Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms.

A central challenge in developing personalized cancer cell immunotherapy is the identification of tumor-reactive T cell receptors (TCRs). By exploiting the distinct transcriptomic profile of tumor-reactive T cells relative to bystander cells, we build and benchmark TRTpred, an antigen-agnostic in silico predictor of tumor-reactive TCRs. We integrate TRTpred with an avidity predictor to derive a combinatorial algorithm of clinically relevant TCRs for personalized T cell therapy and benchmark it in patient-derived xenografts.

Rare Synchronous Lung Cancers in a Nonsmoker with Epidermal Growth Factor Receptor and Mesenchymal-Epithelial Transition Alterations: A Case Report.

Introduction: Lung cancer is the second most common cancer; however, synchronous lung cancer is rare and challenging to treat. Case Presentation: We report the case of an 80-year-old female patient who presented with two lung lesions with primary tumor characteristics, which revealed squamous cell carcinoma and synchronous adenocarcinoma after histological sampling. Next-generation sequencing (NGS) analysis revealed a MET Exon 14 skipping mutation in squamous cell carcinoma and an epidermal growth factor receptor mutation in adenocarcinoma. Capmatinib and stereotactic radiotherapy were initiated for the adenocarcinoma with a good clinical response. Capmatinib treatment had to be discontinued because of stage 3 edema of the lower limbs, after which a left lobectomy was performed. Currently, the patient is considered to be in remission. Conclusion: This case highlights the need for histological analysis of every lung lesion with primary tumor characteristics, as well as for NGS analysis in search of specific mutations enabling the introduction of targeted therapies. mesenchymal-epithelial transition.

Paraneoplastic Autoimmune Limbic Encephalitis Associated with an Atypical Carcinoid Tumor of the Lung: A Case Report.

We report the case of a patient with a history of an atypical lung carcinoid tumor who developed a rapidly progressive memory impairment. The clinical presentation as well as brain MRI, cerebrospinal fluid, and laboratory tests led to the diagnosis of seronegative paraneoplastic autoimmune limbic encephalitis. To the best of our knowledge, this is the first case in literature of such association. This case also highlights an exceptionally favorable outcome, both clinically and radiologically, after immunosuppression and tumor removal.

Unnecessary thyroid surgery rate for suspicious nodule in the absence of molecular testing.

Background: Molecular tests for suspicious thyroid nodules decrease rates of unnecessary surgeries but are not widely used due to reimbursement issues. The aim of this study was to assess the rate of unnecessary surgery performed in real-life setting for Bethesda III, IV and V nodules in the absence of molecular testing. Method: This is a single-center retrospective study of consecutive patients undergoing fine needle aspiration cytology (FNAC) with rapid on-site evaluation between January 2017 and December 2021. Unnecessary surgery was defined as surgery performed because of Bethesda III, IV, or V results in the absence of local compressive symptoms with final benign pathology and as second surgery for completion thyroidectomy. Results: In the 862 patients (640 females, mean age: 54.2 years), 1010 nodules (median size: 24.4 mm) underwent 1189 FNAC. Nodules were EU-TIRADS 2, 3, 4, and 5 in 3%, 34%, 42%, and 22% of cases, respectively. FNAC was Bethesda I, II, III, IV, V, and VI in 8%, 48%, 17%, 17%, 3%, and 6%, respectively. Surgery was performed in 36% of Bethesda III nodules (benign on pathology: 81%), in 74% of Bethesda IV nodules (benign on pathology: 76%) and in 97% of Bethesda V nodules (benign on pathology: 21%). Surgery was considered unnecessary in 56%, 68%, and 21% of patients with Bethesda III, IV, and V nodules, respectively. Conclusion: In this real data cohort surgery was unnecessary in more than half of patients with Bethesda III and IV nodules and in 21% of patients with Bethesda V nodules.

PET/MR Imaging in Head and Neck Cancer.

Head and neck squamous cell carcinoma (HNSCC) can either be examined with hybrid PET/MR imaging systems or sequentially, using PET/CT and MR imaging. Regardless of the acquisition technique, the superiority of MR imaging compared to CT lies in its potential to interrogate tumor and surrounding tissues with different sequences, including perfusion and diffusion. For this reason, PET/MR imaging is preferable for the detection and assessment of locoregional residual/recurrent HNSCC after therapy. In addition, MR imaging interpretation is facilitated when combined with PET. Nevertheless, distant metastases and distant second primary tumors are detected equally well with PET/MR imaging and PET/CT.

