longer time on treatment of bevacizumab (overall: HR 0.91 [0.83-0.99]; pMMR: HR 0.91 [0.83-0.99]). Conclusions: This is the most extensive profiling study to investigate the expression of clock genes in CRC. Our data show that clock genes expression is strongly associated with distinct molecular features, immune cell infiltration, angiogenesis pathway enrichment and patient outcomes. These findings support the clock pathway as a therapeutic target in CRC, with a major role in CRC biology and TME modulation.

Claudin 18 (CLDN18) gene expression and related molecular profile in gastric cancer (GC)

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Background: Claudins are transmembrane proteins which maintain the tight junction between cells. The stomach specific isoform, CLDN18 isoform 2 (CLDN18.2), is emerging as a promising treatment target because of high expression in GC cells, including targeting via adoptive T-cell strategies. We characterized the molecular features associated with CLDN18 isoform 1 and 2 ( CLDN18.1/ 18.2) gene expression in GC. Methods: Tumor profiling was performed from 1967 samples by NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) at Caris Life Sciences (Phoenix, AZ). EBER (Epstein Barr Virus) was tested by CISH. Top quartile transcripts per million for CLDN18.1/18.2 were considered high while bottom quartile low expression. X2, Fisher-exact, and Mann Whitney tests were used and significance adjusted for multiple testing by Benjamini-Hochberg (q <.05). Cell infiltration in the tumor microenvironment (TME) was estimated by quanTIseq. Gene expression profiles were analyzed for a transcriptional signature predictive of response to immunotherapy (T cell-inflamed signature, TIS). Results: CLDN18.2 expression was detected in 97% of the samples and CLDN18.1 in 63%. Primary tumors had significantly higher expression levels of both CLDN18.1/18.2 (Fold Change 18.1: 0.50; 18.2: 0.65), compared to metastatic tumors ( p <.05), thus we focused on the comparison of CLDN18 high and low in primary tumors. CLDN18.2 high expression group had higher CLDN18: ARHGAP26 fusion positive rate (low vs high: 0.91% vs 5.5%, q <.0001), and a trending association with CDH1 mutation (11.7% vs 20.7%, p <.01, q >.05) and EBER (2.15% vs 6.31%, p <.05, q >.05). There were more prevalent ARHGAP26 fusions in the CLDN18.1/18.2 high group (18.1: 9.5% vs 3.86%, p =.001; 18.2: 10.1% vs 0.9%, q <.0001), with the most common fusion between CLDN18 exon 5 and ARHGAP26 exon 12. CLDN18.2 high expression demonstrated an inverse trending correlation with PD-L1 (24.9% vs 18.3%, p <.05; q >.05) and TMB-H (19.6% vs 12.2%, p <.05; q >.05). Similarly, CLDN18.1/18.2 displayed an inverse relationship with M1 Macrophages, NK cells, CD4+ T cells, myeloid dendritic cells in the TME ( q <.05); with higher CLDN18 expression associated with fewer immune cells and a colder TME, especially in isoform 2. The TIS score was significantly higher in the CLDN18.2 high expression group ( q <.05), but lower in CLDN18.1 high expression group ( q <.0001), respectively. Conclusions: This is one of the most comprehensive dedicated analyses on CLDN18 related to tumor molecular features, TME and immunotherapy response in GC. Tumors expressing high CLDN18, especially 18.2, displayed distinct genomic and transcriptomic alterations in immune biomarkers and immune cell infiltration in the TME. Anti-CLDN18.2 monoclonal antibodies are being tested in GC and CLDN18 is a target for ADC and CAR-T therapies. Our data suggest that expression may play a role in guiding patient selection and treatment combinations.

