GENCODE: reference annotation for the human and mouse genomes in 2023

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Global assessment of oil and gas methane ultra-emitters

Methane emissions from oil and gas (O&G) production and transmission represent a considerable contribution to climate change. These emissions comprise sporadic releases of large amounts of methane during maintenance operations or equipment failures not accounted for in current inventory estimates. We collected and analyzed hundreds of very large releases from atmospheric methane images sampled by the TROPOspheric Monitoring Instrument (TROPOMI) between 2019 and 2020. Ultra-emitters are primarily detected over the largest O&G basins throughout the world. With a total contribution equivalent to 8 to 12% (~8 million metric tons of methane per year) of the global O&G production methane emissions, mitigation of ultra-emitters is largely achievable at low costs and would lead to robust net benefits in billions of US dollars for the six major O&G-producing countries when considering societal costs of methane.

Interventional techniques in the management of chronic pain: Part 2.0

The practice guidelines for interventional techniques in the management of chronic pain are systematically developed statements to assist physician and patient decisions about appropriate health care related to chronic pain. These guidelines are professionally derived recommendations for practices in the diagnosis and treatment of chronic or persistent pain. They were developed utilizing a combination of evidence and consensus based techniques, to increase patient access to treatment, improve outcomes and appropriateness of care, and optimize cost-effectiveness. The guidelines include a discussion of their purpose, rationale, and importance, including the patient population served, the methodology and the pathophysiologic basis for intervention. Various interventional techniques will be discussed addressing the rationale for their use in chronic pain with analysis of the outcomes data and cost effectiveness. These guidelines do not constitute inflexible treatment recommendations. It is expected that a provider will establish a plan of care on a case-by-case basis, taking into account an individual patient's medical condition, personal needs, and preferences, and the physician's experience. Based on an individual patient's needs, treatment different from that outlined here could be warranted.

Prognostic factors in ovarian carcinoma in complete histologic remission at second-look surgery

Prognosis of ovarian carcinoma in complete histologic remission (CHR) at second-look surgery is still controversial. In a series of 83 patients in CHR we studied retrospectively several prognostic factors (age, stage, histologic grade, histologic type, initial residual disease after surgery, CA 125 normalization period) to determine which patients present a high risk of relapsing after CHR and could be included in therapeutic protocols for consolidation treatment. Univariate analysis showed that the combination of CA 125 normalization < 8 weeks with absence of macroscopic tumoral residue after initial surgery permits the definition of a group with a very good prognosis, while for patients with CA 125 normalization period > 8 weeks and an initial macroscopic residual tumor, the prognosis is relatively poor (progression-free survival 100% vs. 47%, at 2 years P < 0.05). Using the Cox multivariate analysis, only the initial tumoral residue is of prognostic significance for progression-free survival; there is no prognostic significance for overall survival. The therapeutic strategy for ovarian cancer may be improved for patients in CHR after second-look surgery by determining those at high risk, making it possible to confine consolidation treatment trials to such a group.

Treatment of subdiaphragmatic Hodgkin's disease: long-term results and side effects