The first comprehensive genomic characterization of rectal squamous cell carcinoma.

BACKGROUND: Rectal cancers represent 35% of colorectal cancers; 90% are adenocarcinomas, while squamous cell carcinoma accounts for 0.3% of them. Given its rarity, little is known concerning its pathogenesis, molecular profile and therapeutic management. The current treatment trend is to treat rectal squamous cell carcinoma by analogy to anal squamous cell carcinoma with definitive chemo-radiotherapy, setting aside surgery in case of local recurrence. METHODS: We performed an in-depth genomic analysis (next-generation sequencing, copy number variation, and human papilloma virus characterization) on 10 rectal squamous cell carcinoma samples and compared them in silico to those of anal squamous cell carcinoma and rectal adenocarcinoma. RESULTS: Rectal squamous cell carcinoma shows 100% HPV positivity. It has a mutational (PIK3CA, PTEN, TP53, ATM, BCL6, SOX2) and copy number variation profile (3p, 10p, 10q, 16q deletion and 1q, 3q, 5p, 8q, 20p gain) similar to anal squamous cell carcinoma. PI3K/Akt/mTOR is the most commonly affected signaling pathway similarly to anal squamous cell carcinoma. Most commonly gained or lost genes seen in rectal adenocarcinoma (FLT3, CDX2, GNAS, BCL2, SMAD4, MALT1) are not found in rectal squamous cell carcinoma. CONCLUSION: This study presents the first comprehensive genomic characterization of rectal squamous cell carcinoma. We confirm the existence of this rare histology and its molecular similarity with anal squamous cell carcinoma. This molecular proximity confirms the adequacy of therapeutic management based on histology and not localization, suggesting that rectal squamous cell carcinoma should be treated like anal squamous cell carcinoma and not as a rectal adenocarcinoma.

Characteristics of long-survivor metastatic melanoma after polychemotherapy and interferon: a retrospective study.

BACKGROUND: The development of immunotherapy and tyrosine kinase inhibitors dramatically improved the prognosis of metastatic melanoma. Consequently, chemotherapy is now rarely used. Here, we describe the characteristics of long-surviving patients with metastatic melanoma treated with immunochemotherapy. MATERIAL AND METHODS: We retrieved retrospective clinical and pathological data for patients diagnosed with metastatic melanoma between January 1993 and December 2015 who received the CVD-INF (cisplatin, vinblastine, dacarbazine, and interferon α-2b) regimen at the Hôpitaux Universitaires de Genève. We estimated their progression-free survival and overall survival. This ad hoc study's primary aim was to describe the clinical and biological characteristics of long-term survivors, defined as patients surviving more than two years after immunochemotherapy initiation. The spatial distribution pattern of CD8+ T cells (inflamed, excluded, or desert) was immunohistochemically determined. RESULTS: Ninety patients received CVD-INF. Their median age at metastatic melanoma diagnosis was 55 years (20-75). Their median progression-free survival was 2.8 months, and median overall survival was 7.2 months. Eleven (12%) patients were long-term survivors. In multivariate analysis, central nervous system metastases (hazard ratio [HR]: 2.66; 95% confidence interval [CI]: 1.43-4.95; p = 0.001), multiple metastases (HR: 1.82; 95% CI: 1.01-3.29; p = 0.047), and elevated lactate dehydrogenase (LDH) (HR: 1.92; 95% CI: 1.12-3.30; p = 0.016) were independently associated with shorter survival. Most long-survivors (6/8; 75%) had a tumour-inflamed pattern compared to 25% of non-long survivors (5/20; Fisher's test p = 0.030). CONCLUSIONS: A subset of patients with metastatic melanoma and a tumour-inflamed phenotype treated with CVD-INF survived over two years. Factors associated with prolonged survival are consistent with those previously reported in metastatic melanoma.

Atypical pulmonary phaeohyphomycosis due to Aureobasidium spp. - case report and brief literature review.

We report on a case of probable invasive Auerobasidium spp. pulmonary infection in a patient with myelodysplastic syndrome. The patient was successfully treated with liposomal amphotericin B monotherapy, with transition to orally administered isavuconazole. This case shows an atypical initial radiological presentation with diffuse ground-glass opacities, as previously demonstrated in cases of Aureobasidium spp. hypersensitivity pneumonitis. Moreover this case further highlights the difficulties associated with the diagnosis and complexity in the management of Aureobasidium spp. infections.