Predictive value of MAOB gene expression for targeted therapy in patients (pts) with metastatic colorectal cancer (mCRC) enrolled in CALGB (Alliance)/SWOG 80405

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Background: Monoamine oxidases (MAOs), including MAOA and MAOB, are mitochondrial enzymes responsible for catalyzing monoamine oxidation. Increased expression of MAOs were found in several cancer types and high MAOB was associated with worse disease stage and poorer survival in CRC. Positive and negative correlations of MAOB expression with mesenchymal type and epithelial type gene expressions, respectively, have been reported. Hence, we investigated whether MAOB expression is predictive for targeted therapies in mCRC. Methods: 430 mCRC pts treated with either bevacizumab (BEV, n = 224) or cetuximab (CET, n = 206) in combination with first-line chemotherapy within the CALGB/SWOG 80405 trial were included in the analysis. MAOB RNA was isolated from FFPE tumor samples and sequenced on the HiSeq 2500 (Illumina). Overall survival (OS) and progression-free survival (PFS) were compared between groups of pts categorized by tertiles of MAOB expression into high (H), medium (M) and low (L). Hazard ratios (HR) and 95% confidence intervals (CI) were computed from multivariable Cox proportional hazards model, adjusting for age, sex, location, number of metastases, KRAS, MSI status, and treatment with FOLFOX or FOLFIRI. Sensitivity analyses were conducted after stratifying by sex. Logrank P-values describe differences without adjustment for patient characteristics. Results: In CET-treated pts, MAOB-L showed significantly longer OS (median 39.2 vs 30.9 vs 15.9 months, logrank P = 4.7E-05, L vs H (as reference) adjusted HR 0.42, 95% CI [0.27, 0.65]) and PFS (median 13.2 vs 11.8 vs 7.6 months, logrank P = 0.006, L vs H adjusted HR 0.59 [0.40, 0.88]) compared to MAOB-M and MAOB-H, respectively. Similar results were observed when evaluating MAOB expression as a continuous variable. In BEV-treated pts, no significant differences were observed when comparing MAOB expression tertiles; however, pts with lower MAOB expression had significantly better OS, but not PFS, when evaluating MAOB as a continuous variable (Cox LRT P = 0.015, covariate adjusted). In CET-treated pts, the effect of MAOB expression was observed in male but not female pts (OS: median 40.3 vs 30.9 vs 16.1 months by MAOB-L, M, H, respectively, logrank P = 6.8E-05, L vs H adjusted HR 0.33 [0.19, 0.59]; PFS: median 13.8 vs 12.6 vs 7.9 months, logrank P = 0.001, L vs H adjusted HR 0.46 [0.28, 0.79]). A significant interaction was observed between MAOB expression and treatment for OS ( P = 0.010) in males and females combined, but only in males ( P = 0.018) when stratified by sex. Conclusions: Our results suggest that pts with MAOB-L tumors may have greater benefit from CET-based treatment and that targeting MAOB may be a promising strategy to improve patient outcomes. Further validation studies are warranted to develop a novel personalized approach based on MAOB expression in mCRC pts. Clinical trial information: NCT00265850.

Comprehensive characterization of PTPRT expression in colorectal cancer (CRC)