To evaluate the results, prognostic factors and especially side-effects of the treatment for subdiaphragmatic Hodgkin's disease (SHD) a retrospective study was conducted in the Haematology Departments and in the Cancer Centres of Nancy and Strasbourg between 1976 and 1990; 55 patients corresponding to the IA to IIB SHD stages were analysed. The median age was 45 years. In accordance with Ann Arbor classification, we observed 12 CS IA (21.3%), 2 CS IB (3.5%), 14 CS IIA (25.4%) and 27 CS IIB (49.7%). Twenty-five patients (45.4%) underwent laparotomy with spleen involvement in 10 cases. Fifteen patients (27.3%) had exclusive radiotherapy, 10 by inverted-Y field with or without splenic field, 5 by limited field to inguinal and homolateral iliac nodes. Forty patients had prior chemotherapy, 18 by MOPP protocol, 18 by hybrid MOPP/ABVD protocol and 4 by other schemes. The total dose delivered ranged from 26 to 45 Gy. With a median follow-up of 8 years, the overall and disease specific survival rates are respectively 61% and 83% at 10 years. Nine patients relapsed (16.4%), 4 among the 15 (26.6%) treated by exclusive irradiation and 5 among the 40 (12.5%) treated by combined therapy. We observed 8.3%, 21.4% and 18.5% of relapses respectively among the clinical stages IA, IIA and IIB. Eleven patients (20%) developed a second cancer. Twenty-six long-term complications were noted, nine of which concerned the digestive system. The only significant prognostic factor is age, with 10-year specific survival rates of 96% and 66% respectively for patients younger and older than 50 years (p=0.0003). Our data confirm that the most appropriate treatment for stage IA is exclusive radiotherapy and combined therapy for all other cases. With the use of CT-scan and eventually lymphography, the laparotomy is reserved only for cases with an uncertain diagnosis. Tobacco use is also clearly a risk factor in our series for late vascular complications and second cancers.

Paclitaxel-anthracycline combination chemotherapy in relapsing advanced ovarian cancer after platinum-based chemotherapy: a pilot study

Despite high response rates with platinum-based front-line chemotherapy, the prognosis for advanced ovarian carcinoma (AOC) is poor. Salvage chemotherapy for recurrent AOC was of little benefit before paclitaxel as single-agent therapy showed appreciable efficacy. Anthracyclines are effective, but are not often part of first-line therapy. In this pilot study, we investigated the feasibility of an anthracycline plus paclitaxel combination therapy for recurrent AOC. Twenty-four patients received 150 mg/m2 paclitaxel on day 1, with either 50 mg/m2 doxorubicin on day 1 or 75 mg/m2 epirubicin on day 1 every 3 weeks. A 27% overall response rate was obtained. Myelosuppression was the major toxicity, but was manageable. No myocardiac toxicity was observed. We conclude that paclitaxel-anthracyclines is a promising salvage combination therapy in AOC that should be investigated further.

[Carboplatin and cyclophosphamide in stage Ic-IV ovarian carcinoma: retrospective study of 101 cases]

We report our experience of CBDCA-CPM combination chemotherapy as first line therapy in 101 ovarian cancers. The therapeutic scheme was: initial cytoreductive surgery followed by six chemotherapy cycles (CBDCA 400 mg/m2/d IV dl, CPM 600 mg/m2/d IV dl, dl = d21) and second-look laparotomy. The initial stages were four Ic, three IIa, four IIb, four IIc, 15 IIIa, 28 IIIb, 23 IIIc and 20 IV. After initial surgery, there were 39 macroscopic residual diseases superior to 2 cm, 26 macroscopic residual diseases inferior or equal to 2 cm, four microscopic diseases and no residual disease in 30 cases (unknown in two cases). The overall response rate to chemotherapy was 83% with 56% histologic complete response rate. The main toxicity was haematological with 60% of leucopenia grade III-IV, 52% of thrombopenia grade III-IV. Age at diagnosis, residual disease after first look surgery and length of CA 125 normalization were significant prognostic factors for survival in this series.

Idarubicin and high dose cytarabine: a new salvage treatment for refractory or relapsing non-Hodgkin's lymphoma

Twenty three patients with relapsing (n = 11) or refractory (n = 12) non-Hodgkin's lymphoma (NHL) to one or two prior anthracycline based combination chemotherapy regimens were treated as second or third line regimen with 3 induction cycles of Idarubicin (IDA) (7 mg/m2/d i.v. d1-d3) and high dose cytarabine (HD Ara-C) (1 g/m2/12 h i.v. d1-d3), each cycle was repeated every 3 weeks. Responding patients received a maintenance therapy with monthly cycles of IDA: 15 mg/m2 d1-d3, Etoposide 100 mg/m2 d1-d3, both by oral route. Twenty two patients are evaluable and we observed 13 CR and 1 PR with an overall response rate of 61% (14/23: 95% Cl = 38.5% 80.3%). The median time to progression was 32 months (6.5 - 63 + m.). The response rate to IDA-HD Ara C was not different for patients with (n = 14) or without (n = 9) objective response to the last prior therapy. The main toxicity was hematological: all patients experienced grade 4 neutropenia and 22 patients had grade 4 thrombopenia, but there were no toxic deaths. IDA and HD-Ara-C combination is highly effective in refractory or relapsed. NHL. As hematological toxicity was the limiting factor for further escalation of dose-intensity, further studies might include hematopoietic growth factors support in the therapeutic scheme.