A monoclonal antibody targeting nonjunctional claudin-1 inhibits fibrosis in patient-derived models by modulating cell plasticity.

Tissue fibrosis is a key driver of end-stage organ failure and cancer, overall accounting for up to 45% of deaths in developed countries. There is a large unmet medical need for antifibrotic therapies. Claudin-1 (CLDN1) is a member of the tight junction protein family. Although the role of CLDN1 incorporated in tight junctions is well established, the function of nonjunctional CLDN1 (njCLDN1) is largely unknown. Using highly specific monoclonal antibodies targeting a conformation-dependent epitope of exposed njCLDN1, we show in patient-derived liver three-dimensional fibrosis and human liver chimeric mouse models that CLDN1 is a mediator and target for liver fibrosis. Targeting CLDN1 reverted inflammation-induced hepatocyte profibrogenic signaling and cell fate and suppressed the myofibroblast differentiation of hepatic stellate cells. Safety studies of a fully humanized antibody in nonhuman primates did not reveal any serious adverse events even at high steady-state concentrations. Our results provide preclinical proof of concept for CLDN1-specific monoclonal antibodies for the treatment of advanced liver fibrosis and cancer prevention. Antifibrotic effects in lung and kidney fibrosis models further indicate a role of CLDN1 as a therapeutic target for tissue fibrosis across organs. In conclusion, our data pave the way for further therapeutic exploration of CLDN1-targeting therapies for fibrotic diseases in patients.

Complications of congenital portosystemic shunts: liver tumors are affected by shunt severity, but pulmonary and neurocognitive associations are not.

BACKGROUND AND PURPOSE: Congenital portosystemic shunts (CPSS) are associated with multisystem complications, with the most common being liver tumors. The purpose of this study is to investigate the incidence of complications of CPSS, and to determine the natural history of liver tumors and their relationship with shunt closure. METHODS: Single-center retrospective cohort study of patients with CPSS referred from 1990 to 2020. Data on demographics, laboratory, radiological and histological investigations, clinical evolution, and surgery were reviewed. Mann-Whitney for continuous data and Fisher's exact test for categorical data were used. A p value of 0.05 was considered significant. RESULTS: 54 patients were investigated for CPSS with a median age of 1.1 years (IQR 0.2-11.8 years) at presentation-7 intrahepatic shunts resolved spontaneously and were excluded. Type 1 (without intrahepatic portal flow) had a higher rate of all hepatic tumors than Type 2 (partial intrahepatic portal flow) [18/22(82%) vs. 9/25(36%); p = 0.003); and malignant tumors (6/22(27%) vs 1/25(4%); (p = 0.04). Following shunt closure, 4/11(36%) of patients experienced partial and 3/11(27%) complete tumor regression. Pulmonary hypertension and hepatopulmonary syndrome affected 4(9%), and 3(6%) patients, respectively. Pulmonary complications affected 1 patient with Type 1 and 6 with Type 2 shunts (p = 0.1). Neurocognitive anomalies were identified in 16/47(34%) patients, 8/22(35%) with Type 1 shunts and 8/25(32%) with Type 2 shunts (p = 0.76). 9/47 (19%) required special needs schooling. CONCLUSIONS: Severity of portal venous deprivation (Type 1 CPSS) increases the risk of hepatic tumors and surgical closure is associated with a reduction in size or complete resolution of benign tumors.

Primary Extra-Osseous Ewing Sarcoma of the Thyroid: A Case Report and Review of the Literature.

Extra-osseous Ewing sarcoma (ES) is a rare and aggressive malignant tumor found in a variety of organs. Primary ES of the thyroid is exceedingly rare and few cases have been documented to date. We describe the case of a 54-year old woman with a history of breast carcinoma in whom a unique hypermetabolic left thyroid nodule was identified during a follow-up PET-CT scan. An ultrasound examination showed a hypoechogenic nodule of 3.7 cm. A cytological diagnosis of poorly differentiated thyroid carcinoma was made, and a total thyroidectomy was performed. The surgical specimen revealed a poorly differentiated neoplasm composed of medium-sized cells with scant cytoplasm, expressing pancytokeratin, CD99 and NKX2.2 but lacking p63 and p40 expression. Molecular analysis revealed a EWSR1-FLI1 fusion transcript supporting the diagnosis of a primary extra-osseous ES of the thyroid. The patient received adjuvant chemotherapy and has no evidence of recurrent disease.

MR Imaging of Laryngeal and Hypopharyngeal Cancer.