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Background: PTPRT is a protein coding gene involved in signal transduction and cellular adhesion. It acts as a tumor suppressor gene and mutated PTPRT has been implicated in the early metastasis of CRC. PTPRT mutations have been reported as independent potential biomarkers for bevacizumab resistance in metastatic CRC and linked to improved response and survival of patients treated with checkpoint inhibitors in several tumors. Here we characterized the molecular features and clinical outcomes associated with PTPRT gene expression in CRC. Methods: 15025 CRC tested with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) by Caris Life Sciences (Phoenix, AZ) were analyzed. Top quartile transcripts per million for PTPRT expression were considered high (H) and bottom quartile low (L). Cell infiltration in the tumor microenvironment (TME) was estimated by QuantiSEQ. X2, Fisher-Exact, Mann-Whitney tests were used and significance determined as P-value adjusted for multiple comparisons ( Q <.05). Real world survival was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined patients. Results: PTPRT expression was higher in left- than right-sided CRC and in metastases than primary/local tumors; it was highest in CMS4 and lowest in CMS1 (all Q <.05). PTPRT mutants had lower expression than wild type (0.037 vs 0.064, Q <.05). Overall, PTPRT-H had a lower rate of TMB-H (5% vs 17%), deficient mismatch repair (dMMR) (3% vs 13%) and PD-L1 (2% vs 6%) (H vs L, all Q <.05). In the proficient MMR (pMMR) cohort, PTPRT-H remained inversely correlated with TMB and PD-L1, was negatively associated with rates of mutated KRAS, PIK3CA, SMAD4, FBXW7, and positively associated with mutated TP53 and CDX2 amplification (all Q <.05). Expression of immune related genes was higher in PTPRT-H CRC, including CD274, CD80, CD86, CTLA4, HAVCR2, IDO1, IFNG, LAG3, PDCD1, and PDCD1LG2, regardless of MMR status (all Q <.05). PTPRT-H was associated with higher immune cell infiltration in the TME including B cells, M2 macrophages, neutrophils, NK, Tregs, CD4+ and CD8+ T cells, and myeloid dendritic cells (fold change/FC: 1.21-7.1), but lower M1 macrophages (FC: 0.76), regardless of MMR status (all Q <.05) with the only exception of CD8+ T cells in dMMR. PTPRT expression above median was associated with better OS (overall: HR 0.69, 95% CI [0.64-0.74]; pMMR: HR 0.67 [0.63-0.73]), longer time on treatment of bevacizumab (overall: HR 0.80 [0.74-0.87], pMMR: HR 0.80 [0.74-0.87]), and shorter time on immunotherapy treatment in the dMMR cohort (HR 2.13 [1.33-3.45]). Conclusions: Our data show a strong association between PTPRT expression and distinct molecular features (including CMS and immune biomarkers), TME cell infiltration and targeted treatment outcomes in CRC. These findings support PTPRT as a candidate prognostic and predictive biomarker for bevacizumab and immunotherapy treatment, and as a potential target in CRC.

Patient outcomes following transfer between intensive care units during the COVID-19 pandemic

Transferring critically ill patients between intensive care units (ICU) is often required in the UK, particularly during the COVID-19 pandemic. However, there is a paucity of data examining clinical outcomes following transfer of patients with COVID-19 and whether this strategy affects their acute physiology or outcome. We investigated all transfers of critically ill patients with COVID-19 between three different hospital ICUs, between March 2020 and March 2021. We focused on inter-hospital ICU transfers (those patients transferred between ICUs from different hospitals) and compared this cohort with intra-hospital ICU transfers (patients moved between different ICUs within the same hospital). A total of 507 transfers were assessed, of which 137 met the inclusion criteria. Forty-five patients underwent inter-hospital transfers compared with 92 intra-hospital transfers. There was no significant change in median compliance 6 h pre-transfer, immediately post-transfer and 24 h post-transfer in patients who underwent either intra-hospital or inter-hospital transfers. For inter-hospital transfers, there was an initial drop in median PaO₂ /F_I O₂ ratio: from median (IQR [range]) 25.1 (17.8-33.7 [12.1-78.0]) kPa 6 h pre-transfer to 19.5 (14.6-28.9 [9.8-52.0]) kPa immediately post-transfer (p < 0.05). However, this had resolved at 24 h post-transfer: 25.4 (16.2-32.9 [9.4-51.9]) kPa. For intra-hospital transfers, there was no significant change in PaO₂ /F_I O₂ ratio. We also found no meaningful difference in pH; PaCO₂ ;_, base excess; bicarbonate; or norepinephrine requirements. Our data demonstrate that patients with COVID-19 undergoing mechanical ventilation of the lungs may have short-term physiological deterioration when transferred between nearby hospitals but this resolves within 24 h. This finding is relevant to the UK critical care strategy in the face of unprecedented demand during the COVID-19 pandemic.