Intraperitoneal mitoxantrone as consolidation treatment for patients with ovarian carcinoma in pathologic complete remission

BACKGROUND

Stages II-IV ovarian cancer in pathologic complete remission (pCR) at second-look surgery have a high relapse rate (50%) during the first 2 years. Considering relapse sites (abdomen and/or pelvis), intraperitoneal (IP) therapy is a logical approach. Mitoxantrone is an effective drug against ovarian cancer cells in vitro and is an attractive agent for IP therapy because of its very low peritoneal clearance. The value of IP mitoxantrone was studied as consolidation treatment of ovarian cancer in pCR at second-look surgery.

METHODS

Fifty patients with Stages II-IV ovarian cancer (8, Stage II; 37, Stage III; 5, Stage IV) were included in this Phase II study, which began in June 1988. All patients had undergone initial cytoreductive surgery followed by 6 cyclophosphamide, doxorubicin, and cisplatin cycles. All patients were in pCR, as confirmed by second-look surgery. Consolidation treatment consists of 20 mg (total dose per cycle) IP mitoxantrone every 3 weeks for six cycles.

RESULTS

Toxicity was limited to mild abdominal pain not requiring dose reduction (90% pain grade < or = 2). With a median follow-up of 2 years, the 5-year predicted survival is 59.8% (95% confidence interval [CI], 48.3 - 71.3), and the disease-free survival (DFS) rate is 47.3% (95% CI, 36.7 - 57.9). Patients with no or microscopic residual disease after initial surgery had a better 5-year DFS rate (75.8%) than those with macroscopic residual disease (31.2%) (P = 0.01).

CONCLUSION

IP mitoxantrone (20 mg/cycle) is feasible with an acceptable abdominal toxicity. The results in terms of DFS are encouraging, but a randomized study versus no treatment is necessary to prove the value of this consolidation treatment.

Sodium dithiocarb as adjuvant immunotherapy for high risk breast cancer: a randomized study

Sixty-four patients with non metastatic high risk breast cancer were randomized in a double blind trial of adjuvant immunotherapy with sodium dithiocarb (DDC) versus placebo. All patients underwent prior surgery (mammectomy according to Patey) then adjuvant FAC chemotherapy +/- DDC. With a median follow-up of 5 years we observed 6 relapses and 5 deaths in DDC group; 13 relapses and 12 deaths in control group. At 6 years, overall survival is 81% in DDC group versus 55%. Disease free survival (DFS) is 76% in DDC group versus 55%. DDC associated to chemotherapy and locoregional treatment can improve survival and probably DFS in this high risk breast cancer subgroup.

[Hypothyroid hypertrophic myopathy following mantle irradiation for Hodgkin's disease. A case]

The authors report a case of hypothyroid hypertrophic myopathy consecutive to mantle irradiation for Hodgkin's disease. A rise in TSH level is frequent after mantle irradiation and it justifies prolonged monitoring of these patients' thyroid function, in view of the risk of patent hypothyroidism and perhaps cancer. The patient's age, the pre-irradiation lymphography and the chemotherapy associated with radiotherapy are all factors that influence the incidence of thyroid dysfunction, but there is no agreement concerning their relative importance. Hypertrophic myopathies due to hypothyroidism are rare, and their dramatic clinical presentation contrasts with an almost normal muscle histology. Alterations of energy metabolism and changes in the properties of myosin induced by hormonal deficiency account for the muscular weakness of these patients. On the other hand, the mechanism of muscle hypertrophy remains controverted, the most probable theory being and increase in the number of myotubes. Following irradiation, notably for Hodgkin's disease, the frequency of hypothyroidism requires a regular and systematic laboratory follow-up. Replacement therapy must be instituted if the basal TSH level increases, even if the T4 level is normal.