State-of-the-art MR imaging of the larynx and hypopharynx with high-resolution surface coils, parallel imaging techniques, and DWI has several advantages over CT for assessing submucosal tumor spread, in particular neoplastic involvement of the paraglottic space, laryngeal cartilages, and extralaryngeal soft tissues. Current diagnostic MR imaging criteria based on a combination of distinct imaging features on morphologic sequences combined with DWI allow improved discrimination between tumor, peritumoral inflammation, and fibrosis and, ultimately, an increased precision for submucosal tumor delineation, which is a key prerequisite for tailored treatment options. Multiparametric MR imaging with DWI has a higher diagnostic performance than CT.

The Impact of Variant Allele Frequency in EGFR Mutated NSCLC Patients on Targeted Therapy.

EGFR mutations represent the most common currently targetable oncogenic driver in non-small cell lung cancer. There has been tremendous progress in targeting this alteration over the course of the last decade, and third generation tyrosine kinase inhibitors offer previously unseen survival rates among these patients. Nonetheless, a better understanding is still needed, as roughly a third of patients do not respond to targeted therapy and there is an important heterogeneity among responders. Allelic frequency, or the variant EGFR allele frequency, corresponds to the fraction of sequencing reads harboring the mutation. The allelic fraction is influenced by the proportion of tumor cells in the sample, the presence of copy number alterations but also, most importantly, by the proportion of cells within the tumor that carry the mutation. Mutations that occur early in tumor evolution, often called clonal or truncal, have a higher allelic frequency than late, subclonal mutations, and are more often drivers of cancer evolution and attractive therapeutic targets. Most, but not all, EGFR mutations are clonal. Although an exact estimate of clonal proportion is hard to derive computationally, the allelic frequency is readily available to clinicians and could be a useful surrogate. We hypothesized that tumors with low allelic frequency of the EGFR mutation will respond less favorably to targeted treatment.

Tristetraprolin Promotes Hepatic Inflammation and Tumor Initiation but Restrains Cancer Progression to Malignancy.

BACKGROUND & AIMS: Tristetraprolin (TTP) is a key post-transcriptional regulator of inflammatory and oncogenic transcripts. Accordingly, TTP was reported to act as a tumor suppressor in specific cancers. Herein, we investigated how TTP contributes to the development of liver inflammation and fibrosis, which are key drivers of hepatocarcinogenesis, as well as to the onset and progression of hepatocellular carcinoma (HCC). METHODS: TTP expression was investigated in mouse/human models of hepatic metabolic diseases and cancer. The role of TTP in nonalcoholic steatohepatitis and HCC development was further examined through in vivo/vitro approaches using liver-specific TTP knockout mice and a panel of hepatic cancer cells. RESULTS: Our data demonstrate that TTP loss in vivo strongly restrains development of hepatic steatosis and inflammation/fibrosis in mice fed a methionine/choline-deficient diet, as well as HCC development induced by the carcinogen diethylnitrosamine. In contrast, low TTP expression fostered migration and invasion capacities of in vitro transformed hepatic cancer cells likely by unleashing expression of key oncogenes previously associated with these cancerous features. Consistent with these data, TTP was significantly down-regulated in high-grade human HCC, a feature further correlating with poor clinical prognosis. Finally, we uncover hepatocyte nuclear factor 4 alpha and early growth response 1, two key transcription factors lost with hepatocyte dedifferentiation, as key regulators of TTP expression. CONCLUSIONS: Although TTP importantly contributes to hepatic inflammation and cancer initiation, its loss with hepatocyte dedifferentiation fosters cancer cells migration and invasion. Loss of TTP may represent a clinically relevant biomarker of high-grade HCC associated with poor prognosis.

Portal venous deprivation in patients with portosystemic shunts and its effect on liver tumors.