Identification and characterization of recurrent neoantigens in upper gastrointestinal (GI) cancers

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Background: Neoantigens are short peptides derived from tumor-specific somatic mutations that can bind to HLA molecules and be presented on the cell surface to activate the immune system. Recognition of neoantigens by autologous T cells promotes sensitivity to immune checkpoint blockade of mismatch repair deficient (MMRd)/microsatellite instability high (MSI-H) tumors. Neoantigen-targeted reactivity by autologous T cells has also been reported in microsatellite stable (MSS) tumors. We aimed to comprehensively assess the spectrum of neoantigens in upper GI cancers and identify recurrent immunogenic candidate neoantigens. Methods: 600 tumor specimens including 268 esophageal (EC), 211 gastric (GC), and 121 gastroesophageal junction (GEJ) cancers tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing (NGS) on DNA (whole exome) and RNA (whole transcriptome) were analyzed. MSI status was determined by immunohistochemistry of MMR protein and/or NGS. Immune epitope prediction was performed on translated peptide sequences harboring detected mutations using the NetMHCpan v4.0 method in the Immune Epitope Database, with HLA genotyping performed using arcasHLA. Immune/stromal cell abundance was quantified using the Microenvironment Cell Populations Counter method. Gene expression profiles were analyzed for a transcriptional signature predictive of response to immunotherapy (T cell-inflamed signature, TIS). Results: Overall, the median patient age was 66 years (range 22-90), 72.8% were male, and 33.7% of samples were metastatic site biopsies. MMRd/MSI-H rate was 2.2% in EC, 12.4% in GC, and 2.5% in GEJ. A total of 1172 unique recurrent neoantigens with predicted binding-level affinity for patient specific HLA alleles were identified (317 in EC, 786 in GC, 157 in GEJ), with 442 and 552 neoantigens exclusively associated with MSS and MSI-H tumors, respectively. Across each cancer type, a higher positive TIS score correlated with both immune and stromal cell population abundance in the tumor microenvironment, most notably cytotoxic lymphocyte and monocytic cell types (r > 0.80, P < 0.0001). Recurrent peptides associated with highest average TIS scores resulted from mutation of TP53 (R248W, 2 peptides: 2.8%/3.2% of samples, respectively) and CUX1 (L162F, 1.6%) in MSS EC; REL (D318A, 2.3%) and ERBB2 (V842I, 1.2%) in MSS GC; MSH3 (K383fs, 36%) and ASXL1 (G645fs, 24%) in MMRd/MSI-H GC; and HOXD12 (A70-A71dup , 2.8%) and TP53 (R248Q, 3.7%) in MSS GEJ. Conclusions: This is one of the largest studies to investigate the landscape of recurrent neoantigens in upper GI cancers. We were able to identify candidate recurrent peptides with high HLA binding affinity and an association with a positive TIS signature in both MSI and MSS tumors, supporting the role of recurrent neoantigens as potential cancer immunotherapy targets.

Hippo pathway signaling associated with immune cell trafficking in colorectal cancer