Cisplatin-induced anemia: a potential interference with iron metabolism at erythroid progenitors level

To elucidate the potential mechanisms of anemia induced by cisplatin (CDDP) we have evaluated hemolysis, dyserythropoiesis, ferrokinetics and cytotoxicity on erythroid progenitors in 12 patients treated by a CDDP-containing combination chemotherapy and in 6 patients treated by a similar combination but without CDDP. Eight patients, from the CDDP treated group, experienced a pronounced anemia. None had signs of hemolysis. Ferrokinetic study showed a very deep and protracted decrease of 59Fe incorporation during the chemotherapy cycle and the following 2 weeks. These results, along with a normal medullary erythroblastic cellularity, suggest that CDDP induces a deep but transient erythropoiesis alteration leading to anemia in some cases.

Results of initial doxorubicin, 5-fluorouracil, and cyclophosphamide combination chemotherapy for inflammatory carcinoma of the breast

Forty-three patients with nonmetastatic inflammatory breast carcinoma have been treated by initial doxorubicin, 5-fluorouracil, and cyclophosphamide (FAC) combination chemotherapy. After three chemotherapy cycles, responding patients underwent surgery. Chemotherapy was then completed for nine cycles of FAC followed by locoregional radiation therapy. All patients received tamoxifen 40 mg/day for 1 year from the time of diagnosis. Thirty-eight patients (88%) had a clinical response to chemotherapy and underwent surgery. On histologic examination 17 patients had a residual tumor mass less than 1 cm diameter or a complete tumor disappearance; lymph nodes dissection was negative in 15 patients. With a median follow-up of 48 months, the predicted 5-year disease-free survival (DFS) is 48% (median DFS, 46 months). Analysis of prognosis factors shows that age, menopausal status, and histologic grade have no predictive value. The DFS and overall survival were significantly improved by the presence of hormonal receptors and a low number of positive lymph nodes (less than 4) at surgery. The most significant prognosis factor was the residual tumor mass after initial chemotherapy with an 80% predicted 5-year DFS for the responding patients versus 30% for the no responding patients (P less than 0.001).

Cyclic AMP and cyclic GMP phosphodiesterase activities in Hodgkin's disease lymphocytes

Cyclic nucleotide phosphodiesterase (PDE) activities were studied in peripheral blood monocyte-depleted lymphocytes and enriched T-lymphocyte suspensions from thirteen patients with previously untreated Hodgkin's disease (HD) and fourteen age and sex matched healthy volunteers. Monocyte-depleted lymphocytes from HD patients showed PDE-activities which were two times higher than in their normal counterpart cells. The mean cAMP-PDE activity present in enriched HD T-lymphocyte suspensions was four times higher than in control T-lymphocytes, and the mean cGMP-PDE associated with HD T-lymphocytes was three times higher than in the controls. The hydrolytic activities present in both monocyte-depleted and T-lymphocyte enriched cells suspensions remained unchanged in absence or in the presence of calmodulin and calcium. Since depressed cAMP and cGMP resting levels have been observed in HD lymphocytes and lymphocyte subpopulations, our results suggest that the elevated PDE activities are, at least in part, responsible for the alterations in lymphocyte cyclic nucleotide levels.