AIMS: To outline the use of radiological investigations in patients with congenital portosystemic shunts (CPS) and to assess the degree of portal venous deprivation in relation to the development of liver tumors. METHODS: Single center retrospective cohort study of all patients with CPS referred from 1990 to 2016. Radiological investigations were reviewed for the presence of intrahepatic portal veins. Two groups were defined: Group 1 - without evidence of preservation of an intrahepatic portal venous system and, Group 2 - with evidence of intrahepatic portal venous flow. These groups were compared for the development of liver tumors, serum ammonia, and nature of subsequent surgical intervention. The ratio of infraceliac to supraceliac aortic diameter and hepatic enhancement in biphasic CT scans were also used to infer hepatic arterial in-flow and compared to age matched controls. Nonparametric tests were used throughout. A P value of 0.05 was considered significant. Data are quoted as median (IQR). RESULTS: 45 patients (Group 1, n = 12: Group 2, n = 33) were investigated for CPS at a median age of 8 months (1 month-14 years). Liver tumors were more common in Group 1 than Group 2 [11/12 (92%) versus 10/33 (29%); P < 0.001]. Aortic ratio was significantly lower in patients with CPS compared to control (0.82 versus 0.96; P < 0.001), but there was no difference between patients with or without tumors (0.82 versus 0.82; P = 0.52). Enhancement of the liver parenchyma was greater in portal venous rather than arterial phases by a median difference of 28 (15-50) Hounsfield units in controls, compared to 15 (8.5-23.5) in CPS patients (P = 0.04). A single stage closure was possible in 2/6 (33%) operated patients in Group 1 and 14/20 (70%) in Group 2 (P = 0.32). CONCLUSIONS: Patients without radiological evidence of intrahepatic portal venous flow were significantly more likely to have associated hepatic tumors with a relative risk 3.1. LEVELS OF EVIDENCE: This manuscript includes data that are III and IV Levels-of-Evidence.

Macrofollicular Variant of Follicular Thyroid Carcinoma: A Rare Underappreciated Pitfall in the Diagnosis of Thyroid Carcinoma.

Background: Follicular-patterned thyroid nodules predominantly composed of macrofollicular structures without nuclear atypia are generally regarded as benign (i.e., hyperplastic nodules or follicular adenomas). In line with this concept, fine-needle aspiration cytology (FNAC) also assigns a benign connotation to the presence of macrofollicular structures, unless thyrocytes present papillary thyroid carcinoma (PTC)-related nuclear features that raise the possibility of a macrofollicular variant of PTC. However, cases showing macrofollicular architecture, capsular invasion, and no PTC features can also be observed. Methods: We describe the clinical, cytological, histological, and molecular genetic features of four cases of encapsulated follicular neoplasms that presented histologically with a predominant (>70%) macrofollicular architecture, but which also showed clear signs of capsular invasion, and thus were classified as macrofollicular variant of follicular thyroid carcinoma (MV-FTC). Results: Cytologically, macrofollicular structures were identified in all cases, leading to a benign FNAC diagnosis in three of the four cases. Due to increasing nodule size, thyroidectomy was performed in all cases. Histology showed focal and limited capsular invasion, without vascular invasion. Next-generation sequencing (custom 394 gene panel) of each tumor compared with matched normal DNA revealed a total of 7 somatic variants, including dual (likely biallelic) mutations in the DICER1 gene in 2 patients. The clinical outcome was excellent in all cases. Conclusions: Similar to the classical minimally invasive follicular thyroid carcinoma, MV-FTC appears to behave indolently. MV-FTC has a high rate of false-negative FNAC results, but MV-FTC is very rare (<0.05% of all thyroidectomies) and apparently has an indolent behavior. Further studies comprising larger series are necessary to better clarify the biology of this diagnostically challenging rare tumor.

The impact of short-term machine perfusion on the risk of cancer recurrence after rat liver transplantation with donors after circulatory death.

Hypothermic and normothermic ex vivo liver perfusions promote organ recovery after donation after circulatory death (DCD). We tested whether these perfusions can reduce the risk of hepatocellular carcinoma (HCC) recurrence in a 1h-DCD syngeneic transplantation model, using Fischer F344 rats. DCD grafts were machine perfused for 2h with hypothermic perfusion (HOPE) or normothermic perfusion (NORMO), and transplanted. After reperfusion, we injected HCC cells into the vena porta. On day 28 after transplantation, we assessed tumour volumes by MRI. Control rats included transplantations with Fresh and non-perfused DCD livers. We observed apoptotic-necrotic hepatocyte foci in all DCD grafts, which were more visible than in the Fresh liver grafts. Normothermic perfusion allowed a faster post-transplant recovery, with lower day 1 levels of transaminases compared with the other DCD. Overall, survival was similar in all four groups and all animals developed HCCs. Total tumor volume was lower in the Fresh liver recipients compared to the DCD and DCD+HOPE recipients. Volumes in DCD+NORMO recipients were not significantly different from those in the Fresh group. This experiment confirms that ischemia/reperfusion injury promotes HCC cell engraftment/growth after DCD liver transplantation. Using the present extreme 1h ischemia model, both hypothermic and normothermic perfusions were not effective in reducing this risk.