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Background: Emerging evidence suggests subsets of the Hippo pathway have multiple functions of tumor development and immune response regulation. Increased understanding of the molecular characteristics of its signaling pathways and the impact on immune cell trafficking will be critical to develop colorectal cancer (CRC) therapies. Methods: A total of 13,008 CRC tumors were analyzed at Caris Life Sciences (Phoenix, AZ) with whole transcriptome and whole exome sequencing (NovaSeq). MSI-H/dMMR was tested by NGS (next generation sequencing), immunohistochemistry (IHC), and fragment analysis. Tumor mutational burden (TMB)-High was determined with a 10-mt/MB cutoff. RNA-deconvolution using QuantiSEQ was used to assess immune cell infiltration in the tumor microenvironment. Consensus molecular subtypes (CMS) were developed using RNA expression data. Gene expression was reported as transcripts per million. Z-score totals of 6 core Hippo genes were calculated in groups: MST1+ STK3 (G1), LATS1+ LATS2 (G2), YAP1+ WWTR1 (G3), and all 6 genes together (G4). Tumors with bottom quartile (QL) z-scores were compared with the top quartile (QH) using χ2/Fisher-Exact test and adjusted with the Benjamini-Hochberg method: adjusted p <.05 was considered significant; unadjusted p <.05 trending. Results: Gene expression levels were significantly positively correlated with each other (Spearman rho: 0.30–0.78). Highest expression levels of G1–4 were seen in CMS4 and lowest in CMS3 with significant differences. MSI-H/dMMR were significantly higher in QL than QH in all (G1: 7.4 vs 4.9%, G2: 7.4 vs 4.5, G3: 8.7 vs 4.1, G4: 7.5 vs 4.5). TMB-H prevalence (%) showed inverse relationships with MSI-H significantly in G1–3 (G1: 10.7 vs 7.5, G2: 10.5 vs 7.1, G3: 12.7 vs 6.2) and trending in G4 (11.0 vs 7.0, p =.006). Considering only MSS tumors, TMB-H trended more often in QL than QH in G1, 3, and 4 (3.6–3.7 vs 2.2–2.6). PD-L1 expression by IHC was significantly higher in QH than QL in all (5.3 vs 3.3%) and MSS tumors (2.2 vs 4.2) only in G3. Z-scores of G1–4 were all positively correlated with immune cell infiltrations. Significantly higher fractions of B cells, M2 macrophages, myeloid dendritic cells, NK cells, neutrophils, and CD8+ T cells were seen in QH than QL with a median fold change of 1.39. G1–4 z-scores all positively correlated with the expression of the analyzed immune-related genes. The highest Spearman rho averages were in HAVCR2 (0.54), CD86 (0.54), CD80 (0.53), PD-L2 (0.5), CD274 (0.46), and LAG3 (0.36). Significantly different mutation rates were seen in QH compared to QL in G1 ( TP53, KRAS, PIKCA, SMAD2, AMER1), G2 ( APC), G3 ( PIK3CA, APC), and G4 ( TP53, PIK3CA, KRAS). Conclusions: The Hippo pathway correlated with immune cell trafficking suggesting that YAP1/TAZ signaling may play a critical role in the immune responses. These findings may help develop novel therapeutic strategies targeting the Hippo pathway combined with immune therapies in CRC.

The role of germline polymorphisms in genes involved in the antioxidant system to predict the efficacy of cetuximab for patients with metastatic colorectal cancer (mCRC) enrolled in FIRE-3 trial

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Background: Reactive oxygen species activate RAS/MAPK signaling either through inactivation of phosphatases or by direct oxidation of kinases. We hypothesized that functional genetic variants in genes involved in the antioxidant system may be associated with the efficacy of cetuximab in mCRC patients. Methods: We analyzed genomic and clinical data from FIRE-3, a phase III trial which compared cetuximab and bevacizumab in combination with FOLFIRI in untreated mCRC patients. Genomic DNA extracted from blood samples was genotyped using an OncoArray (Illumina, Inc., San Diego, CA, USA). Candidate 13 functional single nucleotide polymorphisms (SNPs) ( TXN rs2301242, TXN rs2301241, TXN2 rs4821494, TXN2 rs9619611, TXN2 rs59841625, CAT rs7943316, CAT rs564250, CAT rs11604331, CAT rs1001179, CAT rs769217, GPX4 rs757229, GPX4 rs4807542, and GPX4 rs713041) were tested for association with progression-free survival and overall survival (OS), using log-rank test and Cox proportional hazards model. To confirm the predictive value, the treatment-by-SNP interaction was tested. Results: A total of 236 patients were available for the SNP analyses (cetuximab arm, n = 129; bevacizumab arm, n = 107). In the cetuximab arm, two SNPs were significantly associated with clinical outcomes in univariate analyses: TXN2 rs4821494 (T/T vs any G allele, hazard ratio [HR] on OS = 2.17, 95% confidence interval [CI] = 1.04–4.56, log-rank p = 0.04) and GPX4 rs4807542 (G/G vs any A allele, HR on OS = 2.04, 95% CI = 1.05–3.98, log-rank p = 0.03). Multivariate analysis confirmed the significance in TXN2 rs4821494 (T/T vs any G allele, HR on OS = 2.47, 95% CI = 1.06–5.72, p = 0.03). In the bevacizumab arm, univariate analyses did not detect any significant associations between the SNPs and clinical outcomes. Treatment-by-SNP interaction test showed the significant predictive value of TXN2 rs4821494 in terms of OS ( p = 0.03). Conclusions: TXN2 rs4821494 involved in the antioxidant system may predict the efficacy of cetuximab, in comparing with bevacizumab, in the first-line treatment of mCRC. Our novel findings warrant further validation studies.