Decreased membrane "fluidity" of T lymphocytes from untreated patients with Hodgkin's disease

Plasma membrane "fluidity" of peripheral blood T lymphocytes from untreated patients with Hodgkin's disease (HD) and healthy controls was studied using the fluorescent probes 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-(4(trimethylamino)phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH). In 13 consecutive patients a significant increase of T lymphocyte plasma membrane microviscosity was observed with both DPH and TMA-DPH. These alterations seemed unrelated to the cholesterol (Chol) and phospholipid (PL) content of HD T lymphocytes since the Chol/PL ratio was comparable in both HD and control cells. Since prostaglandin E2 (PGE2) from monocytic origin has been claimed to be responsible for the impairment of cell-mediated immunity (CMI) associated with HD, we studied the effect of exogeneously added PGE2 (0.1 microM) on control subjects T lymphocyte membrane "fluidity". Using the fluorescent probe DPH and the spin labelled fatty acid probe 16 NMS for electron paramagnetic resonance study, we observed a PGE2-induced fluidization of control T lymphocyte membranes which is specifically located in the inner part of the plasma membrane, whereas the plasma membrane surface seemed unaffected by PGE2 as judged by the TMA-DPH probe. Thus, PGE2 does not appear to be responsible for the alterations of T lymphocyte membranes observed in HD. Intrinsic alterations and/or other mediators might be involved.

Depressed NK cell activity of peripheral blood mononuclear cells in untreated hodgkin's disease: enhancing effect of interferon in vitro

Natural killer (NK) cell activity of unseparated peripheral blood mononuclear cells from 30 untreated patients with Hodgkin's disease and 22 age- and sex-matched normal controls was evaluated using the classical K 562 cells as targets. A significant defect was demonstrated in the patients with stage I-II and seemed to be more profound in patients with advanced disease (stage III-IV) and in those with B symptoms. The differences between subgroups of patients, however, were not statistically significant, mostly because of the wide dispersion of individual data. Pre-incubation of effector cells with alpha A leucocyte recombinant interferon led to a clear increase in NK cell activity in 4 of 6 patients tested, showing that depressed NK activity in Hodgkin's disease is still susceptible to the enhancing effect of interferon, at least in some patients.

High-dose intravenous IgG for chronic idiopathic thrombocytopenic purpura in adults

Sixteen adult patients of mean age 48 years with chronic ITP were studied for platelet response to high-dose (0.4 g/kg body weight per day for five consecutive days) intravenous polyvalent intact IgG in the absence of any concurrent treatment. The platelet count returned to normal values in nine patients, a partial response (rise in the platelet count between 50 and 150 X 10(9)/1) was observed in three cases. One patient refractory to any other treatment went into a sustained remission. In the other responsive patients the response was only transient. Among seven splenectomised patients only three responded to IgG infusions versus nine in the non-splenectomised group. The length of ITP history appeared as a more critical factor for the response to IgG than previous splenectomy.

Alterations of peripheral blood lymphocyte cyclic AMP and cyclic GMP in untreated patients with hodgkin's disease

Cyclic AMP and cyclic GMP are important regulatory agents of lymphocyte functions. Depressed T-lymphocyte functions are frequently associated with Hodgkin's disease and suppressor monocytes have been implicated in the pathogenesis of this defect. In the present study cAMP and cGMP resting levels were measured in lymphocytes from 18 untreated patients with Hodgkin's disease using a sensitive radioimmunoassay. A significant decrease of cAMP (P less than 0.001) and, to a lesser degree, of cGMP (P less than 0.01) was found in monocyte-depleted lymphocyte suspensions from the patients compared to controls. Studies of patient and control lymphocyte subpopulations showed in patients a clear deficit of cAMP in T-depleted lymphocytes, rather than in T cells, with a low cAMP/cGMP molar ratio in both subpopulations. From this data it is clear that factors other than prostaglandin-mediated suppression of monocyte origin are involved in the pathogenesis of the T-lymphocyte depression associated with Hodgkin's disease.