LRP1B and GRM3 expression in colorectal cancer

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Background: LRP1B is a member of the low-density lipoprotein receptor family and a tumor suppressor found to be downregulated in colon cancer (CRC). GRM3 is a receptor of glutamate, an amino acid and neurotransmitter. Inhibition of GRM3 reduces CRC cell growth. Recent data from CALGB/SWOG 80405 suggests that mutations (MT) of either LRP1B or GRM3 are associated with better and worse overall survival (OS) in patients treated with bevacizumab (Bev), respectively. We investigate the association of LRP1B or GRM3 mRNA levels with outcomes. Methods: A total of 13,780 CRC tumors (male 7,497, female 6,283) underwent comprehensive molecular profiling (Caris Life Sciences). Analyses included next-generation sequencing of DNA (592 genes, NextSeq, WES, NovaSEQ) and RNA (NovaSeq). Significance with multiple correction was indicated with q, otherwise p value. Gene Set Enrichment Analyses (GSEA) were performed (significance p <.05). A Consensus Molecular Subtype (CMS) calling algorithm was developed using mRNA levels (transcripts per million; TPM). Time on treatment (TOT) with Bev was extracted from insurance claims. Results: Male patients had higher GRM3 expression (median TPM.55 vs..52, p <.001). GRM3 and LRP1B were both elevated in brain metastases (1.95 vs..40, q<.01;.53 vs..16, q<.01) and enriched in CMS4 subtype (both p <.001). Overexpression of GRM3 and LRP1B were significantly associated with MSS (.11 vs..07, p <.0001;.54 vs..39, p <.0001) and TMB low status (.11 vs..08, p <.0001;.54 vs..40, p <.0001). For MSS tumors, high LRP1B was associated with lower MT rates of APC (76% vs. 78%), KRAS (49% vs. 51%) and PIK3CA (15% vs. 17%). For MSI tumors, high LRP1B correlated with higher MT of MSH6 (41% vs. 32%), BRCA2 (28% vs. 20%) and PMS2 (12% vs. 6%). MSS tumors with high GRM3 had more APC (79% vs. 75%), less KRAS (47% vs. 52%) and SMAD4 (12% vs. 16%) MT and MSI with high GRM3 carried more APC (42% vs. 35%) and RAD50 (18% vs. 8%) MT. MSS tumors with low LRP1B showed upregulation of the EIF2 pathway while MTOR, RAB, and CDC42 pathways were enriched in MSI with low LRP1B. CDC42 and MTOR pathways were enriched in MSS tumors with low GRM3, and MSI with low GRM3 displayed enrichment of EIF2 and Notch pathways. In MSS tumors, both LRP1B and GRM3 were prognostic and associated with better survival (HR.66, 95% CI [.56-.78], p <.0001 for LRP1B; HR.79, 95% CI [.68-.92], p <.01 for GRM3) and high expression of either one was also associated with better prognosis for patients treated with Bev (HR.85, 95% CI [.70-.92], p <.01 for LRP1B; HR 0.88, 95% CI [.77-.99], p <.05 for GRM3). Conclusions: LRP1B and GRM3 appear to be important regulators in CRC because of their prognostic value and association with response to bevacizumab treatment. Both LRP1B and GRM3 are associated with pathways of cell cycle progression, cell migration, and DNA repair. A better understanding of their role in angiogenic signaling is critical to develop more effective strategies to improve response to bevacizumab or immunotherapy.

The role of genetic variants involved with ferroptosis regulator genes in predicting outcomes in patients (pts) with RAS-mutant metastatic colorectal cancer (mCRC): Data from MAVERICC and TRIBE trials

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Background: Ferroptosis, an iron-dependent programmed cell death, is one of the anti-tumor mechanisms of anti-angiogenesis drugs. RAS mutation can confer ferroptosis in colorectal cancer (CRC). Previous studies suggested that polymorphisms of ferroptosis regulator genes are associated with the increased risk of CRC. Therefore, we hypothesized that genetic variants in the ferroptosis regulator genes may predict first-line treatment outcome in RAS-mutant mCRC pts treated with bevacizumab (bev)-based chemotherapy. Methods: Genomic DNA from blood samples of mCRC pts enrolled in two independent randomized trials, MAVERICC (FOLFIRI+bev arm: discovery cohort, RAS-mutant, n = 56; control-1: RAS-wildtype, n = 87) and TRIBE (FOLFOXIRI+bev arm: validation cohort, RAS-mutant, n = 57; control-2: RAS-wildtype, n = 34), was genotyped through the OncoArray, a customized array manufactured by Illumina including approximately 530K SNP markers. The impact on outcome of 13 selected SNPs in 5 main ferroptosis regulator genes (ACSL4, LPCAT3, SLC3A2, SLC7A11, ALOX15) was analyzed. Results: In the MAVERICC bev cohort, pts with RAS-mutant tumors carrying ALOX15 rs7217186 any C allele (n = 35) showed significant longer overall survival (OS) than carrier of T/T allele (n = 5) in both univariate (24.97 vs. 12.22 months, hazard ratio [HR] = 0.23; 95% confidence interval [CI]: 0.06-0.9; p = 0.02) and multivariate (HR = 0.06; 95%CI 0.007-0.5; p = 0.009) analysis. In the TRIBE bev cohort, RAS-mutant carriers of any C allele (n = 30) showed numerically longer progression-free survival (PFS), compared to carriers of T/T allele (n = 13) in both univariate (11.91 vs. 9.47 months, HR = 0.45; 95%CI 0.2-1.02; p = 0.05) and multivariate (HR = 0.42; 95%CI 0.16-1.1; p = 0.09) analysis. Conversely, RAS-wildtype carriers of any C allele (n = 17) showed significant shorter PFS than T/T carriers in the TRIBE bev cohort (8.91 vs. 15.59 months, univariate HR = 3.39, 95%CI: 1.03-11.18, p = 0.04). Conclusions: Our study demonstrated for the first time that ALOX15 polymorphisms may have different predictive values for the bev-based treatment in mCRC patients based on RAS mutational status. These findings may provide novel insights for the combination of ferroptosis inducers and anti-VEGF treatment.

Point Absorber Limits to Future Gravitational-Wave Detectors

High-quality optical resonant cavities require low optical loss, typically on the scale of parts per million. However, unintended micron-scale contaminants on the resonator mirrors that absorb the light circulating in the cavity can deform the surface thermoelastically and thus increase losses by scattering light out of the resonant mode. The point absorber effect is a limiting factor in some high-power cavity experiments, for example, the Advanced LIGO gravitational-wave detector. In this Letter, we present a general approach to the point absorber effect from first principles and simulate its contribution to the increased scattering. The achievable circulating power in current and future gravitational-wave detectors is calculated statistically given different point absorber configurations. Our formulation is further confirmed experimentally in comparison with the scattered power in the arm cavity of Advanced LIGO measured by in situ photodiodes. The understanding presented here provides an important tool in the global effort to design future gravitational-wave detectors that support high optical power and thus reduce quantum noise.