Immunomodulating effects of a short-term oral treatment with C 1821 in untreated cancer patients: a controlled study

C 1821 is a purified glycoprotein extract from Klebsiella pneumoniae serotype 2 with a molecular weight of about 350,000. It enhances immune responses in animals when given orally and the oral route of administration is devoided of any toxicity even in humans. The present controlled trial showed that C 1821 given per os at the single daily dose of 4 mg for 14 days in untreated cancer patients (mostly lymphomas) significantly enhanced delayed cutaneous hypersensitivity to recall antigens using the Multitest system (7 antigens). It also increased basal levels of lymphocyte cAMP and particularly of cGMP which were decreased in these patients. When incubated in vitro with lymphocytes from either normal controls or patients, C 1821 showed a dose-dependent stimulation of cAMP synthesis which was more pronounced in patients than in controls.

[Idiopathic thrombocytopenic purpura. Treatment by intravenous transfusion of polyvalent immunoglobulins]

Thirteen patients (2 children and 11 adults) with idiopathic thrombocytopenic purpura were treated with high doses of human immunoglobulins intravenously (0.4 g/kg bodyweight/day for 5 days). The platelet count rose sharply in 11 patients, with considerable individual variations in terms of maximum count achieved and delay as well as duration of response. Only two adult patients refractory to previous treatments failed to show any significant response. Complete correction of platelet counts was observed in the two children, whereas most adult patients showed incomplete and transient response. No difference was observed between splenectomized and non splenectomized patients. Survival of 111 Indium-labelled autologous platelets was studied in 2 patients after correction of platelet count and was still found shortened. Circulating immune complexes, when present, were not modified by immunoglobulin infusions. In all patients a significant reduction of the fourth component of serum complement was noted after treatment.

Enhancement of delayed cutaneous hypersensitivity in untreated cancer patients given a short-term oral treatment with C 1821

C 1821 is a purified glycoprotein extract of Klebsiella pneumoniae serotype 2 with immunomodulating properties in animals (in vivo and in vitro) and in humans (in vitro). The compound is devoid of any apparent toxicity when given orally. The aim of the present work was to evaluate the effects of a short term oral administration of C 1821 on delayed cutaneous hypersensitivity to recall antigens in untreated cancer patients (mostly lymphomas). Consecutive patients were alternately allocated to receive C 1821 or placebo for 14 days. C 1821 restored and significantly (P less than 0.02) enhanced skin reactions, as shown using the Multitest system.

Delayed cutaneous hypersensitivity testing in untreated Hodgkin's disease using a standardized new device

Delayed cutaneous hypersensitivity to 7 recall antigens has been tested in 32 patients with untreated Hodgkin's disease using a standardized and reproducible system. Anergy to all 7 antigens was observed in 15/32 patients and hypoergy in 4/32 leading to a cumulative deficiency rate of 59%. Although the defect was distributed throughout all stages, substages and histologic types, it seemed to predominate in less favorable forms of the disease as well as in female patients.

[Persisting deficiency of cell mediated immunity in Hodgkin's disease in complete remission (author's transl)]

There is increasing evidence in the literature for persistent deficiency in cell-mediated immunity (CMI) in Hodgkin's diseases during apparent remissions after discontinuation of the treatment. Patients were followed for 6 months to 2 years after all treatments were stopped. There was a high percentage (41.6) of subjects with skin anergy to seven recall antigens, a highly significant (p less than 0,0001) decrease, as compared with controls, in total and active E rosettes independently from the number of lymphocytes, and a highly significant diminution of T-lymphocyte in vitro reactivity to various doses of phyto haemagglutinine (PHA). There was no difference between the patients tested between 6 months and 1 year and those tested more than 2 years after treatment. No correlation between skin tests and active rosettes was found in this series. Finally, the CMI deficiency is some what different in patients on remission and in untreated patients.

[Autoimmunity and deficiency of cell-mediated immunity in primary myelofibrosis]

Untreated patients with primary myelofibrosis show (1) a high frequency of cutaneous anergy, (2) normal lymphocytosis with decreased level of E-rosette-forming cells in most patients, (3) normal lymphocyte reactivity to PHA and in MLR, and (4) a relative frequency of LE cells and anti-organ antibodies.