Reprogramming CBX8-PRC1 function with a positive allosteric modulator

Canonical targeting of Polycomb repressive complex 1 (PRC1) to repress developmental genes is mediated by cell-type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7, and 8). Based on their central role in silencing and their dysregulation associated with human disease including cancer, CBX proteins are attractive targets for small-molecule chemical probe development. Here, we have used a quantitative and target-specific cellular assay to discover a potent positive allosteric modulator (PAM) of CBX8. The PAM activity of UNC7040 antagonizes H3K27me3 binding by CBX8 while increasing interactions with nucleic acids. We show that treatment with UNC7040 leads to efficient and selective eviction of CBX8-containing PRC1 from chromatin, loss of silencing, and reduced proliferation across different cancer cell lines. Our discovery and characterization of UNC7040 not only reveals the most cellularly potent CBX8-specific chemical probe to date, but also corroborates a mechanism of Polycomb regulation by non-specific CBX nucleotide binding activity.

Immunogenic cell death pathway polymorphisms for predicting oxaliplatin efficacy in metastatic colorectal cancer

Background

Immunogenic cell death (ICD) is a tumor cell death involving both innate and adaptive immune responses. Given published findings that oxaliplatin, but not irinotecan, drives ICD, we investigated whether single nucleotide polymorphisms (SNPs) in the ICD pathway are associated with the efficacy of oxaliplatin-based chemotherapy in metastatic colorectal cancer (mCRC).

Methods

Two randomized clinical trials data were analyzed: discovery cohort, FOLFOX/bevacizumab arm (MAVERICC); validation cohort, FOLFOXIRI/bevacizumab arm (TRIBE); and two control cohorts, FOLFIRI/bevacizumab arms (both trials). Genomic DNA extracted from blood samples was genotyped. Ten SNPs in the ICD pathway were tested for associations with clinical outcomes.

Results

In total, 648 patients were included. In the discovery cohort, three SNPs were significantly associated with clinical outcomes in univariate analysis: CALR rs1010222 with progression-free survival (G/G vs any A, HR=0.61, 95% CI 0.43–0.88), ANXA1 rs1050305 with overall survival (OS) (A/A vs any G, HR=1.87, 95% CI 1.04–3.35), and LRP1 rs1799986 with OS (C/C vs any T, HR=1.69, 95% CI 1.07–2.70). Multivariate analysis confirmed the trend, but statistical significance was not reached. In the validation cohort, ANXA1 rs1050305, and LRP1 rs1799986 were validated to have the significant associations with clinical outcome. No significant associations of these SNPs were observed in the two control cohorts. Treatment-by-SNP interaction test confirmed the predictive values.

Conclusions

The predictive utility of ICD-related SNPs for the efficacy of oxaliplatin-based chemotherapy was demonstrated, warranting further validation studies to be translated into personalized treatment strategies using conventional cytotoxic agents in mCRC.

A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave

Disease modelling has had considerable policy impact during the ongoing COVID-19 pandemic, and it is increasingly acknowledged that combining multiple models can improve the reliability of outputs. Here we report insights from ten weeks of collaborative short-term forecasting of COVID-19 in Germany and Poland (12 October-19 December 2020). The study period covers the onset of the second wave in both countries, with tightening non-pharmaceutical interventions (NPIs) and subsequently a decay (Poland) or plateau and renewed increase (Germany) in reported cases. Thirteen independent teams provided probabilistic real-time forecasts of COVID-19 cases and deaths. These were reported for lead times of one to four weeks, with evaluation focused on one- and two-week horizons, which are less affected by changing NPIs. Heterogeneity between forecasts was considerable both in terms of point predictions and forecast spread. Ensemble forecasts showed good relative performance, in particular in terms of coverage, but did not clearly dominate single-model predictions. The study was preregistered and will be followed up in future phases of the pandemic.